11  msqrob2PTM: DIA-NN case study - Paired phospho-enriched and non-enriched samples

11.1 Background

  • Mass spectrometry–based (MS) proteomics allows the identification and quantification of a myriad of posttranslational modifications (PTMs)
  • This reveals additional complexity and diversity of the proteome.
  • Indeed, PTMs greatly extend the number of different forms of a protein, that is, proteoforms, that can be found.
  • More importantly, these PTMs can impact protein functions
  • They are linked to a variety of diseases and developmental disorders.
  • Aberrant PTM status can cause a number of detrimental effects ranging from the alteration of protein folding to the dysregulation of cell signaling.
  • It is thus of great importance to study these PTMs in detail, not only through their correct identification but also by their correct quantification and subsequent statistical analysis.

11.1.1 Vignette

In this vignette we start from quantified precursor level data to infer

  • Differential abundance (DA) of precursors carrying post-translation-modifications,
  • DA at the protein level
  • Differential usage of precursors, i.e.  DA of precursors upon correction for DA at protein level
  • Differential usage of PTMs, i.e. upon summarising the usages for all precursors that carry the same PTM at a specific residue (position in the protein),

using the msqrob2PTM workflow in the bioconductor package msqrob2.

You can read more about

11.1.2 Experiment

Mutations in tRNAs can lead to mis-incorporation of an amino acid into a growing polypeptide chain that differs from what is specified by the mRNA in a process known as mistranslation. To better understand the impact of mistranslating tRNA variants, Berg et al.  profiled the proteome and phosphoproteome of yeast expressing three different mistranslating tRNAs. The first is a proline tRNA with a G3:U70 base pair in its acceptor stem that mis-incorporates alanine at proline codons (Pro -> Ala; Hoffman et al. 2017). The other two are serine tRNAs with either a UGG proline or UCU arginine anticodon which mis-incorporate serine at proline (Pro -> Ser) or serine at arginine codons (Arg -> Ser), respectively (Berg et al. 2017, 2019b).

Six replicates of each strain were grown. From each replicate an non-enriched (whole proteome) and a phospho-peptide-enriched sample was prepared and quantified using a data independent acquisition workflow.

The data for the non-enriched and phospho-enriched samples are deposited to PRIDE, dataset identifiers PXD068388 and PXD068392).

Summary:

  • Mutations in tRNAs can lead to mis-incorporation of amino acids during protein translation.
  • 4 strains: WT, 3 strains with mutations leading to miss-incorporations (Pro -> Ala, Pro -> Ser and Arg -> Ser).
  • 6 biological repeats per strain
  • For each biological repeat: non-enriched and phospho-enriched MS run.

M. Berg, A. Chang, R. Rodriguez-Mias, J. Villén, Mistranslating tRNA variants impact the proteome and phosphoproteome of Saccharomyces cerevisiae, G3 Genes|Genomes|Genetics, Volume 16, Issue 2, February 2026, jkaf284, https://doi.org/10.1093/g3journal/jkaf284

11.2 Load packages

We load the msqrob2 package, along with additional packages for data manipulation and visualisation.

suppressPackageStartupMessages({
library("QFeatures")  
library("dplyr") 
library("tidyr")
library("ggplot2")
library("msqrob2")    
library("stringr")
library("ExploreModelMatrix")
library("MsCoreUtils") 
library("matrixStats")
library("patchwork")
library("kableExtra")
library("ComplexHeatmap")
library("purrr")
library("tibble")
library("scater")
library("BiocFileCache")
})

11.3 Data

11.3.1 Precursor table

  • We load the output from DIA-NN parquet files.
  • Can be file path to local file or url to file that lives on the web.
  • Here we use BiocFileCache so that we do not need to download the files again each time that the script is knit.
bfc <- BiocFileCache()
precursorFile <- bfcrpath(bfc,"https://zenodo.org/records/20414816/files/WholeProteome_DIANNreport.parquet?download=1")
precursorFilePTM <- bfcrpath(bfc,"https://zenodo.org/records/20414816/files/Phosphoproteome_DIANNreport.parquet?download=1")

We can import the report.parquet file using the read_parquet function from the arrow package.

precursors <- arrow::read_parquet(precursorFile) # function from the arrow package
precursorsPTM <- arrow::read_parquet(precursorFilePTM) # function from the arrow package
#precursors <- data.table::fread(precursorFile) # For older versions the results are stored as tsv files.

We subset the precursor files to reduce the memory footprint and only keep the variables that we need in the downstream analysis.

Note that Protein.Sites refers to the exact modified residue position in the full protein sequence, which will be useful when assessing PTM-level quantification.

Note, that we also filter out the strain with the ProSer variant here.

precursors <- precursors |> 
  filter(!grepl("ProSer",Run)) |>
  select(
         Run, 
         Precursor.Id, 
         Modified.Sequence, 
         Stripped.Sequence, 
         Precursor.Charge, 
         Protein.Group, 
         Protein.Names,
         Protein.Ids,
         Protein.Sites, #exact modified residue position in the full protein sequence
         Genes,
         Precursor.Quantity,
         Precursor.Normalised,
         Normalisation.Factor,
         Ms1.Area,
         Ms1.Normalised,
         PG.MaxLFQ,
         Q.Value, 
         Lib.Q.Value,
         PG.Q.Value,
         Lib.PG.Q.Value,
         Proteotypic,
         Decoy, # Not available in older versions of DIA-NN
         RT)
precursorsPTM <- precursorsPTM |> 
  filter(!grepl("ProSer",Run)) |>
  select(
         Run, 
         Precursor.Id, 
         Modified.Sequence, 
         Stripped.Sequence, 
         Precursor.Charge, 
         Protein.Group, 
         Protein.Names,
         Protein.Ids,
         Protein.Sites, #exact modified residue position in the full protein sequence
         Genes,
         Precursor.Quantity,
         Precursor.Normalised,
         Normalisation.Factor,
         Ms1.Area,
         Ms1.Normalised,
         PG.MaxLFQ,
         Q.Value, 
         Lib.Q.Value,
         PG.Q.Value,
         Lib.PG.Q.Value,
         Proteotypic,
         Decoy, # Not available in older versions of DIA-NN
         RT)
precursorsPTM |> 
  select(Protein.Sites, Modified.Sequence, Stripped.Sequence) |> 
  head(20)
# A tibble: 20 × 3
   Protein.Sites      Modified.Sequence                        Stripped.Sequence
   <chr>              <chr>                                    <chr>            
 1 [P52871:A2,S4]     (UniMod:1)AAS(UniMod:21)VPPGGQR          AASVPPGGQR       
 2 [P52871:A2,S4]     (UniMod:1)AAS(UniMod:21)VPPGGQR          AASVPPGGQR       
 3 [P52871:A2,S4]     (UniMod:1)AAS(UniMod:21)VPPGGQR          AASVPPGGQR       
 4 [P52871:A2,S4]     (UniMod:1)AAS(UniMod:21)VPPGGQR          AASVPPGGQR       
 5 [P52871:A2,S4]     (UniMod:1)AAS(UniMod:21)VPPGGQR          AASVPPGGQR       
 6 [P52871:A2,S4]     (UniMod:1)AAS(UniMod:21)VPPGGQR          AASVPPGGQR       
 7 [P04147:A2,T5]     (UniMod:1)ADIT(UniMod:21)DKTAEQLENLNIQD… ADITDKTAEQLENLNI…
 8 [P04147:A2,T5]     (UniMod:1)ADIT(UniMod:21)DKTAEQLENLNIQD… ADITDKTAEQLENLNI…
 9 [P04147:A2,T5]     (UniMod:1)ADIT(UniMod:21)DKTAEQLENLNIQD… ADITDKTAEQLENLNI…
10 [P04147:A2,T8]     (UniMod:1)ADITDKT(UniMod:21)AEQLENLNIQD… ADITDKTAEQLENLNI…
11 [P04147:A2,T8]     (UniMod:1)ADITDKT(UniMod:21)AEQLENLNIQD… ADITDKTAEQLENLNI…
12 [P04147:A2,T8]     (UniMod:1)ADITDKT(UniMod:21)AEQLENLNIQD… ADITDKTAEQLENLNI…
13 [P04147:A2,T8]     (UniMod:1)ADITDKT(UniMod:21)AEQLENLNIQD… ADITDKTAEQLENLNI…
14 [P04147:A2,T8]     (UniMod:1)ADITDKT(UniMod:21)AEQLENLNIQD… ADITDKTAEQLENLNI…
15 [P04147:A2,T8]     (UniMod:1)ADITDKT(UniMod:21)AEQLENLNIQD… ADITDKTAEQLENLNI…
16 [P04147:A2,T8]     (UniMod:1)ADITDKT(UniMod:21)AEQLENLNIQD… ADITDKTAEQLENLNI…
17 [P04147:A2,T8]     (UniMod:1)ADITDKT(UniMod:21)AEQLENLNIQD… ADITDKTAEQLENLNI…
18 [P40096:A2,T8,M32] (UniMod:1)ADQVPVT(UniMod:21)TQLPPIKPEHE… ADQVPVTTQLPPIKPE…
19 [P40096:A2,T8,M32] (UniMod:1)ADQVPVT(UniMod:21)TQLPPIKPEHE… ADQVPVTTQLPPIKPE…
20 [P40096:A2,T8,M32] (UniMod:1)ADQVPVT(UniMod:21)TQLPPIKPEHE… ADQVPVTTQLPPIKPE…

Garbage collection to free space

gc(); gc()
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used   (Mb)
Ncells 10185124 544.0   17413800  930.0         NA  14212846  759.1
Vcells 61096392 466.2  251102020 1915.8      24576 312075668 2381.0
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used   (Mb)
Ncells 10185233 544.0   17413800  930.0         NA  14212846  759.1
Vcells 61096683 466.2  200881616 1532.7      24576 312075668 2381.0

11.3.2 Subset phospho

In DIA-NN phosphorylation is indicated with (UniMod:21) in the sequence stored in variable Modified.Sequence. This variable contains the precursor sequence along with its modifications.

Here, we only keep precursors that are phosphorylated, i.e. with pattern (UniMod:21) in the variable Modified.Sequence.

precursorsPTM <- precursorsPTM |>
  filter(grepl(pattern = "\\(UniMod:21\\)", Modified.Sequence))

Garbage collection to free space

gc(); gc()
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used   (Mb)
Ncells 10180991 543.8   17413800  930.0         NA  14212846  759.1
Vcells 59444309 453.6  200881616 1532.7      24576 312075668 2381.0
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used   (Mb)
Ncells 10180990 543.8   17413800  930.0         NA  14212846  759.1
Vcells 59444340 453.6  200881616 1532.7      24576 312075668 2381.0

11.3.3 Quick check for imputation

Quick check on distribution of precursors MS2 intensities.

precursors |> 
  filter(is.finite(Precursor.Quantity) & Precursor.Quantity > 0) |>
  ggplot(aes(x = log2(Precursor.Quantity))) +
  geom_density() +
  theme_minimal() +
  labs(subtitle = "Abundances (non-enriched)") + precursorsPTM |> 
  filter(is.finite(Precursor.Quantity) & Precursor.Quantity > 0) |>
  ggplot(aes(x = log2(Precursor.Quantity))) +
  geom_density() +
  theme_minimal() +
  labs(subtitle = "Abundances (phospho-enriched)")

Seems no imputation has been done.

#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used   (Mb)
Ncells 10417304 556.4   17413800  930.0         NA  14442134  771.3
Vcells 99947259 762.6  200881616 1532.7      24576 312075668 2381.0
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used   (Mb)
Ncells 10417285 556.4   17413800  930.0         NA  14442134  771.3
Vcells 99947261 762.6  200881616 1532.7      24576 312075668 2381.0

11.3.4 Sample annotation tables

The sample annotation table is not available and can be generated from the run labels, as the researchers included information on the design in the filenames.

  1. Extract unique Run labels
  2. Split Run label into variables using the “_” separator
  3. Rename the variable Run to runCol (needed for readQFeatures function)
  4. Add sampleId
  5. Sort annotation file according to sampleId
annot <- precursors |> 
  dplyr::distinct(Run) |>  ## 1.
  separate(Run,
           into=c("run","label2","strain","rep","type","acquisition"),
           sep="_",
           remove=FALSE) |>   ## 2.
  rename(runCol = Run) |> ## 3.
  mutate(sampleId = paste0(strain,rep)) |> #4.
  arrange(sampleId) #5.
annot
# A tibble: 18 × 8
   runCol                   run   label2 strain rep   type  acquisition sampleId
   <chr>                    <chr> <chr>  <chr>  <chr> <chr> <chr>       <chr>   
 1 e14629_MB057_ArgSer_01_… e146… MB057  ArgSer 01    Prot… DIA         ArgSer01
 2 e14632_MB057_ArgSer_02_… e146… MB057  ArgSer 02    Prot… DIA         ArgSer02
 3 e14639_MB057_ArgSer_03_… e146… MB057  ArgSer 03    Prot… DIA         ArgSer03
 4 e14644_MB057_ArgSer_04_… e146… MB057  ArgSer 04    Prot… DIA         ArgSer04
 5 e14650_MB057_ArgSer_05_… e146… MB057  ArgSer 05    Prot… DIA         ArgSer05
 6 e14653_MB057_ArgSer_06_… e146… MB057  ArgSer 06    Prot… DIA         ArgSer06
 7 e14627_MB057_Ctrl_01_Pr… e146… MB057  Ctrl   01    Prot… DIA         Ctrl01  
 8 e14635_MB057_Ctrl_02_Pr… e146… MB057  Ctrl   02    Prot… DIA         Ctrl02  
 9 e14638_MB057_Ctrl_03_Pr… e146… MB057  Ctrl   03    Prot… DIA         Ctrl03  
10 e14642_MB057_Ctrl_04_Pr… e146… MB057  Ctrl   04    Prot… DIA         Ctrl04  
11 e14648_MB057_Ctrl_05_Pr… e146… MB057  Ctrl   05    Prot… DIA         Ctrl05  
12 e14654_MB057_Ctrl_06_Pr… e146… MB057  Ctrl   06    Prot… DIA         Ctrl06  
13 e14630_MB057_ProAla_01_… e146… MB057  ProAla 01    Prot… DIA         ProAla01
14 e14634_MB057_ProAla_02_… e146… MB057  ProAla 02    Prot… DIA         ProAla02
15 e14640_MB057_ProAla_03_… e146… MB057  ProAla 03    Prot… DIA         ProAla03
16 e14643_MB057_ProAla_04_… e146… MB057  ProAla 04    Prot… DIA         ProAla04
17 e14647_MB057_ProAla_05_… e146… MB057  ProAla 05    Prot… DIA         ProAla05
18 e14655_MB057_ProAla_06_… e146… MB057  ProAla 06    Prot… DIA         ProAla06

We do the same for the phospho data.

annotPTM <- precursorsPTM |> 
   dplyr::distinct(Run) |>  ## 1.
  separate(Run,
           into=c("label1","label2","strain","rep","type","acquisition"),
           sep="_",
           remove=FALSE) |>   ## 2.
  rename(runCol = Run) |> ## 3.
  mutate(sampleId = paste0(strain,rep)) |> #4.
  arrange(sampleId) #5.
annotPTM
# A tibble: 18 × 8
   runCol                  label1 label2 strain rep   type  acquisition sampleId
   <chr>                   <chr>  <chr>  <chr>  <chr> <chr> <chr>       <chr>   
 1 e14488_MB057_ArgSer_01… e14488 MB057  ArgSer 01    Phos… DIA         ArgSer01
 2 e14491_MB057_ArgSer_02… e14491 MB057  ArgSer 02    Phos… DIA         ArgSer02
 3 e14498_MB057_ArgSer_03… e14498 MB057  ArgSer 03    Phos… DIA         ArgSer03
 4 e14503_MB057_ArgSer_04… e14503 MB057  ArgSer 04    Phos… DIA         ArgSer04
 5 e14509_MB057_ArgSer_05… e14509 MB057  ArgSer 05    Phos… DIA         ArgSer05
 6 e14512_MB057_ArgSer_06… e14512 MB057  ArgSer 06    Phos… DIA         ArgSer06
 7 e14486_MB057_Ctrl_01_P… e14486 MB057  Ctrl   01    Phos… DIA         Ctrl01  
 8 e14494_MB057_Ctrl_02_P… e14494 MB057  Ctrl   02    Phos… DIA         Ctrl02  
 9 e14497_MB057_Ctrl_03_P… e14497 MB057  Ctrl   03    Phos… DIA         Ctrl03  
10 e14501_MB057_Ctrl_04_P… e14501 MB057  Ctrl   04    Phos… DIA         Ctrl04  
11 e14507_MB057_Ctrl_05_P… e14507 MB057  Ctrl   05    Phos… DIA         Ctrl05  
12 e14513_MB057_Ctrl_06_P… e14513 MB057  Ctrl   06    Phos… DIA         Ctrl06  
13 e14489_MB057_ProAla_01… e14489 MB057  ProAla 01    Phos… DIA         ProAla01
14 e14493_MB057_ProAla_02… e14493 MB057  ProAla 02    Phos… DIA         ProAla02
15 e14499_MB057_ProAla_03… e14499 MB057  ProAla 03    Phos… DIA         ProAla03
16 e14502_MB057_ProAla_04… e14502 MB057  ProAla 04    Phos… DIA         ProAla04
17 e14506_MB057_ProAla_05… e14506 MB057  ProAla 05    Phos… DIA         ProAla05
18 e14514_MB057_ProAla_06… e14514 MB057  ProAla 06    Phos… DIA         ProAla06
#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used   (Mb)
Ncells 10429228 557.0   17413800  930.0         NA  14442134  771.3
Vcells 99975022 762.8  200881616 1532.7      24576 312075668 2381.0
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used   (Mb)
Ncells 10429173 557.0   17413800  930.0         NA  14442134  771.3
Vcells 99974964 762.8  200881616 1532.7      24576 312075668 2381.0

11.3.5 Convert to QFeatures

First, recall that the precursor table is file in long format. Every quantitative column in the precursor table contains information for multiple runs. Therefore, the function split the table based on the run identifier, given by the runCol argument (for DIA-NN, that identifier is contained in Run). So, the QFeatures object after import will contain as many sets as there are runs. Next, the function links the annotation table with the PSM data. To achieve this, the annotation table must contain a runCol column that provides the run identifier in which each sample has been acquired, and this information will be used to match the identifiers in the Run column of the precursor table.

Here, we will use the Precursor.Quantity column as quantification input.

  1. We first combine the precursor and precursorPTM table in a list of QFeatures objects,
  2. which we subsequently reduce in one QFeatures object. Note that in QFeatures, the function c() is defined to merge QFeatures objects, stacking all assays together into a single object.

This allows us to store the data of the phospho-enriched and the non-enriched samples in the same QFeatures object.

(qf <- list(
  readQFeatures(assayData = precursors,  
                              colData = annot,
                              quantCols = "Precursor.Quantity",
                              runCol = "Run",
                              fnames = "Precursor.Id"),
  readQFeatures(assayData = precursorsPTM,  
                              colData = annotPTM,
                              quantCols = "Precursor.Quantity",
                              runCol = "Run",
                              fnames = "Precursor.Id") ##1.
) |> purrr::reduce(c) ##2.
)
Checking arguments.
Loading data as a 'SummarizedExperiment' object.
Splitting data in runs.
Formatting sample annotations (colData).
Formatting data as a 'QFeatures' object.
Setting assay rownames.
Checking arguments.
Loading data as a 'SummarizedExperiment' object.
Splitting data in runs.
Formatting sample annotations (colData).
Formatting data as a 'QFeatures' object.
Setting assay rownames.
An instance of class QFeatures (type: bulk) with 36 sets:

 [1] e14627_MB057_Ctrl_01_Proteome_DIA: SummarizedExperiment with 76148 rows and 1 columns 
 [2] e14629_MB057_ArgSer_01_Proteome_DIA: SummarizedExperiment with 74225 rows and 1 columns 
 [3] e14630_MB057_ProAla_01_Proteome_DIA: SummarizedExperiment with 75711 rows and 1 columns 
 ...
 [34] e14512_MB057_ArgSer_06_Phospho_DIA: SummarizedExperiment with 28688 rows and 1 columns 
 [35] e14513_MB057_Ctrl_06_Phospho_DIA: SummarizedExperiment with 29944 rows and 1 columns 
 [36] e14514_MB057_ProAla_06_Phospho_DIA: SummarizedExperiment with 30520 rows and 1 columns

Remove data tables to free space.

rm(precursors, precursorsPTM)
#Garbage collection to free space 
gc(); gc()
            used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells  10467184 559.1   17413800  930.0         NA  17413800  930
Vcells 101505444 774.5  200881616 1532.7      24576 312075668 2381
            used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells  10467180 559.1   17413800  930.0         NA  17413800  930
Vcells 101505471 774.5  200881616 1532.7      24576 312075668 2381

11.4 Data preprocessing

Here we conduct the following processing steps

  1. Replace zero’s by NA.
  2. Precursor filtering and assay joining
  3. Log-transformation
  4. Normalisation
  5. Summarisation for non-enriched runs

11.4.1 Encoding missing values

We first replace any zero in the quantitative data with an NA.

qf <- zeroIsNA(qf, names(qf))

Note that msqrob2 can handle missing data without having to rely on hard-to-verify imputation assumptions, which is our general recommendation. However, msqrob2 does not prevent users from using imputation, which can be performed with impute() from the QFeatures package.

11.4.2 Precursor Filtering

Filtering removes low-quality and unreliable precursors that would otherwise introduce noise and artefacts in the data.

Remove questionable identifications

We apply standard filtering:

  1. q-value threshold of 0.01 for the identification of precursors (Q.Value) and protein groups (PG.Q.Value). If the file is processed via matching between runs, it is also useful to filter on Lib.Q.Value and Lib.PG.Q.Value.

  2. Remove precursors that could not be mapped, i.e. when Precursor.Id column is an empty string.

  3. Filter decoys, i.e. only keep precursors for which the Decoy column equals

  4. (Note, that the Decoy column is not present in the output of older versions of DIA-NN).

  5. Keeping only proteotypic peptides, which map uniquely to a specific protein.

qf <-  qf |>
  filterFeatures(~ Q.Value <= 0.01 & #1.
                     PG.Q.Value <= 0.01 &  #1.
                     Lib.Q.Value <= 0.01 & #1.
                     Lib.PG.Q.Value <= 0.01 & #1.
                     Precursor.Id != "" & #2.
                     Decoy == 0 & #3. (Note, that this filter is not available with previous versions of DIA-NN, as the report.tsv file did not include a Decoy column. So other strategies are needed if Decoys are in the output file.)
                     Proteotypic == 1) #4.
'Q.Value' found in 36 out of 36 assay(s).'PG.Q.Value' found in 36 out of 36 assay(s).'Lib.Q.Value' found in 36 out of 36 assay(s).'Lib.PG.Q.Value' found in 36 out of 36 assay(s).'Precursor.Id' found in 36 out of 36 assay(s).'Decoy' found in 36 out of 36 assay(s).'Proteotypic' found in 36 out of 36 assay(s).

Note, that it is important that the filtering criteria are not distorting the distribution of the test statistics in the downstream analysis for features that are non-DA. It can be shown that filtering will not induce bias results when the filtering criterion is independent of test statistic. The criteria that we proposed above are all based on the results of the identification step, hence, they are independent of the downstream test statistics that will be used to prioritize DA proteins.

#Garbage collection to free space 
gc(); gc()
            used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells  10473136 559.4   17413800  930.0         NA  17413800  930
Vcells 102821103 784.5  200881616 1532.7      24576 312075668 2381
            used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells  10473135 559.4   17413800  930.0         NA  17413800  930
Vcells 102821135 784.5  200881616 1532.7      24576 312075668 2381

Assay joining

  • Up to now, the data from different runs were kept in separate assays.
  • We can now join the filtered sets into an precursor set using joinAssays().
  • Sets are joined by stacking the columns (samples) in a matrix and rows (features) are matched according to a row identifier, here the Precursor.Id.
  • We do this for the non-enriched and phospho samples, which we store in assays with names: precursors and precursorsPTM, respectively.
qf <- joinAssays(
  x = qf,
  i = grep("Proteome",names(qf), value = TRUE),
  fcol = "Precursor.Id",
  name = "precursors"
  )
Using 'Precursor.Id' to join assays.
(qf <- joinAssays(
  x = qf,
  i = grep("Phospho",names(qf), value = TRUE),
  fcol = "Precursor.Id",
  name = "precursorsPTM"
  )
)
Using 'Precursor.Id' to join assays.
An instance of class QFeatures (type: bulk) with 38 sets:

 [1] e14627_MB057_Ctrl_01_Proteome_DIA: SummarizedExperiment with 73741 rows and 1 columns 
 [2] e14629_MB057_ArgSer_01_Proteome_DIA: SummarizedExperiment with 71814 rows and 1 columns 
 [3] e14630_MB057_ProAla_01_Proteome_DIA: SummarizedExperiment with 73265 rows and 1 columns 
 ...
 [36] e14514_MB057_ProAla_06_Phospho_DIA: SummarizedExperiment with 29322 rows and 1 columns 
 [37] precursors: SummarizedExperiment with 88291 rows and 18 columns 
 [38] precursorsPTM: SummarizedExperiment with 59771 rows and 18 columns

Remove the original assays to free space

qf <- qf[,,-c(1:36)]
Warning: 'experiments' dropped; see 'drops()'
harmonizing input:
  removing 36 sampleMap rows not in names(experiments)
#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 10476837 559.6   17413800  930.0         NA  17413800  930
Vcells 66323285 506.1  200881616 1532.7      24576 312075668 2381
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 10476833 559.6   17413800  930.0         NA  17413800  930
Vcells 66323311 506.1  200881616 1532.7      24576 312075668 2381

Filtering: Remove highly missing precursors

We keep peptides that were observed at least 6 times out of the \(n = 18\) samples, so that we can estimate the peptide characteristics.

nObs <- 6
n <- ncol(qf[["precursors"]])

(qf <- filterNA(qf, i = c("precursors", "precursorsPTM"), pNA = (n - nObs) / n))
An instance of class QFeatures (type: bulk) with 2 sets:

 [1] precursors: SummarizedExperiment with 78047 rows and 18 columns 
 [2] precursorsPTM: SummarizedExperiment with 32916 rows and 18 columns 
#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 10477004 559.6   17413800  930.0         NA  17413800  930
Vcells 65062617 496.4  200881616 1532.7      24576 312075668 2381
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 10477003 559.6   17413800  930.0         NA  17413800  930
Vcells 65062648 496.4  200881616 1532.7      24576 312075668 2381

Filter one-hit wonders

We normally remove proteins that can only be found by one peptide, as such proteins may not be trustworthy.

Here, we opt not to do this because we prefer a protein-level summary based on one precursor so that we can estimate usages later on.

We leave the code here for your reference. But commented it out.

  1. We first calculate how many distinct peptides map to each protein group (PG_ProteinGroups). We use the stripped precursor sequence, i.e. sequence of the base peptide for this purpose.

  2. We store this information in the row data of the precursors assay

  3. We filter precursors of one-hit wonder proteins.

## Filter for peptides per protein
# pepsPerProtDf <- qf[["precursors"]] |> 
#    rowData() |> 
#    data.frame() |>
#    dplyr::select("Stripped.Sequence", "Protein.Group") |>
#    group_by(Protein.Group) |>
#    mutate(pepsPerProt = Stripped.Sequence |>
#               unique() |> length()
#           ) #1.

# rowData(qf[["precursors"]])$pepsPerProt <- pepsPerProtDf$pepsPerProt #2. 

#qf <- filterFeatures(qf, 
#                              ~ pepsPerProt > 1, 
#                              keep = TRUE) #3.
#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 10477006 559.6   17413800  930.0         NA  17413800  930
Vcells 65062762 496.4  200881616 1532.7      24576 312075668 2381
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 10477005 559.6   17413800  930.0         NA  17413800  930
Vcells 65062793 496.4  200881616 1532.7      24576 312075668 2381

11.4.3 Log-transformation

We perform log2-transformation with logTransform() from the QFeatures package. We use base = 2 and store the result in a new summarized experiment named precursors_log.

qf <- logTransform(qf, 
                            base = 2, 
                            i = "precursors", 
                            name = "precursors_log")
qf <- logTransform(qf, 
                            base = 2, 
                            i = "precursorsPTM", 
                            name = "precursorsPTM_log")

11.4.4 Normalisation

We first evaluate the distributions of the non-normalised precursors per sample. For this, we perform a short data manipulation pipeline:

  1. We select an assay from the QFeatures object, qf.
  2. We use longForm() to convert the QFeatures object into a long table, where each row contains the quantitative information about one observation, in which column, row and set it was found. Long tables are particularly useful for manipulating data with the tidyverse ecosystem, namely with ggplot2 for visualisation. longForm() also allows to include annotations, and we here include all variables from the colData for filtering and colouring.
  3. longForm() returns a DataFrame which we convert to a data.frame.
  4. We filter out the missing values.
  5. We make a plot with ggplot.
  6. We add aesthetics, we select the log2-intensities (value) as x, and color according to the strain and group according to the colname.
  7. We add a geom_dens layer to add a density plot.
  8. We add a title.
  9. Use a minimal theme.
qf[, , "precursors_log"] |> #1.
  longForm(colvars = colnames(colData(qf))) |>  #2. 
  data.frame() |> #3.
  filter(!is.na(value)) |> #4.
  ggplot() + #5.
  aes(x = value,
      colour = strain,
      group = colname) + #6.
  geom_density() + #7. 
  labs(subtitle = "precursors") + #8.
  theme_minimal() #9.
harmonizing input:
  removing 54 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'

qf[, , "precursorsPTM_log"] |> #1.
  longForm(colvars = colnames(colData(qf))) |>  #2.
  data.frame() |> #3.
  filter(!is.na(value)) |> #4.
  ggplot() + #5.
  aes(x = value, 
      colour = strain,
      group = colname) + #6.
  geom_density() + #7. 
  labs(subtitle = "PTM - precursors") + #8. 
  theme_minimal() #9. 
harmonizing input:
  removing 54 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'

The data seems very clean. However, normalisation is still required.

We use the median of ratio normalisation, which addresses both differences in loading as well as difference in compositionality.

  • This first calculates a reference sample by using the log2 geometric mean, i.e.  the arithmetic mean on a log scale, for every feature.
  • Subsequently log2 fold changes are calculated between each feature of a sample and the reference sample.
  • Finally, the median of these log2 fold changes are used as the log2-tranformed normalisation factor.

The method is the default method for normalisation in bulk RNA-seq data analysis with DESeq2. In our hands it performs very well in a proteomics context.

qf <- sweep( #4. Subtract log2 norm factor column-by-column (MARGIN = 2)
  qf,
  MARGIN = 2,
  STATS = nfLogMedianOfRatios(qf,"precursors_log"),
  i = "precursors_log",
  name = "precursors_norm"
)
This function aims to calculate norm factors on a log scale, 
          the input data are assumed to be on the log-scale!
qf <- sweep( #4. Subtract log2 norm factor column-by-column (MARGIN = 2)
  qf,
  MARGIN = 2,
  STATS = nfLogMedianOfRatios(qf,"precursorsPTM_log"),
  i = "precursorsPTM_log",
  name = "precursorsPTM_norm"
)
This function aims to calculate norm factors on a log scale, 
          the input data are assumed to be on the log-scale!

We explore the effect of the global normalisation in the subsequent plot.

Formally, the function applies the following operation on each sample \(i\) across all precursors \(p\):

\[ y_{ip}^{\text{norm}} = y_{ip} - \log_2(nf_i) \]

with \(y_ip\) the log2-transformed intensities and \(nf_i\) the log2-transformed norm factor.

Upon normalisation, we can see that the distribution of the \(y_{ip}^{\text{norm}}\) nicely overlap (using the same code as above)

qf[, , "precursors_norm"] |>
  longForm(colvars = colnames(colData(qf))) |> 
  data.frame() |> 
  filter(!is.na(value)) |>
  ggplot() + 
  aes(x = value,
      colour = strain,
      group = colname) +
  geom_density() +
  labs(subtitle = "Median normalisation precursors") +
  theme_minimal()
harmonizing input:
  removing 90 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'

qf[, , "precursorsPTM_norm"] |>
  longForm(colvars = colnames(colData(qf))) |> 
  data.frame() |> 
  filter(!is.na(value)) |>
  ggplot() + 
  aes(x = value,
      colour = strain,
      group = colname) +
  geom_density() +
  labs(subtitle = "Median normalisation PTM precursors") +
  theme_minimal()
harmonizing input:
  removing 90 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'

We also explore the normalisation for the common precursors.

precursorsCommon <- assay(qf[, , "precursors_log"]) |> na.exclude() |> rownames()
harmonizing input:
  removing 90 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'
qf[precursorsCommon, , "precursors_norm"] |>
  longForm(colvars = colnames(colData(qf))) |> 
  data.frame() |> 
  filter(!is.na(value)) |>
  ggplot() + 
  aes(x = value,
      colour = strain,
      group = colname) +
  geom_density() +
  theme_minimal() +
   labs(subtitle = "Median normalised log2 precursor intensities (common)")
Warning: 'experiments' dropped; see 'drops()'
harmonizing input:
  removing 90 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'

precursorsCommonPTM <- assay(qf[, , "precursorsPTM_log"]) |> na.exclude() |> rownames()
harmonizing input:
  removing 90 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'
qf[precursorsCommonPTM, , "precursorsPTM_norm"] |>
  longForm(colvars = colnames(colData(qf))) |> 
  data.frame() |> 
  filter(!is.na(value)) |>
  ggplot() + 
  aes(x = value,
      colour = strain,
      group = colname) +
  geom_density() +
  theme_minimal() +
   labs(subtitle = "Median normalised log2 precursor intensities (common)")
Warning: 'experiments' dropped; see 'drops()'
harmonizing input:
  removing 90 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'

Remove temporarily objects

rm(precursorsCommon, precursorsCommonPTM)
#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 10401897 555.6   17413800  930.0         NA  17413800  930
Vcells 31719609 242.1  160705293 1226.1      24576 312075668 2381
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 10401890 555.6   17413800 930.0         NA  17413800  930
Vcells 31719630 242.1  128564235 980.9      24576 312075668 2381

Note, that normalisation could have been avoided by using Precursor.Normalised which is already internally normalised by DIA-NN. However, we do not know the exact procedure for this.

This generally works well for many datasets.

In this vignette we have chosen to conduct the normalisation explicitly ourselves using a method for which we know the underlying rationale.

11.4.5 Summarisation

Here, we summarise the precursor-level data for the non-enriched runs into protein intensities using maxLFQ, which is one of the default methods used in DIA data analysis.

Note, that the maxLFQ implementation can become slow for large datasets. In that case we recommend the median polish method.

  • maxLFQ first calculates all pairwise log ratio’s between samples only using their shared precursors. Particularly, it uses the median of the log ratio’s between the shared precursors, i.e.  \[r_{ij} = median(y_{sj}-y_{si})\].
    Hence, it first eliminates ion effects.

  • It then estimates the summaries by solving

\[ \sum_i\sum_j(y^{prot}_j - y^{prot}_i - r_{ij})^2 \]

It is implemented in the maxLFQ function of the iq package.

aggregateFeatures() in the QFeatures package streamlines summarisation. It requires the name of a rowData column to group the precursors into proteins (or protein groups), here Protein.Group. We provide the summarisation approach through the fun argument.

The function will return a QFeatures object with a new set that we called proteins.

Other summarisation methods are available from the MsCoreUtils package, see ?aggregateFeatures for a comprehensive list.

(qf <- aggregateFeatures(
  qf, i = "precursors_norm", 
  name = "proteins",
  fcol = "Protein.Group", 
  fun = function(X) iq::maxLFQ(X)$estimate
))
Your quantitative data contain missing values. Please read the relevant
section(s) in the aggregateFeatures manual page regarding the effects
of missing values on data aggregation.

Aggregated: 1/1
An instance of class QFeatures (type: bulk) with 7 sets:

 [1] precursors: SummarizedExperiment with 78047 rows and 18 columns 
 [2] precursorsPTM: SummarizedExperiment with 32916 rows and 18 columns 
 [3] precursors_log: SummarizedExperiment with 78047 rows and 18 columns 
 [4] precursorsPTM_log: SummarizedExperiment with 32916 rows and 18 columns 
 [5] precursors_norm: SummarizedExperiment with 78047 rows and 18 columns 
 [6] precursorsPTM_norm: SummarizedExperiment with 32916 rows and 18 columns 
 [7] proteins: SummarizedExperiment with 4607 rows and 18 columns 
#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 10418111 556.4   17413800 930.0         NA  17413800  930
Vcells 32190683 245.6  102851388 784.7      24576 312075668 2381
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 10418113 556.4   17413800 930.0         NA  17413800  930
Vcells 32190719 245.6  102851388 784.7      24576 312075668 2381

11.5 Data exploration and QC

Data exploration aims to highlight the main sources of variation in the data prior to data modelling and can pinpoint to outlying or off-behaving samples.

We first performance the QC for the Phospho-enriched runs then for the non-enriched runs.

11.5.1 Phospho-enriched runs

Marginal distribution at precursor level

qf[, , "precursorsPTM_norm"] |>
  longForm(colvars = colnames(colData(qf))) |> 
  data.frame() |> 
  filter(!is.na(value)) |>
  ggplot() + 
  aes(x = value,
      colour = strain,
      group = colname) +
  geom_density() +
  theme_minimal() +
   labs(subtitle = "Normalised log2 PTM precursor intensities")
harmonizing input:
  removing 108 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'

qf[, , "precursorsPTM_norm"] |>
  longForm(colvars = colnames(colData(qf))) |> 
  data.frame() |> 
  filter(!is.na(value)) |>
  ggplot() + 
  aes(x = sampleId,
      y = value,
      colour = strain,
      group = colname) +
  xlab("sample") +
  geom_boxplot() +
  theme_minimal() +
   labs(subtitle = "Normalised log2 PTM precursor intensities")
harmonizing input:
  removing 108 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'

#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 10447398 558.0   17413800 930.0         NA  17413800  930
Vcells 35837720 273.5  102851388 784.7      24576 312075668 2381
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 10447400 558.0   17413800 930.0         NA  17413800  930
Vcells 35837756 273.5  102851388 784.7      24576 312075668 2381

Charge state

qf[, , "precursorsPTM_norm"] |>
  longForm(colvars = colnames(colData(qf)), rowvars = "Precursor.Charge") |>
  as.data.frame() |>
  filter(!is.na(value)) |>
  filter(Precursor.Charge<=4) |> 
ggplot(aes(x = sampleId)) +
  geom_bar(aes(fill = factor(Precursor.Charge, levels = 4:1)),
           colour = "black") +
  labs(title = "Number of phospho-ions per sample",
       x = "Sample",
       fill = "Charge state") +
  theme_bw() + 
  theme(axis.text.x = element_text(angle = 90))
harmonizing input:
  removing 108 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'

#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 10454906 558.4   17413800 930.0         NA  17413800  930
Vcells 36035084 275.0  102851388 784.7      24576 312075668 2381
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 10454908 558.4   17413800 930.0         NA  17413800  930
Vcells 36035120 275.0  102851388 784.7      24576 312075668 2381

Identifications per sample

qf[,,"precursorsPTM_norm"] |> 
  longForm(colvars = colnames(colData(qf)), 
           rowvars= c("Precursor.Id", 
                      "Protein.Group")) |>
  data.frame() |>
  filter(!is.na(value)) |>
  group_by(strain, sampleId) |>
  summarise(Precursors = length(unique(Precursor.Id)),
            `Protein Groups` = length(unique(Protein.Group))) |> 
  pivot_longer(-(1:2),
               names_to = "Feature",
               values_to = "IDs") |> 
  ggplot(aes(x = sampleId, y = IDs, fill = strain)) +
  geom_col() +
  #scale_fill_observable() +
  facet_wrap(~Feature,
             scales = "free_y") +
  labs(title = "Precursor and protein group identificiations per PTM sample",
       x = "Sample",
       y = "Identifications") +
  theme_bw() + 
  theme(axis.text.x = element_text(angle = 90))
harmonizing input:
  removing 108 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'
`summarise()` has regrouped the output.
ℹ Summaries were computed grouped by strain and sampleId.
ℹ Output is grouped by strain.
ℹ Use `summarise(.groups = "drop_last")` to silence this message.
ℹ Use `summarise(.by = c(strain, sampleId))` for per-operation grouping
  (`?dplyr::dplyr_by`) instead.

# Data Modeling (Robust Regression){#sec-modelling}
#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 10510553 561.4   17413800 930.0         NA  17413800  930
Vcells 29745632 227.0  102851388 784.7      24576 312075668 2381
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 10510525 561.4   17413800 930.0         NA  17413800  930
Vcells 29745618 227.0  102851388 784.7      24576 312075668 2381

Dimensionality reduction plot

A common approach for data exploration is to perform dimension reduction, such as Multi Dimensional Scaling (MDS). We will first extract the set to explore along the sample annotations (used for plot colouring).

getWithColData(qf, "precursorsPTM_norm") |> 
  as("SingleCellExperiment") |> 
  runMDS(exprs_values = 1) |> 
  plotMDS(colour_by = "strain") 

#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 10532620 562.6   17413800 930.0         NA  17413800  930
Vcells 29810557 227.5  102851388 784.7      24576 312075668 2381
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 10532601 562.6   17413800 930.0         NA  17413800  930
Vcells 29810558 227.5  102851388 784.7      24576 312075668 2381

11.5.2 Non-enriched runs

Marginal distribution at precursor and protein level

qf[, , "precursors_norm"] |>
  longForm(colvars = colnames(colData(qf))) |> 
  data.frame() |> 
  filter(!is.na(value)) |>
  ggplot() + 
  aes(x = value,
      colour = strain,
      group = colname) +
  geom_density() +
  theme_minimal() +
   labs(subtitle = "Normalised log2 precursor intensities")
harmonizing input:
  removing 108 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'

qf[, , "precursors_norm"] |>
  longForm(colvars = colnames(colData(qf))) |> 
  data.frame() |> 
  filter(!is.na(value)) |>
  ggplot() + 
  aes(x = sampleId,
      y = value,
      colour = strain,
      group = colname) +
  xlab("sample") +
  geom_boxplot() +
  theme_minimal() +
   labs(subtitle = "Normalised log2 precursor intensities")
harmonizing input:
  removing 108 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'

qf[, , "proteins"] |>
  longForm(colvars = colnames(colData(qf))) |> 
  data.frame() |> 
  filter(!is.na(value)) |>
  ggplot() + 
  aes(x = value,
      colour = strain,
      group = colname) +
  geom_density() +
  theme_minimal() +
   labs(subtitle = "log2 protein intensities (normalised precursors)")
harmonizing input:
  removing 108 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'

qf[, , "proteins"] |>
  longForm(colvars = colnames(colData(qf))) |> 
  data.frame() |> 
  filter(!is.na(value)) |>
  ggplot() + 
  aes(x = sampleId,
      y = value,
      colour = strain,
      group = colname) +
  xlab("sample") +
  geom_boxplot() +
  theme_minimal() +
   labs(subtitle = "log2 protein intensities (normalised precursors)")
harmonizing input:
  removing 108 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'

#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 10533097 562.6   17413800 930.0         NA  17413800  930
Vcells 30936023 236.1  102851388 784.7      24576 312075668 2381
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 10533093 562.6   17413800 930.0         NA  17413800  930
Vcells 30936049 236.1  102851388 784.7      24576 312075668 2381

Charge state

qf[, , "precursors_norm"] |>
  longForm(colvars = colnames(colData(qf)), rowvars = "Precursor.Charge") |>
  as.data.frame() |>
  filter(!is.na(value)) |>
  filter(Precursor.Charge<=4) |> 
ggplot(aes(x = sampleId)) +
  geom_bar(aes(fill = factor(Precursor.Charge, levels = 4:1)),
           colour = "black") +
  labs(title = "Number of precursor ions per sample",
       x = "Sample",
       fill = "Charge state") +
  theme_bw() +
  theme(axis.text.x = element_text(angle = 90))
harmonizing input:
  removing 108 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'

#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 10533093 562.6   17413800 930.0         NA  17413800  930
Vcells 48098249 367.0  102851388 784.7      24576 312075668 2381
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 10533095 562.6   17413800 930.0         NA  17413800  930
Vcells 48098285 367.0  102851388 784.7      24576 312075668 2381

Identifications per sample

qf[,,"precursors_norm"] |> 
  longForm(colvars = colnames(colData(qf)), 
           rowvars= c("Precursor.Id", 
                      "Protein.Group")) |>
  data.frame() |>
  filter(!is.na(value)) |>
  group_by(strain, sampleId) |>
  summarise(Precursors = length(unique(Precursor.Id)),
            `Protein Groups` = length(unique(Protein.Group))) |> 
  pivot_longer(-(1:2),
               names_to = "Feature",
               values_to = "IDs") |> 
  ggplot(aes(x = sampleId, y = IDs, fill = strain)) +
  geom_col() +
  #scale_fill_observable() +
  facet_wrap(~Feature,
             scales = "free_y") +
  labs(title = "Precursor and protein group identificiations per sample",
       x = "Sample",
       y = "Identifications") +
  theme_bw() + 
  theme(axis.text.x = element_text(angle = 90))
harmonizing input:
  removing 108 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'
`summarise()` has regrouped the output.
ℹ Summaries were computed grouped by strain and sampleId.
ℹ Output is grouped by strain.
ℹ Use `summarise(.groups = "drop_last")` to silence this message.
ℹ Use `summarise(.by = c(strain, sampleId))` for per-operation grouping
  (`?dplyr::dplyr_by`) instead.

#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 10533229 562.6   17413800 930.0         NA  17413800  930
Vcells 29796548 227.4  102851388 784.7      24576 312075668 2381
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 10533207 562.6   17413800 930.0         NA  17413800  930
Vcells 29796544 227.4  102851388 784.7      24576 312075668 2381

Dimensionality reduction plot

getWithColData(qf, "proteins") |> 
  as("SingleCellExperiment") |> 
  runMDS(exprs_values = 1) |> 
  plotMDS(colour_by = "strain") 

#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 10532795 562.6   17413800 930.0         NA  17413800  930
Vcells 29797746 227.4  102851388 784.7      24576 312075668 2381
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 10532776 562.6   17413800 930.0         NA  17413800  930
Vcells 29797747 227.4  102851388 784.7      24576 312075668 2381

11.6 Data Modeling at phospho-precursor-level

11.6.1 Model estimation

  1. We first define the model. We only have one source of variability in the experiment that we can model, i.e. the effect of the strain.

  2. We fit the model to each phosphorylated precursor in the precursorsPTM_norm summarised experiment of the QFeatures object qf using the msqrob function.

model <- ~ strain
qf <- msqrob(
  qf,
  i = "precursorsPTM_norm",
  formula = model,
  robust = TRUE)

We enabled M-estimation (robust = TRUE) for improved robustness against outliers.

#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 11265974 601.7   17413800 930.0         NA  17413800  930
Vcells 31917874 243.6  102851388 784.7      24576 312075668 2381
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 11265979 601.7   17413800 930.0         NA  17413800  930
Vcells 31917915 243.6  102851388 784.7      24576 312075668 2381

11.6.2 Inference

We can now convert the research question “Is the abundance of phospho-precursors different between the strains” into a statistical hypotheses.

In other words, we need to translate this question in a null and alternative hypothesis on a single model parameter or a linear combination of model parameters, which is also referred to with a contrast.

To aid defining contrasts, we will visualise the experimental design using the ExploreModelMatrix package.

vd <- ExploreModelMatrix::VisualizeDesign(
    sampleData =  colData(qf),
    designFormula = model,
    textSizeFitted = 4
)
vd$plotlist
[[1]]

We have 3 interesting research questions related to the strain.

  1. Is a precursor DA between ArgSer strain and the WT (control)
  2. Is a precursor DA between ProAla strain and the WT (control)
  3. Is a precursor DA between ProAla strain and the ArgSer strain.

Each of these contrasts can be translated in a log2 FC or a difference in log2 FC and can be estimated with one or a linear combination of the model parameters.

Below we define the contrast and construct the corresponding contrast matrix.

We can generate the null-hypothesess for all pairwise comparisons manually. However, here we will use the createPairwiseContrasts function in msqrob2.

(allHypotheses <- createPairwiseContrasts(
  model, colData(qf), "strain"
  )
)
Warning: the 'nobars' function has moved to the reformulas package. Please update your imports, or ask an upstream package maintainter to do so.
This warning is displayed once per session.
[1] "strainCtrl = 0"                "strainProAla = 0"             
[3] "strainProAla - strainCtrl = 0"

Based on these null hypothesis we now generate the contrast matrix with all three contrasts using the makeContrast function. Note, that experienced users can also define the contrast matrix, directly.

(L <- makeContrast(
  allHypotheses,
  parameterNames = colnames(vd$designmatrix)
))
             strainCtrl strainProAla strainProAla - strainCtrl
(Intercept)           0            0                         0
strainCtrl            1            0                        -1
strainProAla          0            1                         1

We assess the contrast for each precursor.

qf <- hypothesisTest(qf, i = "precursorsPTM_norm", contrast = L, overwrite = TRUE)

We extract the results table from the precursorsPTM_norm summarised experiment in the qf object.

inferencesPTM <- 
  msqrobCollect(qf[["precursorsPTM_norm"]], L)
#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 11422450 610.1   17413800 930.0         NA  17413800  930
Vcells 34474215 263.1  102851388 784.7      24576 312075668 2381
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 11422446 610.1   17413800 930.0         NA  17413800  930
Vcells 34474241 263.1  102851388 784.7      24576 312075668 2381

11.6.3 Report results

We report the results using a results table, volcano plots and heatmaps.

Results table

We use the 5% nominal FDR level to report results

alpha <- 0.05
for (j in colnames(L)) {

  inference <- inferencesPTM |> 
    dplyr::filter(adjPval < alpha & contrast == j)

  cat("**Median - Contrast:**", j, "= 0 (", nrow(inference),
      "significant precursors)\n\n")

  cat('<div style="max-height:300px; overflow-y:auto;">')

  print(
    kable(
      inference |>
        dplyr::arrange(pval) |>
        dplyr::relocate(feature),
      row.names = FALSE
    )
  )

  cat('</div>')

  cat("\n\n\n---\n\n")
}

Median - Contrast: strainCtrl = 0 ( 132 significant precursors)

feature logFC se df t pval adjPval contrast
ETIDDTAS(UniMod:21)QILK2 -1.3878725 0.0868676 16.425974 -15.976871 0.0000000 0.0000005 strainCtrl
GQVVSEEQRPGT(UniMod:21)PLFTVK3 -1.7606517 0.1054288 15.293748 -16.699911 0.0000000 0.0000005 strainCtrl
ETVES(UniMod:21)ESSQTALSK2 -0.9019349 0.0690039 16.403443 -13.070775 0.0000000 0.0000046 strainCtrl
IARPLS(UniMod:21)VPGS(UniMod:21)PK2 0.7155560 0.0647198 16.256685 11.056212 0.0000000 0.0000451 strainCtrl
RGQVVSEEQRPGT(UniMod:21)PLFTVK3 -1.3829874 0.1323581 14.249637 -10.448831 0.0000000 0.0002299 strainCtrl
DLARENS(UniMod:21)LETTFSSVNTR3 -0.8330567 0.0883323 16.386810 -9.430945 0.0000001 0.0002299 strainCtrl
RAT(UniMod:21)YAGFLLADPK3 -2.7224415 0.2243879 11.815432 -12.132749 0.0000001 0.0002299 strainCtrl
LYDLLGVS(UniMod:21)PSANEQELK2 -1.4023471 0.1407479 14.806088 -9.963536 0.0000001 0.0002364 strainCtrl
T(UniMod:21)GAAPQTTFNVAPNSTPIVSTAATGLQHK3 -0.6373352 0.0682631 16.019004 -9.336459 0.0000001 0.0002494 strainCtrl
ETVESESS(UniMod:21)QTALSK2 -1.8228595 0.1448704 10.011209 -12.582688 0.0000002 0.0005918 strainCtrl
LVQIT(UniMod:21)PDGK2 0.8050579 0.0997421 15.547762 8.071393 0.0000006 0.0015085 strainCtrl
GSEIVIAT(UniMod:21)PGR2 -1.0818005 0.1276423 14.091319 -8.475248 0.0000007 0.0015085 strainCtrl
T(UniMod:21)GAAPQTTFNVAPNSTPIVSTAATGLQHK4 -1.1061639 0.1321426 14.224166 -8.370989 0.0000007 0.0015085 strainCtrl
IS(UniMod:21)PPVVAYR2 -1.8161978 0.2294100 15.617433 -7.916820 0.0000007 0.0015085 strainCtrl
GSSS(UniMod:21)LYTLVINDAGK2 1.1815421 0.1540268 16.592491 7.671014 0.0000008 0.0015085 strainCtrl
GSS(UniMod:21)SLYTLVINDAGK3 1.1091290 0.1390355 15.378296 7.977308 0.0000008 0.0015085 strainCtrl
HAS(UniMod:21)PLLEDVEDEEVDRYNESLSR3 -2.0647672 0.2549966 14.690577 -8.097233 0.0000009 0.0016133 strainCtrl
AAS(UniMod:21)FQDSTIPDAR2 -0.7091997 0.0919711 15.887975 -7.711115 0.0000009 0.0016589 strainCtrl
RGQVVSEEQRPGT(UniMod:21)PLFTVK4 -1.5676621 0.1700761 11.266455 -9.217417 0.0000014 0.0023369 strainCtrl
NLS(UniMod:21)NENC(UniMod:4)SFK2 0.6834720 0.0933326 16.375363 7.322972 0.0000015 0.0023875 strainCtrl
DSGYGVS(UniMod:21)VGR2 0.5426223 0.0727577 15.519801 7.457932 0.0000016 0.0025035 strainCtrl
KSDS(UniMod:21)GTVLGAIPLNSR2 -0.5679243 0.0748780 14.361829 -7.584663 0.0000022 0.0029837 strainCtrl
VDIIANDQGNRT(UniMod:21)TPSFVAFTDTER3 -0.7321217 0.0926959 13.314083 -7.898105 0.0000022 0.0029837 strainCtrl
VSSFNHS(UniMod:21)SSGMTSSDSLASEEVPSNK3 4.1866327 0.2650858 6.417882 15.793502 0.0000022 0.0029837 strainCtrl
SHS(UniMod:21)NILKPPVR3 -0.6884790 0.0982175 15.727572 -7.009740 0.0000032 0.0041514 strainCtrl
ENSTIQSSS(UniMod:21)SSNLR2 -0.7781743 0.0997623 12.534773 -7.800283 0.0000037 0.0045667 strainCtrl
AC(UniMod:4)VVYGGS(UniMod:21)PIGNQLR2 -0.7870067 0.1152159 15.669475 -6.830714 0.0000045 0.0053546 strainCtrl
S(UniMod:21)FIFPETSNQSK2 -0.5135915 0.0773459 16.609444 -6.640194 0.0000047 0.0053751 strainCtrl
SIS(UniMod:21)SVTNSDSNISSSK2 -0.4492690 0.0684650 16.778774 -6.562022 0.0000052 0.0053980 strainCtrl
KSDS(UniMod:21)GTVLGAIPLNSR3 -0.5644426 0.0833325 15.546547 -6.773382 0.0000052 0.0053980 strainCtrl
EAS(UniMod:21)LQEELEPLR2 -1.1595078 0.1670403 14.722408 -6.941485 0.0000052 0.0053980 strainCtrl
IETES(UniMod:21)TTIPNDSDR2 0.4523919 0.0683473 16.110299 6.619020 0.0000057 0.0057061 strainCtrl
YDETTFSGS(UniMod:21)PER2 0.5824588 0.0856507 14.947062 6.800393 0.0000061 0.0059222 strainCtrl
M(UniMod:35)TEAGS(UniMod:21)LDLIDDAGENS(UniMod:21)DLEDRIDNSLPGSQR4 -2.8911505 0.2386328 6.894347 -12.115480 0.0000067 0.0063329 strainCtrl
(UniMod:28)QLRDS(UniMod:21)FVTPNYSR2 0.9210333 0.1409903 15.674488 6.532602 0.0000076 0.0068143 strainCtrl
QLRDS(UniMod:21)FVTPNYSR3 0.5476409 0.0848089 16.109896 6.457351 0.0000077 0.0068143 strainCtrl
NNEGSSNMNMNRNDLDDVS(UniMod:21)HYEMK3 3.8354156 0.4188686 8.778774 9.156609 0.0000088 0.0076065 strainCtrl
DPIPSDPS(UniMod:21)ER2 -0.6050658 0.0947838 15.912926 -6.383639 0.0000093 0.0077894 strainCtrl
NTTATPIQFADFNT(UniMod:21)SSNNLTPSQSVTNSGTQVAHGNNMEVDR4 3.0634251 0.2064334 5.664072 14.839777 0.0000095 0.0077894 strainCtrl
RPTYSSS(UniMod:21)KSNNWTPGEASDTPPLPPHATPK4 -3.0020708 0.3623045 9.778774 -8.286042 0.0000100 0.0079776 strainCtrl
NGLNELASS(UniMod:21)ATK2 0.8320405 0.1330646 16.277252 6.252907 0.0000107 0.0083329 strainCtrl
PAPLTLAET(UniMod:21)HS(UniMod:21)PNASVENSHTIVR3 0.9826436 0.1288764 10.592238 7.624700 0.0000128 0.0097375 strainCtrl
NIDEDVNNLTAT(UniMod:21)TDEEDRDPESQK3 0.7167712 0.1029303 12.330727 6.963656 0.0000131 0.0097375 strainCtrl
ETNNNLSNM(UniMod:35)NSS(UniMod:21)PAQNPK3 -3.5401580 0.1985585 4.778774 -17.829298 0.0000148 0.0106251 strainCtrl
FEIGESGGNDPYMVSS(UniMod:21)PK3 2.1737356 0.2262873 7.677795 9.606088 0.0000151 0.0106251 strainCtrl
ERNPS(UniMod:21)ESVK2 -0.5644133 0.0923857 15.935255 -6.109316 0.0000153 0.0106251 strainCtrl
NEHS(UniMod:21)NLAVEDNIPEEEPK3 -0.5397225 0.0886019 15.966583 -6.091542 0.0000157 0.0106251 strainCtrl
IARPLSVPGS(UniMod:21)PK2 0.8082425 0.1350037 16.684810 5.986819 0.0000159 0.0106251 strainCtrl
GT(UniMod:21)QSQYESGLTSNK2 -0.5062964 0.0840562 16.142088 -6.023309 0.0000171 0.0111594 strainCtrl
NDNLDDKS(UniMod:21)TVC(UniMod:4)YSEK2 0.6221338 0.1037637 16.246350 5.995675 0.0000175 0.0112171 strainCtrl
ENS(UniMod:21)SLSSIK2 -0.7305715 0.1246591 16.626655 -5.860556 0.0000207 0.0128360 strainCtrl
SFGSGLKLKITDS(UniMod:21)NLENMEDVEAK3 2.9625200 0.2431345 5.906460 12.184698 0.0000208 0.0128360 strainCtrl
EEVS(UniMod:21)QLAELHLR3 -1.6458966 0.2710728 14.854436 -6.071789 0.0000223 0.0134745 strainCtrl
MSES(UniMod:21)PMFAANGMPK2 2.8704162 0.4061935 10.778774 7.066623 0.0000232 0.0137454 strainCtrl
TQLENS(UniMod:21)DNFEEQK2 0.5186244 0.0872310 15.223153 5.945413 0.0000253 0.0147092 strainCtrl
SNDSFINDDRNS(UniMod:21)FTNATTNAR3 -0.5750153 0.1004951 16.433641 -5.721824 0.0000284 0.0161043 strainCtrl
YTNST(UniMod:21)DSSESSLDFLK2 0.5622813 0.0926632 14.034977 6.068010 0.0000287 0.0161043 strainCtrl
(UniMod:27)EKSPT(UniMod:21)PQT(UniMod:21)STASLSSVTK3 3.2218326 0.4668367 10.439206 6.901412 0.0000337 0.0184493 strainCtrl
EAS(UniMod:21)TQEPAK2 -0.7501469 0.1318051 15.928709 -5.691333 0.0000340 0.0184493 strainCtrl
M(UniMod:35)TDPHLNTPQVSTS(UniMod:21)PTFER3 -2.4208678 0.3560428 10.587112 -6.799373 0.0000358 0.0188791 strainCtrl
NAESKDS(UniMod:21)DGVQVANESEEDPELK3 -0.5313498 0.0946522 16.287672 -5.613708 0.0000363 0.0188791 strainCtrl
KSDSGTVLGAIPLNS(UniMod:21)R3 -0.5127535 0.0903414 15.751351 -5.675734 0.0000365 0.0188791 strainCtrl
SNNWTPGEAS(UniMod:21)DT(UniMod:21)PPLPPHATPK3 4.9273214 0.4363360 5.778774 11.292492 0.0000373 0.0189449 strainCtrl
ESS(UniMod:21)LEGQDLTK2 -0.6936983 0.1188949 14.459240 -5.834549 0.0000381 0.0190580 strainCtrl
LSHFS(UniMod:21)NLEDASFK2 -0.6353741 0.1099548 14.354496 -5.778502 0.0000433 0.0213438 strainCtrl
(UniMod:1)SS(UniMod:21)EDIIYDPQFK2 0.4769651 0.0856592 15.739046 5.568172 0.0000451 0.0216395 strainCtrl
PYTEES(UniMod:21)E1 -1.7433153 0.2978099 13.735713 -5.853786 0.0000453 0.0216395 strainCtrl
TYS(UniMod:21)AENVPLTSTVSNDK2 0.4302315 0.0764934 15.184784 5.624429 0.0000462 0.0217806 strainCtrl
TFVS(UniMod:21)ETADDIEK2 0.5048344 0.0929629 16.778774 5.430492 0.0000471 0.0218525 strainCtrl
DIPVKS(UniMod:21)DDTPAK2 0.4511292 0.0828855 16.449479 5.442800 0.0000492 0.0225142 strainCtrl
NHS(UniMod:21)PDPIGIDNYK3 -0.3728104 0.0679928 15.756398 -5.483083 0.0000529 0.0238636 strainCtrl
AGSHS(UniMod:21)VGLLPM(UniMod:35)2 -2.4501832 0.2758181 6.778774 -8.883329 0.0000562 0.0247747 strainCtrl
KS(UniMod:21)SY(UniMod:21)GSNNDDSYGSNNDDSYGSSNK3 2.7718095 0.2618620 5.727599 10.585000 0.0000565 0.0247747 strainCtrl
QQTIDEQS(UniMod:21)QISPEK2 -0.3835711 0.0714394 16.187780 -5.369182 0.0000602 0.0260650 strainCtrl
QQADQAPPPYS(UniMod:21)SQSTPQVQAGAQAQQPR3 -0.6221011 0.1072449 13.015840 -5.800753 0.0000614 0.0262152 strainCtrl
HNES(UniMod:21)DLFWDNVHR3 -0.9515637 0.1702609 14.224294 -5.588858 0.0000630 0.0265338 strainCtrl
TLLEAIDAIEQPSRPT(UniMod:21)DK3 -0.4956322 0.0912516 15.108844 -5.431490 0.0000677 0.0274984 strainCtrl
(UniMod:27)EAVVDDGS(UniMod:21)ENAFGIPEFTR2 1.1828555 0.2142261 14.410270 5.521530 0.0000678 0.0274984 strainCtrl
NATGAAIPVAGPSS(UniMod:21)TPSPVIPVADASK3 2.2539326 0.3980817 13.439453 5.661985 0.0000685 0.0274984 strainCtrl
SDEEHTFENADAGAS(UniMod:21)ATYPM(UniMod:35)QC(UniMod:4)SALR3 3.0720165 0.2620513 5.114026 11.722959 0.0000687 0.0274984 strainCtrl
RSS(UniMod:21)GALVDDDKR3 -0.5512225 0.1051295 16.449544 -5.243273 0.0000735 0.0290634 strainCtrl
EQATDPILTATGPEDM(UniMod:35)QQSAS(UniMod:21)IVGPSSNANPVTATAATENQPK4 -3.3455175 0.5190276 9.957563 -6.445741 0.0000753 0.0294241 strainCtrl
EVS(UniMod:21)GFGSLNR2 -0.7191145 0.1380936 16.364419 -5.207443 0.0000803 0.0310072 strainCtrl
IRVESLLVS(UniMod:21)PISK3 -0.6407075 0.1222378 15.911847 -5.241485 0.0000821 0.0313248 strainCtrl
KEIS(UniMod:21)DIKK2 -0.8966197 0.1731766 16.449828 -5.177489 0.0000840 0.0316451 strainCtrl
DASQNGSGDS(UniMod:21)QSVISVDK2 -0.4400907 0.0854709 16.531767 -5.149012 0.0000876 0.0324558 strainCtrl
S(UniMod:21)S(UniMod:21)IPAGTDPGSC(UniMod:4)GANFK3 -3.6838365 0.4349142 6.598290 -8.470260 0.0000881 0.0324558 strainCtrl
RAT(UniMod:21)YAGFLLADPK2 -2.2362537 0.3634073 10.396416 -6.153574 0.0000914 0.0332551 strainCtrl
IPVIS(UniMod:21)SGK2 -0.4715652 0.0917836 16.297037 -5.137793 0.0000937 0.0337267 strainCtrl
NNSS(UniMod:21)RINLQDIC(UniMod:4)K3 0.3763185 0.0738274 16.481740 5.097273 0.0000983 0.0348219 strainCtrl
PLS(UniMod:21)VPGS(UniMod:21)PK2 0.8361467 0.1618861 15.740967 5.165032 0.0000989 0.0348219 strainCtrl
AALDEPDLNAVMT(UniMod:21)NEDSIDLNASEVDHSSR3 2.0035872 0.3073812 9.150121 6.518250 0.0001012 0.0352474 strainCtrl
AES(UniMod:21)DAVAEANDIDD2 -0.4631132 0.0914704 16.517439 -5.062984 0.0001047 0.0358421 strainCtrl
SDYGGS(UniMod:21)RDS(UniMod:21)FQSSGSR2 -1.9521263 0.2707220 7.778774 -7.210815 0.0001052 0.0358421 strainCtrl
QSLSNSS(UniMod:21)PM(UniMod:35)K2 -2.3025826 0.3682962 9.717155 -6.251986 0.0001074 0.0361768 strainCtrl
RNS(UniMod:21)SHVSSLTSR3 -0.5101551 0.0980835 14.960268 -5.201230 0.0001084 0.0361768 strainCtrl
NISNT(UniMod:21)PLVK2 1.0309356 0.1558726 8.778774 6.613962 0.0001095 0.0361768 strainCtrl
TYS(UniMod:21)LHEPTDAVHANIDTAPDGC(UniMod:4)K3 0.4464849 0.0888503 16.474509 5.025136 0.0001141 0.0372857 strainCtrl
LLAPS(UniMod:21)IEDVDANPEELR2 -0.7328891 0.1446215 15.912475 -5.067635 0.0001161 0.0375731 strainCtrl
TRDT(UniMod:21)PEDVSTAGAK2 -0.5458667 0.1089830 16.330868 -5.008732 0.0001211 0.0387358 strainCtrl
DASM(UniMod:35)QHDLIPLNSSDDYHNDASVTAATSNNFLSS(UniMod:21)PSSSDSLSK4 -2.7280898 0.4437936 9.728813 -6.147204 0.0001221 0.0387358 strainCtrl
NVSTEHQNQSHPVNS(UniMod:21)ESHLIAEPNILTPYVPSESSQTPVMK4 2.8984043 0.2569333 4.778774 11.280767 0.0001263 0.0390807 strainCtrl
ENS(UniMod:21)LETTFSSVNTR2 -0.6277617 0.1269173 16.778774 -4.946228 0.0001273 0.0390807 strainCtrl
RNT(UniMod:21)AIPTK2 0.7287215 0.1461134 16.198597 4.987369 0.0001295 0.0390807 strainCtrl
SLEAS(UniMod:21)AADES(UniMod:21)DEDEEAIR3 2.6823707 0.4531544 10.312439 5.919331 0.0001301 0.0390807 strainCtrl
(UniMod:1)SSTHSNNVGHPQSS(UniMod:21)PQGPLTEQQR3 0.4169189 0.0835204 16.114179 4.991821 0.0001303 0.0390807 strainCtrl
AEALNLANTDSQYLTPTSGS(UniMod:21)PVR3 0.3709410 0.0723372 14.744739 5.127943 0.0001305 0.0390807 strainCtrl
DPNNQTSENTFDPNRFTMLS(UniMod:21)DDDLKK3 -1.7223627 0.2483631 7.763226 -6.934857 0.0001386 0.0405033 strainCtrl
RQLANT(UniMod:21)PAK2 0.5229703 0.1054671 16.130599 4.958609 0.0001390 0.0405033 strainCtrl
TQTQPPS(UniMod:21)HLLSTSR3 1.5168155 0.1972348 6.769153 7.690404 0.0001391 0.0405033 strainCtrl
NGEDEDTDNLMGTENS(UniMod:21)FSLPPTR3 1.3509999 0.1932935 7.603629 6.989371 0.0001451 0.0416707 strainCtrl
ENS(UniMod:21)LETTFSSVNTR3 -0.5794016 0.1147484 14.940585 -5.049321 0.0001457 0.0416707 strainCtrl
NVFGT(UniMod:21)LQR2 1.0754536 0.2171622 15.778774 4.952306 0.0001500 0.0425244 strainCtrl
TGQLSALQS(UniMod:21)PVNITSSNK2 0.3469371 0.0701778 15.640654 4.943688 0.0001565 0.0432979 strainCtrl
LGS(UniMod:21)APNNAGEDSDNNSIR2 0.4570661 0.0943069 16.756205 4.846580 0.0001573 0.0432979 strainCtrl
NAVSTKPTPPPAPEASAESGLSS(UniMod:21)K3 -0.4215249 0.0853487 15.659249 -4.938854 0.0001575 0.0432979 strainCtrl
YAS(UniMod:21)SSSTDIENDDEK2 -0.3976706 0.0797551 15.144492 -4.986147 0.0001581 0.0432979 strainCtrl
TPNAVYREENS(UniMod:21)PIQSPVQPILSSPK3 -0.2987311 0.0614189 16.097275 -4.863833 0.0001695 0.0460223 strainCtrl
MQNIAPS(UniMod:21)RSSESTPTSGPPLLPPR3 3.9118948 0.3526906 4.590457 11.091576 0.0001732 0.0466343 strainCtrl
NNEES(UniMod:21)REEATAALK3 -0.4283977 0.0874418 15.328848 -4.899235 0.0001811 0.0480255 strainCtrl
RRS(UniMod:21)QIDTDYALR3 -0.4018705 0.0834938 16.311130 -4.813177 0.0001814 0.0480255 strainCtrl
FIELSQQQPAPVEAEIT(UniMod:21)GGEVAANGDNTLFTIK4 -0.9485678 0.1933808 14.966335 -4.905181 0.0001916 0.0498572 strainCtrl
HAS(UniMod:21)PLLEDVEDEEVDRYNESLSR4 -1.1693781 0.2183149 11.572649 -5.356382 0.0001946 0.0498572 strainCtrl
MSEES(UniMod:21)LFESSPQK2 -2.9476160 0.6108699 15.749257 -4.825276 0.0001947 0.0498572 strainCtrl
IS(UniMod:21)M(UniMod:35)SPNRELLK3 -2.8756712 0.3444515 5.778774 -8.348551 0.0001952 0.0498572 strainCtrl
TSQPQQQS(UniMod:21)PSLLQGEIR3 0.3641770 0.0745655 15.061615 4.883985 0.0001962 0.0498572 strainCtrl
YASSS(UniMod:21)STDIENDDEK2 -0.4484113 0.0900753 14.075441 -4.978183 0.0001994 0.0498572 strainCtrl
VDFSAPPLVPTNSTT(UniMod:21)K3 -0.8339604 0.1515542 10.778774 -5.502720 0.0001995 0.0498572 strainCtrl
VC(UniMod:4)S(UniMod:21)SHTGLVR2 0.9496776 0.1928233 14.518706 4.925118 0.0002012 0.0498572 strainCtrl
LETDES(UniMod:21)PIQTK2 0.3624824 0.0755521 15.820619 4.797781 0.0002033 0.0498572 strainCtrl
QNFIAENGT(UniMod:21)Y(UniMod:21)LPETIWPGK3 1.9954199 0.3221820 8.494879 6.193455 0.0002039 0.0498572 strainCtrl
QTYNVGS(UniMod:21)EAETNEK2 0.3328000 0.0703759 16.609290 4.728894 0.0002060 0.0499845 strainCtrl

Median - Contrast: strainProAla = 0 ( 136 significant precursors)

feature logFC se df t pval adjPval contrast
(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2 2.0438618 0.0998935 15.949529 20.460402 0.0000000 0.0000000 strainProAla
S(UniMod:21)DSEVNQEAKPEVK2 2.0942845 0.1662582 16.220860 12.596576 0.0000000 0.0000137 strainProAla
RNT(UniMod:21)AIPTK2 1.5267558 0.1488333 16.198597 10.258159 0.0000000 0.0001815 strainProAla
S(UniMod:21)DSEVNQEAKPEVK3 2.2676641 0.2059957 14.273891 11.008309 0.0000000 0.0001841 strainProAla
NNEES(UniMod:21)REEATAALK3 -0.8475604 0.0848461 15.328848 -9.989384 0.0000000 0.0002373 strainProAla
LYDLLGVS(UniMod:21)PSANEQELK2 -1.4134161 0.1388533 14.806088 -10.179204 0.0000000 0.0002373 strainProAla
AINS(UniMod:21)PIIR2 1.2304097 0.1289973 15.871674 9.538260 0.0000001 0.0002582 strainProAla
TT(UniMod:21)PSFVAFTDTER2 0.8267539 0.0958953 16.703475 8.621423 0.0000001 0.0005934 strainProAla
INMGGGLFLSPEDIT(UniMod:21)KIASGLIS(UniMod:21)PVLGEVSER4 -4.9540273 0.3810121 8.870392 -13.002283 0.0000004 0.0015780 strainProAla
S(UniMod:21)FIFPETSNQSK2 -0.5790829 0.0767904 16.609444 -7.541090 0.0000009 0.0029830 strainProAla
(UniMod:1)TT(UniMod:21)ASSSASQLQQR2 1.1062218 0.1471155 15.615069 7.519409 0.0000014 0.0041384 strainProAla
M(UniMod:35)TDPHLNTPQVSTS(UniMod:21)PTFER3 -3.1544089 0.3382423 10.587112 -9.325886 0.0000020 0.0050395 strainProAla
VSSFNHS(UniMod:21)SSGMTSSDSLASEEVPSNK3 4.3404584 0.2711614 6.417882 16.006919 0.0000021 0.0050395 strainProAla
T(UniMod:21)GAAPQTTFNVAPNSTPIVSTAATGLQHK3 -0.4979321 0.0705833 16.019004 -7.054528 0.0000027 0.0061606 strainProAla
M(UniMod:35)TEAGS(UniMod:21)LDLIDDAGENS(UniMod:21)DLEDRIDNSLPGSQR4 -2.9746263 0.2170261 6.894347 -13.706307 0.0000030 0.0062902 strainProAla
VDIIANDQGNRT(UniMod:21)TPSFVAFTDTER3 0.7766528 0.1024428 13.314083 7.581328 0.0000035 0.0069052 strainProAla
QAGS(UniMod:21)PSSTVSSLAK2 1.0257423 0.1466699 15.163703 6.993543 0.0000041 0.0074274 strainProAla
HSRPLS(UniMod:21)IS(UniMod:21)ST(UniMod:21)TPLDLQR3 5.2389750 0.3146317 5.778774 16.651134 0.0000042 0.0074274 strainProAla
APVAS(UniMod:21)PRPAAT(UniMod:21)PNLSK3 -0.7080543 0.1050468 15.931263 -6.740372 0.0000049 0.0077670 strainProAla
VVEATPEDGTASS(UniMod:21)QK2 -0.4386139 0.0652099 15.891375 -6.726189 0.0000050 0.0077670 strainProAla
DADLPQLQNTLS(UniMod:21)IRK3 -0.9345877 0.1289767 13.554754 -7.246174 0.0000051 0.0077670 strainProAla
GSSS(UniMod:21)LYTLVINDAGK2 0.9959429 0.1531520 16.592491 6.502970 0.0000061 0.0088352 strainProAla
FEIGESGGNDPYMVSS(UniMod:21)PK3 2.5509100 0.2381191 7.677795 10.712749 0.0000069 0.0095752 strainProAla
LVQIT(UniMod:21)PDGK2 0.6554916 0.0995412 15.547762 6.585130 0.0000072 0.0096173 strainProAla
GSS(UniMod:21)SLYTLVINDAGK3 0.9045271 0.1375883 15.378296 6.574158 0.0000078 0.0099412 strainProAla
IVGNT(UniMod:21)DAEK2 -0.7866964 0.1239718 16.171112 -6.345772 0.0000092 0.0104381 strainProAla
SNSS(UniMod:21)NSYELESGR2 -0.4450880 0.0699790 16.046468 -6.360307 0.0000093 0.0104381 strainProAla
ASLDYDPSVPNTSYAPVQSAS(UniMod:21)PVVK3 0.4901483 0.0763844 15.664312 6.416864 0.0000094 0.0104381 strainProAla
QQADQAPPPYS(UniMod:21)SQSTPQVQAGAQAQQPR3 -0.7487753 0.1072449 13.015840 -6.981921 0.0000095 0.0104381 strainProAla
AALDEPDLNAVMT(UniMod:21)NEDSIDLNASEVDHSSR3 2.5701718 0.2943942 9.150121 8.730376 0.0000098 0.0104381 strainProAla
T(UniMod:21)GAAPQTTFNVAPNSTPIVSTAATGLQHK4 -0.8559111 0.1309358 14.224166 -6.536875 0.0000122 0.0125542 strainProAla
MSEES(UniMod:21)LFESSPQK2 -3.7881920 0.6068464 15.749257 -6.242423 0.0000126 0.0125895 strainProAla
NNEGSSNMNMNRNDLDDVS(UniMod:21)HYEMK3 3.5678770 0.4104057 8.778774 8.693537 0.0000133 0.0128478 strainProAla
GT(UniMod:21)QSQYESGLTSNK2 -0.5139302 0.0838901 16.142088 -6.126229 0.0000141 0.0131757 strainProAla
SFGSGLKLKITDS(UniMod:21)NLENMEDVEAK3 3.1535974 0.2431345 5.906460 12.970590 0.0000146 0.0132754 strainProAla
KDS(UniMod:21)PSFLPGQQR3 0.4930127 0.0801687 15.370943 6.149692 0.0000167 0.0147504 strainProAla
APVAS(UniMod:21)PRPAAT(UniMod:21)PNLSK2 -0.7615531 0.1204927 14.303299 -6.320325 0.0000171 0.0147504 strainProAla
MSES(UniMod:21)PMFAANGMPK2 2.9151155 0.4061935 10.778774 7.176668 0.0000202 0.0166381 strainProAla
ETIDDTAS(UniMod:21)QILK2 -0.5151723 0.0874094 16.425974 -5.893788 0.0000204 0.0166381 strainProAla
LGLPHGS(UniMod:21)GPT(UniMod:21)SVYNNK2 -2.0434402 0.1981212 6.750729 -10.314092 0.0000223 0.0177158 strainProAla
QIVFEIPS(UniMod:21)ETH2 -0.6845834 0.1177475 16.601886 -5.813998 0.0000228 0.0177158 strainProAla
NSTPSDASS(UniMod:21)TK2 -1.1378697 0.1818170 13.540264 -6.258323 0.0000244 0.0185210 strainProAla
MS(UniMod:21)DSEVNQEAKPEVK3 2.6430660 0.4240863 13.361813 6.232377 0.0000270 0.0196162 strainProAla
S(UniMod:21)S(UniMod:21)IPAGTDPGSC(UniMod:4)GANFK3 -3.8667196 0.3796015 6.598290 -10.186261 0.0000282 0.0196162 strainProAla
SQSNGDEEDS(UniMod:21)ILK2 0.4317453 0.0750542 16.158940 5.752445 0.0000286 0.0196162 strainProAla
EYVPLDNAEQSTSSS(UniMod:21)QETK3 -0.4465230 0.0776795 16.182125 -5.748272 0.0000286 0.0196162 strainProAla
SDEEHTFENADAGAS(UniMod:21)ATYPM(UniMod:35)QC(UniMod:4)SALR3 3.5211132 0.2524711 5.114026 13.946601 0.0000289 0.0196162 strainProAla
(UniMod:28)QAGS(UniMod:21)PSSTVSSLAK2 1.3576363 0.2340737 15.528924 5.800038 0.0000305 0.0198067 strainProAla
SNNWTPGEAS(UniMod:21)DT(UniMod:21)PPLPPHATPK3 5.5794322 0.4779822 5.778774 11.672887 0.0000310 0.0198067 strainProAla
KGDEESGADT(UniMod:21)VTS(UniMod:21)PITFEK3 3.9054104 0.3914110 6.630576 9.977773 0.0000311 0.0198067 strainProAla
SST(UniMod:21)EHMLISPGR3 3.4131192 0.1804936 4.189280 18.909920 0.0000324 0.0202611 strainProAla
NTTATPIQFADFNT(UniMod:21)SSNNLTPSQSVTNSGTQVAHGNNMEVDR4 3.4370326 0.2905149 5.664072 11.830830 0.0000330 0.0202611 strainProAla
TGLGTPNQQVSVPNIVS(UniMod:21)PK3 3.4958101 0.4129454 7.778774 8.465550 0.0000343 0.0206312 strainProAla
LRDLY(UniMod:21)LEQTESDSDFDEGSQANGSVPPLK3 -4.8438586 0.6618835 9.369851 -7.318295 0.0000361 0.0206468 strainProAla
EIQEALS(UniMod:21)EKPTREPTPSVK3 -0.4227109 0.0754868 16.408134 -5.599796 0.0000363 0.0206468 strainProAla
AGSFGAPSS(UniMod:21)PTSGIPNPK2 0.4066255 0.0735320 16.695571 5.529912 0.0000392 0.0206468 strainProAla
NTPAESIS(UniMod:21)DLEGM(UniMod:35)TTFAPTTGGENR3 -2.7351240 0.1897330 4.778774 -14.415646 0.0000403 0.0206468 strainProAla
(UniMod:1)MDPLS(UniMod:21)SVQPASYVGFDTITNQIEHR3 1.2544947 0.1889409 10.778774 6.639613 0.0000404 0.0206468 strainProAla
THT(UniMod:21)QPVPASFDR3 -0.4200633 0.0756008 16.190202 -5.556337 0.0000416 0.0206468 strainProAla
SAHPARFS(UniMod:21)PDDK3 -0.3948870 0.0717848 16.683356 -5.500980 0.0000417 0.0206468 strainProAla
ATILALTSAVSS(UniMod:21)PK2 0.4519060 0.0811199 15.972815 5.570842 0.0000425 0.0206468 strainProAla
TVDPAS(UniMod:21)APNHSPEIDNLDDLVVLK4 2.2886059 0.3697558 12.249622 6.189506 0.0000426 0.0206468 strainProAla
AAYGDIS(UniMod:21)DEEEK2 0.3904622 0.0692277 15.370158 5.640258 0.0000429 0.0206468 strainProAla
QSLSNSS(UniMod:21)PM(UniMod:35)K2 -2.5621254 0.3670676 9.717155 -6.979983 0.0000440 0.0206468 strainProAla
ALLELLDDS(UniMod:21)PVTPGETR3 1.6392509 0.2202209 8.778774 7.443667 0.0000448 0.0206468 strainProAla
APVAS(UniMod:21)PRPAATPNLSK2 -0.5955712 0.1054773 15.142621 -5.646438 0.0000448 0.0206468 strainProAla
KDS(UniMod:21)PSFLPGQQR2 0.9710568 0.1704048 14.760314 5.698529 0.0000449 0.0206468 strainProAla
DLGVNVLS(UniMod:21)QSSLEEK2 -0.5003727 0.0910732 16.362042 -5.494184 0.0000453 0.0206468 strainProAla
DIPGDEAYNS(UniMod:21)DDIM(UniMod:35)APLREK3 -3.8455940 0.3529715 5.778774 -10.894913 0.0000455 0.0206468 strainProAla
EASAAYEILS(UniMod:21)DPEK2 -1.9883711 0.2090392 6.531127 -9.511951 0.0000460 0.0206468 strainProAla
QTHSDDEDLPAVS(UniMod:21)PYPNEK3 0.6869457 0.1170817 13.577251 5.867234 0.0000464 0.0206468 strainProAla
ETNNNLSNM(UniMod:35)NSS(UniMod:21)PAQNPK3 -2.7728760 0.1985585 4.778774 -13.965036 0.0000467 0.0206468 strainProAla
TGAAPQTTFNVAPNSTPIVSTAAT(UniMod:21)GLQHK3 -1.0323271 0.1772420 13.738445 -5.824392 0.0000476 0.0206468 strainProAla
APVAS(UniMod:21)PRPAATPNLSK3 -0.5581158 0.1001923 15.458035 -5.570447 0.0000479 0.0206468 strainProAla
TPTPTPPVVAEPAIS(UniMod:21)PRPVSQR3 -0.3675392 0.0670477 16.116081 -5.481758 0.0000489 0.0208065 strainProAla
NVSTEHQNQSHPVNS(UniMod:21)ESHLIAEPNILTPYVPSESSQTPVMK4 3.2752621 0.2422390 4.778774 13.520787 0.0000544 0.0228021 strainProAla
S(UniMod:21)SSVYM(UniMod:35)DSEPAVNK2 -3.9124251 0.3816181 5.895808 -10.252200 0.0000561 0.0232405 strainProAla
LET(UniMod:21)DESPIQTK2 0.4530457 0.0822945 15.218199 5.505179 0.0000574 0.0233255 strainProAla
MS(UniMod:21)DSEVNQEAKPEVK2 3.0843475 0.5578444 15.001883 5.529046 0.0000578 0.0233255 strainProAla
SHS(UniMod:21)NILKPPVR3 -0.5445265 0.1004937 15.727572 -5.418515 0.0000603 0.0240495 strainProAla
DASM(UniMod:35)QHDLIPLNSSDDYHNDASVTAATSNNFLSS(UniMod:21)PSSSDSLSK4 -2.9578157 0.4425956 9.728813 -6.682885 0.0000625 0.0245995 strainProAla
RNS(UniMod:21)YISANSEEER2 -0.9710622 0.1796784 15.524175 -5.404446 0.0000649 0.0252242 strainProAla
EGSSS(UniMod:21)QVSQTLNIPIK2 -0.5341941 0.0976658 14.749758 -5.469611 0.0000686 0.0263572 strainProAla
YGIYHGDDDS(UniMod:21)TLNNVFDK2 -1.1117145 0.1981822 13.612653 -5.609558 0.0000715 0.0271272 strainProAla
KYFDS(UniMod:21)GDYALQK3 -0.8704276 0.1503587 12.463574 -5.789006 0.0000743 0.0278532 strainProAla
IS(UniMod:21)M(UniMod:35)SPNRELLK3 -3.1178396 0.3144398 5.778774 -9.915538 0.0000765 0.0283553 strainProAla
NPWLTGNLVEEANS(UniMod:21)QGIIQNR3 -0.6370447 0.1146406 13.378643 -5.556886 0.0000835 0.0305953 strainProAla
YIDDS(UniMod:21)SFDTEK2 -0.8708320 0.1656818 15.604941 -5.256050 0.0000851 0.0308148 strainProAla
SSS(UniMod:21)FAHLQAPSPIPDPLQVSK3 0.7667350 0.1450611 15.106822 5.285601 0.0000894 0.0320229 strainProAla
ITIDS(UniMod:21)PYLVC(UniMod:4)TEGEK2 0.4741006 0.0920611 16.303973 5.149847 0.0000913 0.0323529 strainProAla
TLTPQNKQS(UniMod:21)PANTK3 -0.4975451 0.0961171 15.745063 -5.176446 0.0000966 0.0338578 strainProAla
S(UniMod:21)DS(UniMod:21)EVNQEAKPEVK3 2.0831402 0.3050262 8.508632 6.829382 0.0001001 0.0342282 strainProAla
ASSVAS(UniMod:21)IHNQR2 0.7385730 0.1454690 16.532687 5.077183 0.0001015 0.0342282 strainProAla
SFPLT(UniMod:21)QEEEHHGAVS(UniMod:21)PAVDTR3 -0.4009682 0.0774774 15.503839 -5.175293 0.0001017 0.0342282 strainProAla
RPLS(UniMod:21)QPTTSIGFPALEK2 -0.5688363 0.1116148 16.292430 -5.096422 0.0001020 0.0342282 strainProAla
SST(UniMod:21)PLSGAASSSC(UniMod:4)FQYNNVR2 0.5601824 0.1094401 15.997291 5.118619 0.0001032 0.0342608 strainProAla
PEQEPLS(UniMod:21)PNGRK2 -0.4908709 0.0973179 16.645621 -5.043996 0.0001064 0.0349778 strainProAla
(UniMod:27)ES(UniMod:21)VHNHSDGDDVDIPM(UniMod:35)DDSPVNEEAR4 2.9098591 0.2153623 4.311582 13.511461 0.0001082 0.0352058 strainProAla
FSES(UniMod:21)VDSLR2 1.0184164 0.1914348 13.590265 5.319913 0.0001196 0.0382454 strainProAla
GPPDATLTSGGSLPVS(UniMod:21)PRPLVT(UniMod:21)TLVSSQNTTSSGATGVAALEM(UniMod:35)K4 -2.1516504 0.2944180 7.438274 -7.308147 0.0001200 0.0382454 strainProAla
YTNST(UniMod:21)DSSESSLDFLK2 0.4856047 0.0925422 14.034977 5.247388 0.0001224 0.0385490 strainProAla
ALLELLDDSPVT(UniMod:21)PGETR2 1.5821619 0.2397254 8.583504 6.599893 0.0001233 0.0385490 strainProAla
MQNIAPS(UniMod:21)RSSESTPTSGPPLLPPR3 4.0017564 0.3352922 4.590457 11.935130 0.0001249 0.0386730 strainProAla
LVPADS(UniMod:21)DEEEYETSHISDTPVSLSSANDR4 4.3459892 0.3895351 4.778774 11.156862 0.0001329 0.0402499 strainProAla
SFFKES(UniMod:21)NDETYDPDTLAPALDGR3 -0.6930931 0.1351605 14.637538 -5.127928 0.0001336 0.0402499 strainProAla
VIEEYSLS(UniMod:21)QGSGPSNDSWK2 -0.6870535 0.1289239 13.032622 -5.329138 0.0001357 0.0402499 strainProAla
MKT(UniMod:21)TDTYPSLPK2 0.8584211 0.1585147 12.485991 5.415403 0.0001359 0.0402499 strainProAla
S(UniMod:21)NSSNSYELESGR2 -0.3719125 0.0756945 16.778774 -4.913335 0.0001363 0.0402499 strainProAla
(UniMod:1)SS(UniMod:21)VQLSR2 -0.8055954 0.1496451 12.534782 -5.383372 0.0001414 0.0413621 strainProAla
VTNVSHS(UniMod:21)QEAEK2 -0.6398439 0.1279019 15.414066 -5.002615 0.0001453 0.0421270 strainProAla
TGQLSALQS(UniMod:21)PVNITSSNK2 0.3547601 0.0715015 15.640654 4.961578 0.0001511 0.0423445 strainProAla
VDPETLHEALPPPNAS(UniMod:21)PISHLR3 -0.8275245 0.1671202 15.728605 -4.951674 0.0001516 0.0423445 strainProAla
DAQIVVGT(UniMod:21)PGR2 0.3649481 0.0747550 16.527254 4.881921 0.0001518 0.0423445 strainProAla
M(UniMod:35)PEDTTDVEQVAS(UniMod:21)PNDNESNPSEAK3 -3.2637816 0.3015715 4.778774 -10.822578 0.0001530 0.0423445 strainProAla
FEQASESEPT(UniMod:21)TVSYEIAGNS(UniMod:21)PNAER3 2.7397648 0.2532714 4.778774 10.817505 0.0001533 0.0423445 strainProAla
WYPS(UniMod:21)EDVAALK2 0.7244876 0.1467957 15.805244 4.935346 0.0001545 0.0423445 strainProAla
NTSS(UniMod:21)MDFLNSMENTPK2 2.6896305 0.2440824 4.699695 11.019354 0.0001554 0.0423445 strainProAla
RTHT(UniMod:21)QPVPASFDR3 -0.4636329 0.0949001 16.292061 -4.885485 0.0001568 0.0423798 strainProAla
DSTNEFVGS(UniMod:21)PSLTSPQYIPS(UniMod:21)PLSSTK3 1.4971002 0.2982813 14.776535 5.019088 0.0001596 0.0427707 strainProAla
RPFS(UniMod:21)SSSAEESQK3 4.7599164 0.4450965 4.778774 10.694122 0.0001617 0.0427749 strainProAla
ISRPIASQNS(UniMod:21)LGWNEV2 0.6510056 0.1304045 14.951297 4.992201 0.0001623 0.0427749 strainProAla
GTSQVGELSQS(UniMod:21)STK2 0.4039483 0.0828293 16.056453 4.876876 0.0001663 0.0434490 strainProAla
LGS(UniMod:21)APNNAGEDSDNNSIR2 0.4528356 0.0943069 16.756205 4.801721 0.0001728 0.0447914 strainProAla
STESIC(UniMod:4)S(UniMod:21)LTK2 0.4661840 0.0972364 16.778774 4.794339 0.0001749 0.0449610 strainProAla
TNLNNPS(UniMod:21)GTSGWR2 0.5842211 0.1220310 16.775309 4.787481 0.0001775 0.0452723 strainProAla
EASPAQYSHS(UniMod:21)LHER3 -0.4019816 0.0831277 15.708002 -4.835712 0.0001920 0.0483881 strainProAla
AQLHHDSHTNAGT(UniMod:21)PVLTPAPVPAGS(UniMod:21)NPWGVTQSATPVTSINLSK4 -2.3498923 0.2808006 5.778774 -8.368544 0.0001927 0.0483881 strainProAla
VEVDS(UniMod:21)FSGAK2 -0.4454321 0.0932104 16.293604 -4.778781 0.0001953 0.0484281 strainProAla
RNIS(UniMod:21)MALDDDDEEK3 1.4451151 0.2728304 11.878375 5.296752 0.0001959 0.0484281 strainProAla
SC(UniMod:4)ETQDES(UniMod:21)EIKDAET(UniMod:21)SC(UniMod:4)DNYHPM(UniMod:35)NIDETSDEVSR4 -3.6884673 0.3611647 4.778774 -10.212703 0.0001999 0.0490197 strainProAla
T(UniMod:21)RNPLTHSTPK3 -2.3402880 0.2700335 5.520111 -8.666659 0.0002034 0.0495019 strainProAla
NGEDEDTDNLMGTENS(UniMod:21)FSLPPTR3 1.2868687 0.1941766 7.603629 6.627312 0.0002065 0.0495019 strainProAla
SSDKDAT(UniMod:21)TDGKNDDEEEEK3 -0.7019555 0.1392841 13.369627 -5.039740 0.0002079 0.0495019 strainProAla
DASQNGSGDS(UniMod:21)QSVISVDK2 -0.4025890 0.0851434 16.531767 -4.728365 0.0002087 0.0495019 strainProAla
IETES(UniMod:21)TTIPNDSDR2 -0.3193642 0.0671409 16.110299 -4.756626 0.0002106 0.0495019 strainProAla
AQTQS(UniMod:21)SVQLK2 0.4473760 0.0946738 16.496598 4.725447 0.0002112 0.0495019 strainProAla

Median - Contrast: strainProAla - strainCtrl = 0 ( 377 significant precursors)

feature logFC se df t pval adjPval contrast
(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2 2.1457286 0.0985026 15.949529 21.783474 0.0000000 0.0000000 strainProAla - strainCtrl
GQVVSEEQRPGT(UniMod:21)PLFTVK3 2.2079917 0.1015815 15.293748 21.736164 0.0000000 0.0000000 strainProAla - strainCtrl
ETVES(UniMod:21)ESSQTALSK2 0.9567824 0.0681487 16.403443 14.039626 0.0000000 0.0000015 strainProAla - strainCtrl
TT(UniMod:21)PSFVAFTDTER2 1.2734144 0.0961995 16.703475 13.237224 0.0000000 0.0000022 strainProAla - strainCtrl
VDIIANDQGNRT(UniMod:21)TPSFVAFTDTER3 1.5087745 0.0997399 13.314083 15.127092 0.0000000 0.0000057 strainProAla - strainCtrl
RGQVVSEEQRPGT(UniMod:21)PLFTVK3 1.7450085 0.1333930 14.249637 13.081708 0.0000000 0.0000123 strainProAla - strainCtrl
S(UniMod:21)DSEVNQEAKPEVK2 1.9615652 0.1684383 16.220860 11.645602 0.0000000 0.0000123 strainProAla - strainCtrl
IETES(UniMod:21)TTIPNDSDR2 -0.7717561 0.0676291 16.110299 -11.411593 0.0000000 0.0000156 strainProAla - strainCtrl
RAT(UniMod:21)YAGFLLADPK3 2.9490160 0.2201907 11.815432 13.393010 0.0000000 0.0000592 strainProAla - strainCtrl
ETIDDTAS(UniMod:21)QILK2 0.8727002 0.0877898 16.425974 9.940795 0.0000000 0.0000740 strainProAla - strainCtrl
IS(UniMod:21)PPVVAYR2 2.2530264 0.2294100 15.617433 9.820959 0.0000000 0.0001268 strainProAla - strainCtrl
AINS(UniMod:21)PIIR2 1.1924405 0.1270271 15.871674 9.387290 0.0000001 0.0001860 strainProAla - strainCtrl
IARPLS(UniMod:21)VPGS(UniMod:21)PK2 -0.5916613 0.0648979 16.256685 -9.116802 0.0000001 0.0002090 strainProAla - strainCtrl
RGQVVSEEQRPGT(UniMod:21)PLFTVK4 2.0049637 0.1689532 11.266455 11.866980 0.0000001 0.0002187 strainProAla - strainCtrl
S(UniMod:21)DSEVNQEAKPEVK3 1.9560306 0.1999615 14.273891 9.782038 0.0000001 0.0002187 strainProAla - strainCtrl
ENSTIQSSS(UniMod:21)SSNLR2 0.9052793 0.0864436 12.534773 10.472482 0.0000001 0.0002903 strainProAla - strainCtrl
ETVESESS(UniMod:21)QTALSK2 1.8695628 0.1471488 10.011209 12.705251 0.0000002 0.0003014 strainProAla - strainCtrl
NAVSTKPTPPPAPEASAES(UniMod:21)GLSS(UniMod:21)K3 1.0783927 0.1215856 15.626159 8.869409 0.0000002 0.0003014 strainProAla - strainCtrl
KSDS(UniMod:21)GTVLGAIPLNSR3 0.7027831 0.0816803 15.546547 8.604076 0.0000003 0.0004421 strainProAla - strainCtrl
SQSNGDEEDS(UniMod:21)ILK2 0.6426236 0.0769869 16.158940 8.347177 0.0000003 0.0004690 strainProAla - strainCtrl
DYGDAFEGIENTSLS(UniMod:21)PK2 0.6039379 0.0733338 16.432406 8.235470 0.0000003 0.0004732 strainProAla - strainCtrl
(UniMod:1)SS(UniMod:21)AITALTPNQVNDELNK2 0.7000865 0.0847613 16.156940 8.259511 0.0000003 0.0004908 strainProAla - strainCtrl
GSEIVIAT(UniMod:21)PGR2 1.1399213 0.1282532 14.091319 8.888052 0.0000004 0.0005162 strainProAla - strainCtrl
HAS(UniMod:21)PLLEDVEDEEVDRYNESLSR3 2.1953862 0.2557564 14.690577 8.583897 0.0000004 0.0005522 strainProAla - strainCtrl
VDIIANDQGNRTT(UniMod:21)PSFVGFTDTER3 0.8608398 0.1010680 14.662834 8.517433 0.0000005 0.0005661 strainProAla - strainCtrl
THT(UniMod:21)QPVPASFDR3 -0.6202817 0.0771104 16.190202 -8.044071 0.0000005 0.0005661 strainProAla - strainCtrl
KSDS(UniMod:21)GTVLGAIPLNSR2 0.6609357 0.0768360 14.361829 8.601900 0.0000005 0.0005661 strainProAla - strainCtrl
NILPQRT(UniMod:21)PRS(UniMod:21)AAK3 -0.8462716 0.1024949 15.285069 -8.256717 0.0000005 0.0005765 strainProAla - strainCtrl
(UniMod:1)TT(UniMod:21)ASSSASQLQQR2 1.2647945 0.1557140 15.615069 8.122551 0.0000005 0.0005776 strainProAla - strainCtrl
INMGGGLFLSPEDIT(UniMod:21)KIASGLIS(UniMod:21)PVLGEVSER4 -4.7816203 0.3767745 8.870392 -12.690935 0.0000005 0.0005776 strainProAla - strainCtrl
ASYPLT(UniMod:21)PR2 1.0696951 0.1348908 15.948870 7.930084 0.0000006 0.0006490 strainProAla - strainCtrl
PTPPPAPEASAESGLSS(UniMod:21)K2 0.6264556 0.0781918 15.487838 8.011782 0.0000007 0.0006734 strainProAla - strainCtrl
YIDDS(UniMod:21)SFDTEK2 -1.2836303 0.1656818 15.604941 -7.747561 0.0000010 0.0009477 strainProAla - strainCtrl
SNDSFINDDRNS(UniMod:21)FTNATTNAR3 0.7538401 0.1004951 16.433641 7.501262 0.0000011 0.0009984 strainProAla - strainCtrl
NIDEDVNNLTAT(UniMod:21)TDEEDRDPESQK3 -0.8527360 0.0981565 12.330727 -8.687511 0.0000013 0.0011923 strainProAla - strainCtrl
EIVFAS(UniMod:21)PPRK2 1.0056196 0.1373600 16.579153 7.321049 0.0000014 0.0012225 strainProAla - strainCtrl
TTPSFVAFT(UniMod:21)DTER2 1.1296270 0.1562866 16.133240 7.227919 0.0000019 0.0016448 strainProAla - strainCtrl
PYTEES(UniMod:21)E1 2.3271509 0.2976433 13.735713 7.818589 0.0000020 0.0016596 strainProAla - strainCtrl
NGLNELASS(UniMod:21)ATK2 -0.9490251 0.1324904 16.277252 -7.162970 0.0000020 0.0016596 strainProAla - strainCtrl
SAES(UniMod:21)EFTDK2 0.5528463 0.0767348 15.625822 7.204636 0.0000024 0.0019075 strainProAla - strainCtrl
ALLELLDDSPVT(UniMod:21)PGETR2 2.9596170 0.2741487 8.583504 10.795664 0.0000028 0.0021318 strainProAla - strainCtrl
YAANLQES(UniMod:21)PKR2 -0.5932887 0.0862900 16.740316 -6.875522 0.0000029 0.0021981 strainProAla - strainCtrl
QIDGASSPSSNEDALES(UniMod:21)DNNEK3 -0.5553974 0.0800319 16.326025 -6.939699 0.0000030 0.0021981 strainProAla - strainCtrl
IRS(UniMod:21)EPTLNASSSDHK3 0.7251664 0.1057823 16.543679 6.855270 0.0000032 0.0023280 strainProAla - strainCtrl
KSDSGTVLGAIPLNS(UniMod:21)R3 0.6206246 0.0895807 15.751351 6.928103 0.0000037 0.0026071 strainProAla - strainCtrl
PTPPPAPEASAESGLSS(UniMod:21)K3 0.5189550 0.0766184 16.393795 6.773247 0.0000039 0.0026903 strainProAla - strainCtrl
SGLPEPNSQIVS(UniMod:21)PELAK2 -0.6047688 0.0869723 15.394746 -6.953580 0.0000040 0.0026903 strainProAla - strainCtrl
NAVSTKPTPPPAPEASAESGLSS(UniMod:21)K3 0.5814791 0.0843802 15.659249 6.891181 0.0000041 0.0026903 strainProAla - strainCtrl
KDS(UniMod:21)PSFLPGQQR3 0.5490593 0.0791417 15.370943 6.937673 0.0000042 0.0026903 strainProAla - strainCtrl
DFS(UniMod:21)PVHK2 -1.4614796 0.2105403 14.993826 -6.941567 0.0000047 0.0029979 strainProAla - strainCtrl
AQHESSS(UniMod:21)PVLC(UniMod:4)TR3 0.7727350 0.1046311 13.159562 7.385327 0.0000049 0.0030692 strainProAla - strainCtrl
QAGS(UniMod:21)PSSTVSSLAK2 0.9614995 0.1400635 15.163703 6.864739 0.0000051 0.0030888 strainProAla - strainCtrl
TGLGTPNQQVSVPNIVS(UniMod:21)PK3 3.4213372 0.3121574 7.778774 10.960295 0.0000053 0.0031662 strainProAla - strainCtrl
YDETTFSGS(UniMod:21)PER2 -0.5767658 0.0843059 14.947062 -6.841343 0.0000057 0.0033405 strainProAla - strainCtrl
DNADLPVDPYHLS(UniMod:21)PQQQPSNNLFGSGR3 -0.6696073 0.0963622 14.409570 -6.948857 0.0000058 0.0033405 strainProAla - strainCtrl
SSS(UniMod:21)FAHLQAPSPIPDPLQVSK3 1.0428171 0.1542288 15.106822 6.761496 0.0000062 0.0034891 strainProAla - strainCtrl
VNSELEES(UniMod:21)PAAVHQER2 -0.5879418 0.0902672 16.357689 -6.513349 0.0000064 0.0035650 strainProAla - strainCtrl
DSGYGVS(UniMod:21)VGR2 -0.5112562 0.0771772 15.519801 -6.624449 0.0000068 0.0037230 strainProAla - strainCtrl
TQFYRDS(UniMod:21)AHNS(UniMod:21)PVAPNR3 -0.4656164 0.0729877 16.599855 -6.379386 0.0000077 0.0041212 strainProAla - strainCtrl
AELPANIS(UniMod:21)LQESSSAK2 -0.9053757 0.1414030 16.388243 -6.402803 0.0000078 0.0041216 strainProAla - strainCtrl
EERS(UniMod:21)NNLLTPQPTNFTTK3 -0.6215513 0.0983405 16.778774 -6.320400 0.0000082 0.0041830 strainProAla - strainCtrl
HSRPLS(UniMod:21)IS(UniMod:21)ST(UniMod:21)TPLDLQR3 4.6554330 0.3146317 5.778774 14.796451 0.0000082 0.0041830 strainProAla - strainCtrl
RNS(UniMod:21)YISANSEEER2 -1.1527967 0.1775821 15.524175 -6.491628 0.0000086 0.0043321 strainProAla - strainCtrl
GIDIVVNEVS(UniMod:21)NR2 0.7623403 0.1185524 15.482350 6.430408 0.0000097 0.0048193 strainProAla - strainCtrl
DKT(UniMod:21)SSDDLLNWLQSR3 0.7081810 0.1101200 15.353916 6.430992 0.0000101 0.0048925 strainProAla - strainCtrl
RPTYSSS(UniMod:21)KSNNWTPGEASDTPPLPPHATPK4 2.9942171 0.3623045 9.778774 8.264365 0.0000102 0.0048925 strainProAla - strainCtrl
KIEENSNSPFNPLLS(UniMod:21)GEK3 -0.6700065 0.1065598 15.837860 -6.287613 0.0000113 0.0052697 strainProAla - strainCtrl
RAS(UniMod:21)NDNLLIPGENAHK3 0.4599824 0.0708280 14.649663 6.494358 0.0000114 0.0052697 strainProAla - strainCtrl
ATILALTSAVSS(UniMod:21)PK2 0.5078011 0.0811199 15.972815 6.259885 0.0000115 0.0052697 strainProAla - strainCtrl
PSQNLVPVT(UniMod:21)PSTTK2 0.5523103 0.0896856 16.342648 6.158296 0.0000125 0.0056690 strainProAla - strainCtrl
NDNLDDKS(UniMod:21)TVC(UniMod:4)YSEK2 -0.6201642 0.1013263 16.246350 -6.120465 0.0000138 0.0060182 strainProAla - strainCtrl
AC(UniMod:4)VVYGGS(UniMod:21)PIGNQLR2 0.7096441 0.1143746 15.669475 6.204561 0.0000139 0.0060182 strainProAla - strainCtrl
RRS(UniMod:21)FYTAS(UniMod:21)PLLSSGSIPK3 0.4932063 0.0800265 15.939976 6.163039 0.0000139 0.0060182 strainProAla - strainCtrl
DDEKHS(UniMod:21)FSTTQQVV3 -0.6781507 0.1080001 15.095925 -6.279168 0.0000143 0.0061169 strainProAla - strainCtrl
SC(UniMod:4)SLSS(UniMod:21)PTYSK2 -0.7303520 0.1137078 14.283432 -6.423062 0.0000145 0.0061169 strainProAla - strainCtrl
DASLT(UniMod:21)PLK2 -0.6718793 0.1078070 15.229477 -6.232241 0.0000150 0.0061918 strainProAla - strainCtrl
ERNPS(UniMod:21)ESVK2 0.5558866 0.0908487 15.935255 6.118818 0.0000151 0.0061918 strainProAla - strainCtrl
DPIPSDPS(UniMod:21)ER2 0.5954517 0.0973552 15.912926 6.116281 0.0000152 0.0061918 strainProAla - strainCtrl
(UniMod:28)QAGS(UniMod:21)PSSTVSSLAK2 1.4938586 0.2429815 15.528924 6.148034 0.0000160 0.0064185 strainProAla - strainCtrl
SSSFAHLQAPS(UniMod:21)PIPDPLQVSKPETR4 0.6654696 0.1059823 14.663397 6.279064 0.0000164 0.0064926 strainProAla - strainCtrl
RAT(UniMod:21)YAGFLLADPK2 2.6696468 0.3571293 10.396416 7.475295 0.0000171 0.0066738 strainProAla - strainCtrl
DNNLDNT(UniMod:21)YLNGK2 -0.4993728 0.0835871 16.187136 -5.974282 0.0000185 0.0071500 strainProAla - strainCtrl
YSS(UniMod:21)PVSGFYDHDINGY2 0.6880763 0.1164752 16.652864 5.907493 0.0000187 0.0071500 strainProAla - strainCtrl
SQS(UniMod:21)NGDEEDSILK2 1.2307213 0.1944519 13.946414 6.329180 0.0000190 0.0071500 strainProAla - strainCtrl
DLLTIGGANAS(UniMod:21)PIEK2 0.6477492 0.1102515 16.778774 5.875198 0.0000194 0.0072164 strainProAla - strainCtrl
LSHFS(UniMod:21)NLEDASFK2 0.6885021 0.1105956 14.354496 6.225404 0.0000198 0.0072993 strainProAla - strainCtrl
AVSTANDNS(UniMod:21)FLQPPHR3 -0.5287453 0.0887748 16.014654 -5.956030 0.0000201 0.0073039 strainProAla - strainCtrl
LSALC(UniMod:4)KT(UniMod:21)PPS(UniMod:21)LIK3 -0.7587202 0.1165483 12.901241 -6.509922 0.0000205 0.0073693 strainProAla - strainCtrl
EAS(UniMod:21)LQEELEPLR2 1.0222166 0.1670403 14.722408 6.119580 0.0000213 0.0075805 strainProAla - strainCtrl
SSSFAHLQAPS(UniMod:21)PIPDPLQVSK3 1.1797709 0.2020069 16.470900 5.840249 0.0000223 0.0078644 strainProAla - strainCtrl
S(UniMod:21)FELC(UniMod:4)EDR2 0.9268253 0.1589467 16.354499 5.831046 0.0000234 0.0081467 strainProAla - strainCtrl
TVAADQSATAPSS(UniMod:21)PTMNSSVTTINR3 -0.6033236 0.0894602 11.655469 -6.744043 0.0000239 0.0082177 strainProAla - strainCtrl
NLYLT(UniMod:21)PES(UniMod:21)PLNR2 -0.6753827 0.1142058 15.604771 -5.913735 0.0000242 0.0082374 strainProAla - strainCtrl
QPQS(UniMod:21)PLSSQSTQNQAIPR3 -0.4076059 0.0711533 16.704672 -5.728561 0.0000263 0.0088728 strainProAla - strainCtrl
S(UniMod:21)LFISPTLQVSQYEK2 -0.7639050 0.1318334 16.060132 -5.794475 0.0000270 0.0090023 strainProAla - strainCtrl
NHS(UniMod:21)PDPIGIDNYK3 0.4054766 0.0696429 15.756398 5.822221 0.0000276 0.0090630 strainProAla - strainCtrl
TGNEDVGNNNPSNS(UniMod:21)IPK2 -0.4465081 0.0767371 15.764670 -5.818671 0.0000277 0.0090630 strainProAla - strainCtrl
VNSELEES(UniMod:21)PAAVHQER3 -0.4679343 0.0804920 15.602780 -5.813428 0.0000292 0.0094402 strainProAla - strainCtrl
EIQEALS(UniMod:21)EKPTREPTPSVK3 -0.4351807 0.0767193 16.408134 -5.672376 0.0000315 0.0100808 strainProAla - strainCtrl
DSTNEFVGS(UniMod:21)PSLTSPQYIPS(UniMod:21)PLSSTK3 1.7519599 0.2983178 14.776535 5.872797 0.0000326 0.0103208 strainProAla - strainCtrl
(UniMod:1)ST(UniMod:21)DVAAAQAQSK2 0.4022153 0.0707539 15.908224 5.684712 0.0000346 0.0108042 strainProAla - strainCtrl
KMS(UniMod:21)FEELMK2 0.7469108 0.1172539 12.048226 6.370031 0.0000349 0.0108042 strainProAla - strainCtrl
AGSFGAPSS(UniMod:21)PTSGIPNPK2 0.4121028 0.0737901 16.695571 5.584801 0.0000351 0.0108042 strainProAla - strainCtrl
DAQIVVGT(UniMod:21)PGR2 0.4180993 0.0750842 16.527254 5.568409 0.0000377 0.0114740 strainProAla - strainCtrl
DYGDAFEGIENTSLS(UniMod:21)PK3 0.7214764 0.1203167 13.225628 5.996475 0.0000416 0.0124497 strainProAla - strainCtrl
AFESFLRPPSTPDLPS(UniMod:21)DDDNFAANSR3 -0.8304565 0.1467065 15.332904 -5.660667 0.0000416 0.0124497 strainProAla - strainCtrl
SRS(UniMod:21)PQIK2 -0.8063425 0.1459456 16.358491 -5.524952 0.0000426 0.0126183 strainProAla - strainCtrl
QTHSDDEDLPAVS(UniMod:21)PYPNEK3 0.6632387 0.1124520 13.577251 5.897971 0.0000440 0.0129097 strainProAla - strainCtrl
LGLPHGS(UniMod:21)GPT(UniMod:21)SVYNNK2 -1.7684178 0.1916041 6.750729 -9.229539 0.0000453 0.0131613 strainProAla - strainCtrl
NS(UniMod:21)PLAPIK1 -0.5972149 0.1097546 16.778774 -5.441367 0.0000460 0.0131937 strainProAla - strainCtrl
MS(UniMod:21)DSEVNQEAKPEVK3 2.3382932 0.3958100 13.361813 5.907615 0.0000462 0.0131937 strainProAla - strainCtrl
SLGTNINTAPAS(UniMod:21)PEEPK2 -0.7835756 0.1362331 14.206532 -5.751726 0.0000473 0.0133839 strainProAla - strainCtrl
S(UniMod:21)SPVQLQSNVDDSVLR2 -0.4933111 0.0874934 14.948434 -5.638266 0.0000478 0.0134022 strainProAla - strainCtrl
SST(UniMod:21)EHMLISPGR3 3.8501477 0.2244615 4.189280 17.152816 0.0000486 0.0135073 strainProAla - strainCtrl
THT(UniMod:21)QPVPASFDR2 -0.7557105 0.1357484 15.355566 -5.566995 0.0000494 0.0135406 strainProAla - strainCtrl
NSS(UniMod:21)DNDSVTNEEGLIR2 0.5307146 0.0912533 13.647482 5.815840 0.0000496 0.0135406 strainProAla - strainCtrl
VVVNT(UniMod:21)PREPVR3 -0.7950995 0.1442710 15.701748 -5.511154 0.0000507 0.0137377 strainProAla - strainCtrl
QTYNVGS(UniMod:21)EAETNEK2 -0.3790050 0.0703759 16.609290 -5.385440 0.0000534 0.0142508 strainProAla - strainCtrl
NFHAEVST(UniMod:21)PQVLS(UniMod:21)AKK2 -0.7474102 0.1384674 16.478698 -5.397733 0.0000535 0.0142508 strainProAla - strainCtrl
ILEDLLDSS(UniMod:21)NIHPSYTK2 -0.8018978 0.1486253 16.394257 -5.395434 0.0000547 0.0143861 strainProAla - strainCtrl
T(UniMod:21)LYQNPQTPTVLPSTYHPINK3 -0.5801105 0.1005876 13.580548 -5.767219 0.0000549 0.0143861 strainProAla - strainCtrl
ALLELLDDS(UniMod:21)PVTPGETR3 1.4879429 0.2059978 8.778774 7.223102 0.0000564 0.0146455 strainProAla - strainCtrl
EIVFAS(UniMod:21)PPR2 0.9918870 0.1800178 15.159235 5.509940 0.0000577 0.0146569 strainProAla - strainCtrl
RLSSVVTTS(UniMod:21)PDK2 -0.4506346 0.0835327 16.091484 -5.394706 0.0000584 0.0146569 strainProAla - strainCtrl
QSAVT(UniMod:21)PNQS(UniMod:21)GTPTPSASTTSLTSLNEK4 0.9078942 0.1260560 8.731966 7.202311 0.0000592 0.0146569 strainProAla - strainCtrl
TLTPQNKQS(UniMod:21)PANTK3 -0.5214962 0.0961171 15.745063 -5.425632 0.0000593 0.0146569 strainProAla - strainCtrl
DASLT(UniMod:21)PLK1 -1.1254599 0.2029526 14.767819 -5.545432 0.0000594 0.0146569 strainProAla - strainCtrl
DIPVKS(UniMod:21)DDTPAK2 -0.4431475 0.0828855 16.449479 -5.346502 0.0000597 0.0146569 strainProAla - strainCtrl
ETERS(UniMod:21)PSSSPIHNATK3 0.4784936 0.0877844 15.492375 5.450780 0.0000598 0.0146569 strainProAla - strainCtrl
S(UniMod:21)LDEIIGSNK1 -0.7197101 0.1299888 14.719101 -5.536707 0.0000611 0.0146569 strainProAla - strainCtrl
KPPVTT(UniMod:21)PR2 -0.5936714 0.1113194 16.428895 -5.333046 0.0000616 0.0146569 strainProAla - strainCtrl
RNS(UniMod:21)YISANSEEER3 -0.8783462 0.1660242 16.778774 -5.290470 0.0000626 0.0146569 strainProAla - strainCtrl
RNT(UniMod:21)AIPTK2 0.7980342 0.1493423 16.198597 5.343657 0.0000632 0.0146569 strainProAla - strainCtrl
KVES(UniMod:21)LGSPSGATK2 0.4251165 0.0783003 15.410382 5.429305 0.0000634 0.0146569 strainProAla - strainCtrl
SSAVPQTS(UniMod:21)PGQPR2 -0.3602244 0.0670883 15.932625 -5.369410 0.0000635 0.0146569 strainProAla - strainCtrl
IHS(UniMod:21)HDDIINLGK3 0.3826335 0.0701190 15.165732 5.456915 0.0000637 0.0146569 strainProAla - strainCtrl
(UniMod:27)ES(UniMod:21)VHNHSDGDDVDIPM(UniMod:35)DDSPVNEEAR4 3.2976353 0.2153623 4.311582 15.312038 0.0000637 0.0146569 strainProAla - strainCtrl
IEAPS(UniMod:21)PSVNKK2 -0.4233100 0.0787415 15.851016 -5.375948 0.0000638 0.0146569 strainProAla - strainCtrl
ILGTS(UniMod:21)PDMIDSAENR2 0.6980048 0.1192180 12.367498 5.854859 0.0000689 0.0157127 strainProAla - strainCtrl
KGDEESGADT(UniMod:21)VTS(UniMod:21)PITFEK3 3.8703155 0.4434093 6.630576 8.728539 0.0000713 0.0161335 strainProAla - strainCtrl
(UniMod:27)EKSPT(UniMod:21)PQT(UniMod:21)STASLSSVTK3 -2.9807091 0.4716709 10.439206 -6.319467 0.0000718 0.0161335 strainProAla - strainCtrl
(UniMod:1)SDWDTNT(UniMod:21)IIGSR2 0.4333520 0.0827309 16.532628 5.238093 0.0000731 0.0163053 strainProAla - strainCtrl
SFYPNS(UniMod:21)NKK2 -1.4947691 0.2407873 10.691926 -6.207839 0.0000752 0.0166384 strainProAla - strainCtrl
VTPT(UniMod:21)KTEVIIR2 1.0951846 0.1913825 12.746029 5.722492 0.0000758 0.0166384 strainProAla - strainCtrl
LINTISDDDAPQS(UniMod:21)PR2 0.3608420 0.0689248 16.351894 5.235303 0.0000761 0.0166384 strainProAla - strainCtrl
NILPQRT(UniMod:21)PRS(UniMod:21)AAK2 -1.1277986 0.1998267 13.123065 -5.643884 0.0000773 0.0166972 strainProAla - strainCtrl
NHS(UniMod:21)PDPIGIDNYK2 0.4047564 0.0762365 15.522070 5.309221 0.0000780 0.0166972 strainProAla - strainCtrl
HNES(UniMod:21)DLFWDNVHR3 0.9807014 0.1792967 14.224294 5.469712 0.0000780 0.0166972 strainProAla - strainCtrl
RS(UniMod:21)PLQTK2 -0.5324029 0.0970073 14.068041 -5.488279 0.0000785 0.0166972 strainProAla - strainCtrl
ERGS(UniMod:21)C(UniMod:4)VDIGK2 -0.8030260 0.1538895 16.311934 -5.218198 0.0000794 0.0167797 strainProAla - strainCtrl
NDNLDDKS(UniMod:21)TVC(UniMod:4)YSEK3 -0.6413542 0.1192677 14.803359 -5.377435 0.0000805 0.0168851 strainProAla - strainCtrl
RYDT(UniMod:21)ATAADLR2 0.9492420 0.1804635 15.782467 5.260021 0.0000813 0.0169542 strainProAla - strainCtrl
RPS(UniMod:21)VGNIQEANNLLNIIK3 1.1237968 0.2155754 16.178249 5.213011 0.0000824 0.0170675 strainProAla - strainCtrl
(UniMod:1)SS(UniMod:21)AITALTPNQVNDELNK3 0.5675682 0.1096120 16.501261 5.177976 0.0000831 0.0170922 strainProAla - strainCtrl
SQGS(UniMod:21)HLNLAANTQGNPIPGTTAWK3 0.6807750 0.1228157 13.346649 5.543064 0.0000863 0.0175189 strainProAla - strainCtrl
THT(UniMod:21)QPVPASFDREDGQHAQNR4 -0.6836470 0.1323541 16.417538 -5.165287 0.0000866 0.0175189 strainProAla - strainCtrl
S(UniMod:21)PVSLGSGSLPPINTK2 -0.5999031 0.1167229 16.684966 -5.139549 0.0000868 0.0175189 strainProAla - strainCtrl
DLARENS(UniMod:21)LETTFSSVNTR3 0.4557135 0.0883323 16.386810 5.159084 0.0000882 0.0176429 strainProAla - strainCtrl
DTVDSGNVT(UniMod:21)TTESTER2 -0.4863501 0.0945799 16.550120 -5.142216 0.0000885 0.0176429 strainProAla - strainCtrl
QELNKLS(UniMod:21)PEK2 -0.5258270 0.1023034 16.419336 -5.139878 0.0000912 0.0179634 strainProAla - strainCtrl
SGLEPQC(UniMod:4)S(UniMod:21)REEEENIDR3 0.5008430 0.0937170 14.505210 5.344207 0.0000918 0.0179634 strainProAla - strainCtrl
ITAQESIKS(UniMod:21)PEAAR2 -0.4695868 0.0887933 14.959347 -5.288538 0.0000918 0.0179634 strainProAla - strainCtrl
TIDIQQDS(UniMod:21)SDENDNFK2 0.4196937 0.0806479 15.564988 5.204025 0.0000950 0.0184590 strainProAla - strainCtrl
ASTAVES(UniMod:21)LDNHPPK2 0.6831740 0.1320011 15.650743 5.175517 0.0000987 0.0190658 strainProAla - strainCtrl
ISNVS(UniMod:21)FDSK2 -0.8235889 0.1615068 16.281043 -5.099406 0.0001016 0.0192803 strainProAla - strainCtrl
S(UniMod:21)SVATTASTESSEQGPK2 1.4009742 0.2505947 12.463086 5.590598 0.0001025 0.0192803 strainProAla - strainCtrl
FFNFSTDIS(UniMod:21)GEK2 -0.9515524 0.1746137 13.300899 -5.449471 0.0001027 0.0192803 strainProAla - strainCtrl
EGPSS(UniMod:21)PASILPAK2 -0.4989846 0.0981388 16.384085 -5.084477 0.0001027 0.0192803 strainProAla - strainCtrl
ESDAS(UniMod:21)LNVTTGNNTSR2 -0.4207281 0.0830290 16.570701 -5.067242 0.0001028 0.0192803 strainProAla - strainCtrl
NAVSTKPTPPPAPEASAES(UniMod:21)GLSSK4 0.5580520 0.1036185 13.666420 5.385639 0.0001044 0.0194646 strainProAla - strainCtrl
HAS(UniMod:21)PLLEDVEDEEVDRYNESLSR4 1.2298673 0.2139989 11.572649 5.747073 0.0001060 0.0195880 strainProAla - strainCtrl
TLSLIQSYS(UniMod:21)LLDKPDEAIEK3 1.1235071 0.1991263 12.068296 5.642183 0.0001063 0.0195880 strainProAla - strainCtrl
YDS(UniMod:21)STDLQAGR2 0.3698327 0.0726638 16.102585 5.089645 0.0001072 0.0196285 strainProAla - strainCtrl
QPQS(UniMod:21)PLSSQSTQNQAIPR2 -0.4075059 0.0792151 15.270660 -5.144297 0.0001133 0.0206414 strainProAla - strainCtrl
NTPAESIS(UniMod:21)DLEGM(UniMod:35)TTFAPTTGGENR3 -2.9293431 0.2545536 4.778774 -11.507767 0.0001151 0.0208503 strainProAla - strainCtrl
DDEKHSFS(UniMod:21)TTQQVV2 -0.5805399 0.1054316 12.470592 -5.506316 0.0001174 0.0210549 strainProAla - strainCtrl
KNDSDVPELAT(UniMod:21)IPAAK3 -0.3787394 0.0756737 16.536287 -5.004898 0.0001176 0.0210549 strainProAla - strainCtrl
KES(UniMod:21)PEIRDYER3 0.8730840 0.1721316 15.739516 5.072189 0.0001190 0.0210974 strainProAla - strainCtrl
S(UniMod:21)FELC(UniMod:4)EDRWWER3 0.9678313 0.1895069 15.380389 5.107103 0.0001192 0.0210974 strainProAla - strainCtrl
LIGQNGEES(UniMod:21)EKEKEDTPEHDEEEEGK4 0.7300602 0.1413423 14.778774 5.165191 0.0001207 0.0212360 strainProAla - strainCtrl
KS(UniMod:21)EIFSTYADNQPGVLIQVFEGER3 1.2693332 0.2496072 15.506266 5.085322 0.0001213 0.0212360 strainProAla - strainCtrl
ANEDDLKPPS(UniMod:21)QHEAC(UniMod:4)GNSALQSSITDFSDR4 -3.0273813 0.3156051 5.491433 -9.592309 0.0001234 0.0213869 strainProAla - strainCtrl
VSSATSNSANIT(UniMod:21)PNNLR3 -0.4267747 0.0845308 15.786776 -5.048748 0.0001235 0.0213869 strainProAla - strainCtrl
NFHAEVSTPQVLS(UniMod:21)AKK3 -0.6310794 0.1265787 16.427181 -4.985670 0.0001247 0.0214816 strainProAla - strainCtrl
ATS(UniMod:21)PLLESDSIEK2 0.3555638 0.0716513 16.577545 4.962423 0.0001274 0.0218288 strainProAla - strainCtrl
NQS(UniMod:21)SLGLIPVASATSNTSSPK2 -0.5243274 0.0930833 11.516555 -5.632885 0.0001286 0.0219074 strainProAla - strainCtrl
S(UniMod:21)PVVDGIVR2 0.7606990 0.1442317 13.592584 5.274148 0.0001297 0.0219115 strainProAla - strainCtrl
NS(UniMod:21)PLAPIK2 -0.5743647 0.1139883 15.622580 -5.038802 0.0001300 0.0219115 strainProAla - strainCtrl
EEVLT(UniMod:21)PTTSASTPHR2 -0.4267613 0.0853613 15.987159 -4.999470 0.0001313 0.0219484 strainProAla - strainCtrl
STS(UniMod:21)AGNSITANAPVVPK2 -0.3687551 0.0736446 15.891077 -5.007228 0.0001316 0.0219484 strainProAla - strainCtrl
SDT(UniMod:21)PLLYR2 1.0685017 0.2075697 14.426672 5.147677 0.0001347 0.0223369 strainProAla - strainCtrl
S(UniMod:21)SPLLDITNK2 -0.9868683 0.2007107 16.778774 -4.916868 0.0001353 0.0223369 strainProAla - strainCtrl
DGTSSVSSS(UniMod:21)PIK2 -0.5042304 0.0966601 13.776002 -5.216529 0.0001376 0.0223519 strainProAla - strainCtrl
ITAQESIKS(UniMod:21)PEAARK3 -0.6367942 0.1287497 16.295553 -4.945987 0.0001385 0.0223519 strainProAla - strainCtrl
GNLGNRFS(UniMod:21)PTK2 -0.5423347 0.1097686 16.336166 -4.940707 0.0001390 0.0223519 strainProAla - strainCtrl
T(UniMod:21)RNPLTHSTPK3 -2.3138663 0.2482041 5.520111 -9.322432 0.0001391 0.0223519 strainProAla - strainCtrl
YGIYHGDDDS(UniMod:21)TLNNVFDK2 -1.0415433 0.1991205 13.612653 -5.230718 0.0001395 0.0223519 strainProAla - strainCtrl
PQEEAPEDESLIVISS(UniMod:21)PQVEK3 0.5124027 0.1032034 16.027637 4.964978 0.0001398 0.0223519 strainProAla - strainCtrl
RPIS(UniMod:21)TIVEQELPK2 -1.0455429 0.2068522 15.075112 -5.054540 0.0001404 0.0223519 strainProAla - strainCtrl
APQKEES(UniMod:21)KESEPMEVDEDDSK3 1.2102755 0.2130534 10.937685 5.680620 0.0001453 0.0230213 strainProAla - strainCtrl
(UniMod:28)QHQHQPVAT(UniMod:21)PAK3 -0.5066726 0.1034332 16.465274 -4.898549 0.0001482 0.0231963 strainProAla - strainCtrl
PEQEPLS(UniMod:21)PNGRK2 -0.4746343 0.0973179 16.645621 -4.877154 0.0001503 0.0231963 strainProAla - strainCtrl
AAFDEDGNIS(UniMod:21)NVK2 -0.5310329 0.1074344 15.869398 -4.942859 0.0001504 0.0231963 strainProAla - strainCtrl
LIS(UniMod:21)TEDVTSK2 -0.7605480 0.1528319 15.499906 -4.976369 0.0001506 0.0231963 strainProAla - strainCtrl
SSAES(UniMod:21)S(UniMod:21)NATNNNTLGTESK2 -1.5561538 0.2647893 10.078480 -5.876951 0.0001511 0.0231963 strainProAla - strainCtrl
SVS(UniMod:21)TTNDNIGESGNR2 0.4416234 0.0876779 14.874691 5.036883 0.0001512 0.0231963 strainProAla - strainCtrl
TQLENS(UniMod:21)DNFEEQK2 -0.4589481 0.0918131 15.223153 -4.998719 0.0001520 0.0231963 strainProAla - strainCtrl
NEEIVAT(UniMod:21)PIK2 -0.6163339 0.1262525 16.508963 -4.881756 0.0001523 0.0231963 strainProAla - strainCtrl
AQHESSS(UniMod:21)PVLC(UniMod:4)TR2 1.0990324 0.1717509 8.601388 6.398991 0.0001530 0.0231963 strainProAla - strainCtrl
KSS(UniMod:21)PDAVDSVGK2 0.5271737 0.1057616 15.193688 4.984547 0.0001571 0.0237104 strainProAla - strainCtrl
AST(UniMod:21)AVES(UniMod:21)LDNHPPK2 0.7515004 0.1492136 14.660721 5.036406 0.0001581 0.0237494 strainProAla - strainCtrl
(UniMod:27)ENSSELPDS(UniMod:21)YDYSDSEFEDNLERR3 -3.6337608 0.3394465 4.778774 -10.704959 0.0001609 0.0239584 strainProAla - strainCtrl
VGDQVLIPQFGGS(UniMod:21)TIK2 1.0933703 0.2113775 13.445958 5.172595 0.0001610 0.0239584 strainProAla - strainCtrl
AYLAS(UniMod:21)DSDESDGQVDEEAK2 -0.4291973 0.0878984 16.122941 -4.882877 0.0001624 0.0240404 strainProAla - strainCtrl
SNDS(UniMod:21)FINDDRNSFTNATTNAR3 0.5976026 0.1238694 16.778774 4.824456 0.0001642 0.0241961 strainProAla - strainCtrl
LAS(UniMod:21)LDNLR2 0.9170016 0.1828224 14.635503 5.015805 0.0001653 0.0242538 strainProAla - strainCtrl
NIS(UniMod:21)PDSSLSHNASSNTYVTAAAAAPR3 -0.3554483 0.0714542 14.973697 -4.974494 0.0001673 0.0243829 strainProAla - strainCtrl
LDFSS(UniMod:21)PRPNNDGGR3 -0.4179372 0.0867667 16.744577 -4.816792 0.0001677 0.0243829 strainProAla - strainCtrl
TSS(UniMod:21)ENT(UniMod:21)NVFEIVHQK3 -0.8921415 0.1808358 15.342768 -4.933434 0.0001689 0.0244325 strainProAla - strainCtrl
EVPTLSQLNTTVS(UniMod:21)RDK2 0.4789120 0.0992890 16.537728 4.823415 0.0001711 0.0246441 strainProAla - strainCtrl
SFFKES(UniMod:21)NDETYDPDTLAPALDGR3 -0.6443931 0.1294949 14.637538 -4.976204 0.0001782 0.0255554 strainProAla - strainCtrl
VPTVGS(UniMod:21)YGVAGATLPETIPTSK2 -0.4377999 0.0899941 15.757738 -4.864763 0.0001795 0.0256268 strainProAla - strainCtrl
IEDT(UniMod:21)SNVGTEQLVAEK3 -0.7313340 0.1505551 15.797798 -4.857583 0.0001809 0.0257018 strainProAla - strainCtrl
YAS(UniMod:21)SSSTDIENDDEK2 0.3785207 0.0772001 15.144492 4.903109 0.0001860 0.0261200 strainProAla - strainCtrl
S(UniMod:21)NPC(UniMod:4)LIGEPGIGK2 0.4818066 0.0998521 16.010082 4.825205 0.0001862 0.0261200 strainProAla - strainCtrl
NFHAEVST(UniMod:21)PQVLS(UniMod:21)AK3 -0.4065553 0.0854090 16.778774 -4.760098 0.0001879 0.0261200 strainProAla - strainCtrl
DSAHNS(UniMod:21)PVAPNR3 -0.6062111 0.1272176 16.678781 -4.765151 0.0001889 0.0261200 strainProAla - strainCtrl
QVS(UniMod:21)ELQDLVK2 0.6335240 0.1318316 16.159107 4.805553 0.0001890 0.0261200 strainProAla - strainCtrl
GFVFNS(UniMod:21)VQK1 -0.5530516 0.1115387 14.479379 -4.958383 0.0001904 0.0261200 strainProAla - strainCtrl
NNS(UniMod:21)HC(UniMod:4)EVESYPQVPPVTHDIHK4 0.6337824 0.1319322 16.135999 4.803850 0.0001904 0.0261200 strainProAla - strainCtrl
GYHIIDTTTYNELVSNFNS(UniMod:21)PTLK3 0.7469410 0.1550970 15.988670 4.815960 0.0001904 0.0261200 strainProAla - strainCtrl
TAYSGS(UniMod:21)PSK2 -0.6363302 0.1323648 15.980318 -4.807398 0.0001940 0.0265024 strainProAla - strainCtrl
INGNSLRS(UniMod:21)PFLVGTDK2 -0.4676198 0.0967245 15.552243 -4.834554 0.0001978 0.0269031 strainProAla - strainCtrl
RSTASSVNAT(UniMod:21)PSSAR3 -0.4311481 0.0907764 16.563709 -4.749563 0.0001987 0.0269063 strainProAla - strainCtrl
TVDPAS(UniMod:21)APNHSPEIDNLDDLVVLK4 1.9821758 0.3802101 12.249622 5.213370 0.0002030 0.0273666 strainProAla - strainCtrl
ETQS(UniMod:21)LDRPQFK2 -0.4081395 0.0838598 15.003804 -4.866927 0.0002050 0.0275289 strainProAla - strainCtrl
TSDLNQEHGNGS(UniMod:21)AILGK3 -0.3959506 0.0819830 15.373386 -4.829668 0.0002062 0.0275646 strainProAla - strainCtrl
KDS(UniMod:21)PSFLPGQQR2 0.7490754 0.1534027 14.760314 4.883067 0.0002081 0.0275646 strainProAla - strainCtrl
VSIS(UniMod:21)HDDLQAVAVAVSTK2 1.3442872 0.2636894 12.920432 5.097994 0.0002084 0.0275646 strainProAla - strainCtrl
SSES(UniMod:21)ASNIPDAVNTR2 0.6427725 0.1317921 14.799879 4.877169 0.0002089 0.0275646 strainProAla - strainCtrl
DIPGDEAYNS(UniMod:21)DDIM(UniMod:35)APLREK3 -4.1127541 0.4991771 5.778774 -8.239068 0.0002096 0.0275646 strainProAla - strainCtrl
EYVPLDNAEQSTSSS(UniMod:21)QETK3 -0.3727518 0.0784920 16.182125 -4.748917 0.0002115 0.0276952 strainProAla - strainCtrl
RNS(UniMod:21)SHVSSLTSR3 0.4603150 0.0949556 14.960268 4.847689 0.0002146 0.0277211 strainProAla - strainCtrl
ERDGS(UniMod:21)TEETLNSLK2 0.5019891 0.1060914 16.308785 4.731665 0.0002147 0.0277211 strainProAla - strainCtrl
AGFKPEEEPEDSS(UniMod:21)YDDFGK3 -0.3654878 0.0761935 15.510466 -4.796835 0.0002149 0.0277211 strainProAla - strainCtrl
VVVNT(UniMod:21)PREPVR2 -0.7532240 0.1485916 12.998057 -5.069089 0.0002152 0.0277211 strainProAla - strainCtrl
LANS(UniMod:21)FEFPITTNNVNAQDR2 -0.4414564 0.0925725 15.779147 -4.768765 0.0002171 0.0278569 strainProAla - strainCtrl
(UniMod:1)SIC(UniMod:4)EQY(UniMod:21)YPEEPTKPTVK2 1.7453952 0.3598901 14.721255 4.849800 0.0002236 0.0285644 strainProAla - strainCtrl
VVSS(UniMod:21)DSLDIAQGIDLVR2 0.8844359 0.1849877 15.373576 4.781053 0.0002272 0.0288720 strainProAla - strainCtrl
VSLSSSYIDQYT(UniMod:21)PR2 -0.4614401 0.0983330 16.448969 -4.692629 0.0002278 0.0288720 strainProAla - strainCtrl
SEAIT(UniMod:21)PRPK2 -0.4496419 0.0954354 16.047242 -4.711480 0.0002335 0.0294310 strainProAla - strainCtrl
GTDDDNIDIS(UniMod:21)NGHVSK2 -0.3688742 0.0773766 15.344772 -4.767256 0.0002347 0.0294310 strainProAla - strainCtrl
APVAS(UniMod:21)PRPAAT(UniMod:21)PNLSK3 -0.4955124 0.1050468 15.931263 -4.717065 0.0002352 0.0294310 strainProAla - strainCtrl
AGANS(UniMod:21)MIQNVVDSDTISETAAR3 0.9222397 0.1687759 10.447011 5.464285 0.0002359 0.0294310 strainProAla - strainCtrl
SDS(UniMod:21)GTVLGAIPLNSR2 0.7815083 0.1506233 11.807227 5.188497 0.0002383 0.0296157 strainProAla - strainCtrl
SENPDVT(UniMod:21)FGQVGR2 -0.4013784 0.0842807 15.272722 -4.762400 0.0002399 0.0297006 strainProAla - strainCtrl
(UniMod:1)SNENLS(UniMod:21)PNSSNPDLTK2 0.3366232 0.0706357 15.167828 4.765625 0.0002429 0.0299439 strainProAla - strainCtrl
TLT(UniMod:21)PTSTR2 0.6086878 0.1271147 14.804552 4.788491 0.0002479 0.0303374 strainProAla - strainCtrl
TIESGPVEELVS(UniMod:21)PSK2 -0.7159505 0.1504260 15.112862 -4.759485 0.0002482 0.0303374 strainProAla - strainCtrl
AHLDDS(UniMod:21)GIEK2 -0.3675228 0.0782163 15.811878 -4.698803 0.0002489 0.0303374 strainProAla - strainCtrl
PLS(UniMod:21)VPGS(UniMod:21)PK2 -0.7513663 0.1598583 15.740967 -4.700202 0.0002511 0.0304874 strainProAla - strainCtrl
AVVIDDPPLRQT(UniMod:21)PEPFDEQSAYNPQSPIAIDFGSSK4 -0.4270279 0.0915313 16.155141 -4.665375 0.0002523 0.0305182 strainProAla - strainCtrl
TPTPTPPVVAEPAIS(UniMod:21)PRPVSQR3 -0.3146302 0.0674653 16.116081 -4.663584 0.0002548 0.0305951 strainProAla - strainCtrl
NES(UniMod:21)ISNIVSILPEGAK2 0.6588503 0.1426506 16.731572 4.618629 0.0002549 0.0305951 strainProAla - strainCtrl
RRGS(UniMod:21)EDDSFLSSQGNR3 0.8464095 0.1830463 16.591335 4.624020 0.0002573 0.0307155 strainProAla - strainCtrl
NNEES(UniMod:21)REEATAALK3 -0.4191627 0.0887793 15.328848 -4.721403 0.0002578 0.0307155 strainProAla - strainCtrl
APVAS(UniMod:21)PRPAAT(UniMod:21)PNLSK2 -0.5635135 0.1171509 14.303299 -4.810150 0.0002613 0.0310110 strainProAla - strainCtrl
PSRLS(UniMod:21)DEVK2 0.4987814 0.1039350 14.342597 4.798976 0.0002649 0.0313229 strainProAla - strainCtrl
EVSNSTVDADNGAS(UniMod:21)DFEAGQQFATELDQGEK3 1.4036744 0.2525505 9.730728 5.557995 0.0002664 0.0313862 strainProAla - strainCtrl
S(UniMod:21)VPRPGDASNTEK2 -0.4570015 0.0923221 12.945126 -4.950077 0.0002687 0.0315396 strainProAla - strainCtrl
TLLEAIDAIEQPSRPT(UniMod:21)DK3 0.4525394 0.0959375 15.108844 4.717022 0.0002701 0.0315883 strainProAla - strainCtrl
DAVNSAPSNS(UniMod:21)LLK2 -1.0149653 0.2044123 12.734589 -4.965286 0.0002747 0.0317973 strainProAla - strainCtrl
AIDISS(UniMod:21)LSGETSSGYK2 -0.3666962 0.0792071 16.079941 -4.629585 0.0002749 0.0317973 strainProAla - strainCtrl
TTS(UniMod:21)NPSSILHDLPR2 -0.5677010 0.1198247 14.778774 -4.737762 0.0002749 0.0317973 strainProAla - strainCtrl
YAANLQES(UniMod:21)PKR3 -0.4240164 0.0895228 14.732513 -4.736409 0.0002780 0.0320313 strainProAla - strainCtrl
IHFPLVSYS(UniMod:21)PVLSK3 1.0479328 0.2125070 12.925189 4.931286 0.0002791 0.0320417 strainProAla - strainCtrl
NTSNET(UniMod:21)DGNAFTGSC(UniMod:4)SISSK2 1.2368744 0.2248371 9.756376 5.501204 0.0002853 0.0325906 strainProAla - strainCtrl
VWDVRS(UniMod:21)PSIPR3 0.7984159 0.1674728 14.257686 4.767438 0.0002859 0.0325906 strainProAla - strainCtrl
IKS(UniMod:21)NPC(UniMod:4)LIGEPGIGK3 0.8632966 0.1824828 14.554894 4.730839 0.0002902 0.0329607 strainProAla - strainCtrl
SYDGNGTGIMVS(UniMod:21)PMK2 -0.5887130 0.1177844 12.163813 -4.998227 0.0002978 0.0337006 strainProAla - strainCtrl
S(UniMod:21)VDVSSPYINLYYNR2 -0.4860936 0.1062296 16.144181 -4.575876 0.0003041 0.0342133 strainProAla - strainCtrl
S(UniMod:21)RALGTPAFFAPELC(UniMod:4)STEK3 0.7793877 0.1709572 16.373891 4.558965 0.0003045 0.0342133 strainProAla - strainCtrl
APVAS(UniMod:21)PRPAATPNLSKDK3 -1.3457307 0.2173259 7.687325 -6.192225 0.0003079 0.0344107 strainProAla - strainCtrl
FYS(UniMod:21)YADMLSDDNNNNVSNATSTSSTANPLR3 0.6551829 0.1326100 12.423946 4.940677 0.0003084 0.0344107 strainProAla - strainCtrl
(UniMod:1)SSST(UniMod:21)T(UniMod:21)PDLLYPSADK2 1.2530498 0.2032950 7.706617 6.163703 0.0003141 0.0349250 strainProAla - strainCtrl
DSAHNS(UniMod:21)PVAPNR2 -0.5453454 0.1198520 16.257095 -4.550159 0.0003155 0.0349250 strainProAla - strainCtrl
ELS(UniMod:21)DNEK2 0.4539977 0.1003051 16.586663 4.526168 0.0003163 0.0349250 strainProAla - strainCtrl
IQAFVWGSPADEEEES(UniMod:21)VVPLSK3 -0.4808394 0.1047748 15.671795 -4.589267 0.0003181 0.0350034 strainProAla - strainCtrl
M(UniMod:35)PEDTTDVEQVAS(UniMod:21)PNDNESNPSEAK3 -3.7259039 0.4046007 4.778774 -9.208843 0.0003211 0.0352053 strainProAla - strainCtrl
RKLS(UniMod:21)EDGVTDGDGK3 0.7871168 0.1469142 9.953540 5.357663 0.0003252 0.0354481 strainProAla - strainCtrl
T(UniMod:21)LQFVIQEK2 0.4798589 0.1046085 15.552576 4.587187 0.0003255 0.0354481 strainProAla - strainCtrl
LSALC(UniMod:4)KT(UniMod:21)PPS(UniMod:21)LIK2 -1.3208976 0.2686094 12.292734 -4.917540 0.0003311 0.0359281 strainProAla - strainCtrl
DNDNPVRT(UniMod:21)IS(UniMod:21)LT(UniMod:21)NIEQQSQLNQR3 0.4587614 0.1005091 15.663686 4.564376 0.0003351 0.0362406 strainProAla - strainCtrl
RTHT(UniMod:21)QPVPASFDR3 -0.4378883 0.0969719 16.292061 -4.515620 0.0003373 0.0363562 strainProAla - strainCtrl
RSVS(UniMod:21)DAELR2 0.5457772 0.1162184 14.062750 4.696133 0.0003397 0.0364868 strainProAla - strainCtrl
TFVS(UniMod:21)ETADDIEK2 -0.4161837 0.0929629 16.778774 -4.476878 0.0003418 0.0365954 strainProAla - strainCtrl
(UniMod:28)QLRDS(UniMod:21)FVTPNYSR2 -0.6237810 0.1371108 15.674488 -4.549468 0.0003449 0.0367941 strainProAla - strainCtrl
GQVVSEEQRPGT(UniMod:21)PLFTVK2 2.2538252 0.4475626 11.345046 5.035776 0.0003461 0.0367996 strainProAla - strainCtrl
STS(UniMod:21)PMYTITR2 1.2457033 0.2573246 12.506460 4.840980 0.0003596 0.0381110 strainProAla - strainCtrl
LESHPTEQTEVSS(UniMod:21)Q2 0.4073290 0.0894246 15.304530 4.555001 0.0003613 0.0381628 strainProAla - strainCtrl
SITQHEVERES(UniMod:21)VSSK2 1.0158290 0.2248225 15.726718 4.518360 0.0003646 0.0383806 strainProAla - strainCtrl
RVVVNT(UniMod:21)PREPVR3 -0.6288564 0.1407328 16.396409 -4.468444 0.0003668 0.0384921 strainProAla - strainCtrl
SSS(UniMod:21)NSSVTSTGQSSR2 0.5417719 0.1202293 15.778774 4.506155 0.0003709 0.0387884 strainProAla - strainCtrl
ASLSTFSSTFSDS(UniMod:21)PSK2 -0.4723145 0.1046135 15.514877 -4.514853 0.0003792 0.0393895 strainProAla - strainCtrl
KS(UniMod:21)SY(UniMod:21)GSNNDDSYGSNNDDSYGSSNK3 -1.9405909 0.2612958 5.727599 -7.426798 0.0003802 0.0393895 strainProAla - strainCtrl
EGEVEPVDMYTPDT(UniMod:21)AADEEARK3 6.6005366 0.7151450 4.608072 9.229648 0.0003830 0.0393895 strainProAla - strainCtrl
TRDT(UniMod:21)PEDVSTAGAK2 0.4828737 0.1084828 16.330868 4.451156 0.0003839 0.0393895 strainProAla - strainCtrl
LSNINSNSVQSVIS(UniMod:21)PKK2 -0.3821184 0.0860456 16.466308 -4.440881 0.0003850 0.0393895 strainProAla - strainCtrl
S(UniMod:21)NENLS(UniMod:21)PNSSNPDLTK3 0.4349204 0.0928712 13.531525 4.683049 0.0003852 0.0393895 strainProAla - strainCtrl
AQLHHDSHTNAGT(UniMod:21)PVLTPAPVPAGS(UniMod:21)NPWGVTQSATPVTSINLSK4 -1.8835695 0.2563347 5.778774 -7.348086 0.0003862 0.0393895 strainProAla - strainCtrl
ETPLLYNDTHT(UniMod:21)P2 0.3775119 0.0854283 16.778774 4.419052 0.0003866 0.0393895 strainProAla - strainCtrl
LRDLY(UniMod:21)LEQTESDSDFDEGSQANGSVPPLK3 -3.8878817 0.7237947 9.369851 -5.371525 0.0003920 0.0398094 strainProAla - strainCtrl
RRS(UniMod:21)DNPATNEYVR3 1.0391418 0.2296165 15.118001 4.525554 0.0003948 0.0399685 strainProAla - strainCtrl
VVDFSQEVS(UniMod:21)K2 -0.5774136 0.1269241 14.628651 -4.549281 0.0004079 0.0411661 strainProAla - strainCtrl
AQTQS(UniMod:21)SVQLK2 0.4205253 0.0953652 16.496598 4.409631 0.0004095 0.0411966 strainProAla - strainCtrl
KIEENSNS(UniMod:21)PFNPLLSGEK3 -0.3724174 0.0829843 15.318457 -4.487803 0.0004128 0.0412859 strainProAla - strainCtrl
ITAQESIKS(UniMod:21)PEAAR3 -0.4616766 0.1050156 16.644979 -4.396266 0.0004130 0.0412859 strainProAla - strainCtrl
PAQPSGGLFGAT(UniMod:21)NNTTSK3 -1.0635434 0.2058592 10.001549 -5.166362 0.0004211 0.0419629 strainProAla - strainCtrl
INVSNDVHSLGNS(UniMod:21)DTESR3 0.5374212 0.1230548 16.778774 4.367331 0.0004316 0.0428769 strainProAla - strainCtrl
SDYGGS(UniMod:21)RDS(UniMod:21)FQSSGSR2 1.6634143 0.2853660 7.778774 5.829055 0.0004356 0.0430696 strainProAla - strainCtrl
NNNTSQISSTNT(UniMod:21)PDVIDLK2 0.5348878 0.1164946 13.778774 4.591525 0.0004363 0.0430696 strainProAla - strainCtrl
NNLWDDDVLARFDS(UniMod:21)SK3 0.5414890 0.1222150 15.686142 4.430628 0.0004390 0.0430714 strainProAla - strainCtrl
NAESKDS(UniMod:21)DGVQVANESEEDPELK3 0.4163760 0.0948942 16.287672 4.387790 0.0004410 0.0430714 strainProAla - strainCtrl
EVDKS(UniMod:21)PSVSTLK2 -0.4204938 0.0957848 16.243912 -4.389984 0.0004416 0.0430714 strainProAla - strainCtrl
ETQS(UniMod:21)LDRPQFK3 -0.3833255 0.0877327 16.542965 -4.369241 0.0004433 0.0430714 strainProAla - strainCtrl
TTSTNHS(UniMod:21)VGHTASQNAR2 -0.6999162 0.1593514 16.155423 -4.392282 0.0004448 0.0430714 strainProAla - strainCtrl
IPGQLFSGTLGLLRPSQQANSDNNKPPQS(UniMod:21)PK4 0.5627490 0.1287934 16.513405 4.369392 0.0004449 0.0430714 strainProAla - strainCtrl
RTS(UniMod:21)QSQSLSGSTFK3 1.0601409 0.2365634 14.862423 4.481424 0.0004489 0.0430714 strainProAla - strainCtrl
AS(UniMod:21)LDLPGINHAETLLSQR3 -0.4755472 0.1072132 15.463864 -4.435528 0.0004490 0.0430714 strainProAla - strainCtrl
YDITIDEES(UniMod:21)PRPGQQTFEK3 0.3107807 0.0702038 15.576702 4.426838 0.0004495 0.0430714 strainProAla - strainCtrl
S(UniMod:21)S(UniMod:21)AITALTPNQVNDELNK2 0.4772312 0.1085265 15.996563 4.397369 0.0004499 0.0430714 strainProAla - strainCtrl
STS(UniMod:21)TNDFSENSLDAPHDQEVIHTSNPFLK4 0.3683744 0.0833305 15.587982 4.420645 0.0004545 0.0433769 strainProAla - strainCtrl
TNS(UniMod:21)PQPTSLTSDNDTSSVTTAK2 0.5754017 0.1313647 16.106046 4.380184 0.0004593 0.0437071 strainProAla - strainCtrl
S(UniMod:21)NLSS(UniMod:21)PSSASSSASPATTVTK2 0.7391254 0.1673338 15.542750 4.417072 0.0004608 0.0437140 strainProAla - strainCtrl
DIEEINSTSS(UniMod:21)NVGK2 0.3012831 0.0686945 15.963549 4.385841 0.0004629 0.0437140 strainProAla - strainCtrl
NNVNHSNSEPIDT(UniMod:21)PNDDIQENVK3 0.4972730 0.1138297 16.176824 4.368571 0.0004661 0.0437140 strainProAla - strainCtrl
TSTFLHS(UniMod:21)PIQK2 -0.7874446 0.1732184 13.886659 -4.545963 0.0004664 0.0437140 strainProAla - strainCtrl
TGVKIS(UniMod:21)PVVDK2 -0.4619054 0.1053024 15.889804 -4.386467 0.0004671 0.0437140 strainProAla - strainCtrl
TENNSNHNYNNSNVSSNSIGS(UniMod:21)PNFHSLR3 -0.8845629 0.1787314 10.742562 -4.949120 0.0004681 0.0437140 strainProAla - strainCtrl
HRES(UniMod:21)LGLDDDEAEEQAM(UniMod:35)YTR4 -3.3638699 0.3971874 4.778774 -8.469225 0.0004697 0.0437140 strainProAla - strainCtrl
FGTEIIT(UniMod:21)ETVSK2 0.8052664 0.1819687 15.289217 4.425301 0.0004704 0.0437140 strainProAla - strainCtrl
VSSATSNSANIT(UniMod:21)PNNLR2 -0.3786909 0.0858595 15.460738 -4.410590 0.0004726 0.0437850 strainProAla - strainCtrl
ETPLHSSSS(UniMod:21)T(UniMod:21)SLSSLFRPTK3 0.4402234 0.0961908 13.460174 4.576565 0.0004759 0.0438672 strainProAla - strainCtrl
INSSLNIAS(UniMod:21)PSHLK3 -0.6234482 0.1440171 16.649182 -4.328986 0.0004762 0.0438672 strainProAla - strainCtrl
VNDS(UniMod:21)VLVK2 -0.5198446 0.1196349 16.300521 -4.345261 0.0004814 0.0439190 strainProAla - strainCtrl
KTS(UniMod:21)SDLGIFGHR3 0.7300494 0.1677336 16.139126 4.352434 0.0004845 0.0439190 strainProAla - strainCtrl
S(UniMod:21)RSAINIETESR3 0.3570136 0.0812661 15.532018 4.393144 0.0004846 0.0439190 strainProAla - strainCtrl
PAPLTLAET(UniMod:21)HS(UniMod:21)PNASVENSHTIVR3 -0.6523553 0.1316938 10.592238 -4.953577 0.0004848 0.0439190 strainProAla - strainCtrl
LEAEEIPS(UniMod:21)EDQNEFLLER3 0.9433243 0.2131380 15.080972 4.425884 0.0004848 0.0439190 strainProAla - strainCtrl
PHTPFIS(UniMod:21)KLNTHQDSSYLSPNT(UniMod:21)TST(UniMod:21)TTPSNNNSNSNQAK4 4.0210348 0.6346579 6.629613 6.335751 0.0004869 0.0439190 strainProAla - strainCtrl
GIPGLTDAPES(UniMod:21)NKK3 -0.8566828 0.1677135 9.800088 -5.108012 0.0004887 0.0439190 strainProAla - strainCtrl
IS(UniMod:21)PSAPSK1 -0.5471030 0.1264221 16.467973 -4.327589 0.0004889 0.0439190 strainProAla - strainCtrl
EVPTLSQLNTTVS(UniMod:21)RDK3 0.3705265 0.0851849 16.109740 4.349676 0.0004893 0.0439190 strainProAla - strainCtrl
NS(UniMod:21)QDC(UniMod:4)VPLQWQAK2 -0.5092443 0.1163600 15.675792 -4.376454 0.0004913 0.0439821 strainProAla - strainCtrl
PTSNAS(UniMod:21)PPPASSGFNAR3 -4.5350511 0.7286086 6.778774 -6.224262 0.0004942 0.0440621 strainProAla - strainCtrl
TIS(UniMod:21)NEPLTTGNER2 0.7953274 0.1848237 16.778774 4.303167 0.0004950 0.0440621 strainProAla - strainCtrl
LDPT(UniMod:21)S(UniMod:21)YEAY(UniMod:21)QQQTQQK3 2.5726548 0.4870312 9.013651 5.282321 0.0005030 0.0446492 strainProAla - strainCtrl
SSS(UniMod:21)FAHLQAPSPIPDPLQVSKPETR4 0.5139542 0.1183819 15.944552 4.341494 0.0005089 0.0449383 strainProAla - strainCtrl
S(UniMod:21)PEVIEID2 0.3156353 0.0724162 15.683724 4.358628 0.0005091 0.0449383 strainProAla - strainCtrl
TNLAPNNTS(UniMod:21)TSSLM(UniMod:35)K2 -3.7962010 0.5328409 5.618498 -7.124455 0.0005142 0.0452637 strainProAla - strainCtrl
RNHS(UniMod:21)PDPIGIDNYK3 0.4888570 0.1121077 15.506400 4.360601 0.0005199 0.0456332 strainProAla - strainCtrl
VADELRS(UniMod:21)VGETVDYIASNPDAN3 1.3330196 0.2952684 13.505949 4.514604 0.0005297 0.0461953 strainProAla - strainCtrl
ELGTANGTGHST(UniMod:21)PLSK2 -0.4279639 0.1001742 16.761907 -4.272199 0.0005300 0.0461953 strainProAla - strainCtrl
LPASSSPSPSPTSS(UniMod:21)ASPSR3 -0.5247805 0.1162686 13.507548 -4.513519 0.0005306 0.0461953 strainProAla - strainCtrl
RGS(UniMod:21)EDDSFLSSQGNR3 0.5796785 0.1350887 16.386382 4.291095 0.0005336 0.0462597 strainProAla - strainCtrl
AKEDS(UniMod:21)LIK1 -0.4798242 0.1116752 16.285697 -4.296604 0.0005343 0.0462597 strainProAla - strainCtrl
S(UniMod:21)FDVPPPPIDASSPFSQK2 -0.4164482 0.0955060 15.278372 -4.360442 0.0005373 0.0463903 strainProAla - strainCtrl
DSNLS(UniMod:21)SPARDILPLPPK2 -0.4868734 0.1129671 15.876863 -4.309868 0.0005484 0.0472209 strainProAla - strainCtrl
TTFKT(UniMod:21)PR2 -0.6198351 0.1454682 16.547433 -4.260965 0.0005574 0.0478654 strainProAla - strainCtrl
NLQRES(UniMod:21)C(UniMod:4)EDILDLK3 0.4194066 0.0977818 16.025890 4.289210 0.0005613 0.0480696 strainProAla - strainCtrl
VVS(UniMod:21)GEAASDEHFSR2 0.4850957 0.1110680 14.861238 4.367557 0.0005632 0.0481009 strainProAla - strainCtrl
TVSSESYQS(UniMod:21)EQESSTPLLK2 0.3635594 0.0852124 16.264862 4.266510 0.0005708 0.0485212 strainProAla - strainCtrl
STLNS(UniMod:21)VKK2 -0.7336983 0.1718628 16.216889 -4.269092 0.0005711 0.0485212 strainProAla - strainCtrl
REENTIINSET(UniMod:21)ESTTHSAPFLK3 0.4581279 0.1000181 12.442716 4.580450 0.0005763 0.0488249 strainProAla - strainCtrl
EST(UniMod:21)PPISPK2 1.0403955 0.2278031 12.511516 4.567081 0.0005819 0.0491727 strainProAla - strainCtrl
SEPVGT(UniMod:21)PNIEENK2 0.2772306 0.0656164 16.778774 4.225019 0.0005851 0.0491822 strainProAla - strainCtrl
QET(UniMod:21)LTESLK2 0.4180162 0.0976485 15.842201 4.280827 0.0005851 0.0491822 strainProAla - strainCtrl

Volcanoplots

plotVolcano(inferencesPTM) + 
  facet_wrap(~contrast) + 
  labs(title = "Precursor-level Phospho DA")

inferencesPTM |> 
  filter(adjPval < alpha) |> 
  mutate(DA = sign(logFC) |> as.factor() |> recode("-1"= "down","1" = "up")) |>
  group_by(contrast, DA) |> 
  ggplot(aes(x = contrast)) +
  geom_bar(aes(fill = factor(DA)),
           colour = "black") +
  theme_minimal() +
  theme(axis.text.x = element_text(angle = 90))

Heatmaps

We will make a heatmap for each contrast. Note that we cluster the rows ourselves to avoid issues with missing values.

lapply(colnames(L),
                   function(contrast, se, alpha)
{
                     sig <- rowData(se)[[contrast]] |> 
                       filter(adjPval < alpha) |> 
                       rownames()
                     if (length(sig) > 2)
                     {
                     quants <- t(scale(t(assay(se[sig,]))))
                     colnames(quants) <- se$sampleId #specific to this dataset to get short colnames
                     rowclushlp <- quants
                     rowclushlp[is.na(rowclushlp)] <- min(quants,na.rm=TRUE) - 2
                     rowclus <- hclust(dist(rowclushlp))
                     annotations <- columnAnnotation(
                       group = se$strain
                       ) #3.
                     set.seed(1234) ## annotation colours are randomly generated by default
                     return(
                       Heatmap(show_row_names = FALSE,
                       quants, 
                       name = "log2 intensity",
                       top_annotation = annotations, 
                       column_title = paste0(contrast, " = 0"),
                       cluster_rows = rowclus
                       )
                     )
                     } else return(ggplot() + theme_minimal() + ggtitle(paste0(contrast, " = 0")))
                   },
                   se = getWithColData(qf, "precursorsPTM_norm"),
                   alpha = alpha)
[[1]]


[[2]]


[[3]]

#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 11644169 621.9   17413800 930.0         NA  17413800  930
Vcells 34950819 266.7  102851388 784.7      24576 312075668 2381
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 11644171 621.9   17413800 930.0         NA  17413800  930
Vcells 34950855 266.7  102851388 784.7      24576 312075668 2381

Detail plots

We can explore the data for a precursor to validate the statistical inference results. For example, let’s explore the precursor and the normalised precursor intensities for the precursor with the most significant log2 fold change.

(target_feature <- inferencesPTM |> 
   dplyr::slice(which.min(pval)) |> 
   pull(feature)
)
[1] "(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2"
inferencesPTM |> 
  filter(feature == target_feature)
                                                                    logFC
strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2                -0.1018668
strainProAla.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2               2.0438618
strainProAla - strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2  2.1457286
                                                                       se
strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2                0.09779209
strainProAla.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2              0.09989353
strainProAla - strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2 0.09850259
                                                                     df
strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2                15.94953
strainProAla.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2              15.94953
strainProAla - strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2 15.94953
                                                                       t
strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2                -1.041667
strainProAla.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2              20.460402
strainProAla - strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2 21.783474
                                                                       pval
strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2                3.130993e-01
strainProAla.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2              7.155345e-13
strainProAla - strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2 2.721245e-13
                                                                    adjPval
strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2                7.174904e-01
strainProAla.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2              2.281339e-08
strainProAla - strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2 8.623080e-09
                                                                                contrast
strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2                               strainCtrl
strainProAla.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2                           strainProAla
strainProAla - strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2 strainProAla - strainCtrl
                                                                                            feature
strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2                (UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2
strainProAla.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2              (UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2
strainProAla - strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2 (UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2

To obtain the required data, we perform a little data manipulation pipeline:

  • We use the QFeatures subsetting functionality to retrieve all data related to ion data used for model fitting.
  • We then convert the data with longForm() for plotting.
  • Finally, we plot the log2 normalised intensities for each sample for the unnormalised and normalised phospho precursors.
qf[target_feature, , c("precursorsPTM_log","precursorsPTM_norm")] |> #1
  longForm(colvars = colnames(colData(qf))) |> #2
  data.frame() |> 
  ggplot() +
  aes(x = sampleId,
      y = value) +
  geom_line(aes(group = rowname), linewidth = 0.1) +
  geom_point(aes(colour = strain)) +
  facet_wrap(~ assay, scales = "free") +
  ggtitle(target_feature) +
  theme_minimal() +
  theme(axis.text.x = element_blank())
Warning: 'experiments' dropped; see 'drops()'
harmonizing input:
  removing 90 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'

qf[target_feature, , c("precursorsPTM_log","precursorsPTM_norm")] |> #1
  longForm(colvars = colnames(colData(qf))) |> #2
  data.frame() |>
  filter(!is.na(value)) %>% 
  {
  ggplot(.) +
  aes(x = strain,
      y = value) +
  geom_boxplot(aes(colour = strain)) +
  facet_wrap(~ assay, scales = "free") +
  geom_jitter(aes(shape = rowname)) +
  scale_shape_manual(values = seq_len(dplyr::n_distinct(.$rowname))) +
  ggtitle(target_feature) +
  theme_minimal() +
  theme(axis.text.x = element_blank()) +
  guides(shape = "none")
  }
Warning: 'experiments' dropped; see 'drops()'
harmonizing input:
  removing 90 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'

We now compare the intensities for the top 5 DA phospo-precursors for the first contrast to these of their corresponding protein in the non-enriched assay.

contr = colnames(L)[1]
top5 <- inferencesPTM |> 
  filter(contrast == contr) |> 
  arrange(pval) |> 
  head(n = 5) |> 
  pull(feature)

for (feat in top5)
{
  ptm_data <- qf[,,c("precursorsPTM_norm")] |> 
    longForm(colvars = colnames(colData(qf)), rowvars = "Protein.Group") |>
    data.frame() |> 
    filter(rowname==feat)
  feature_protein <- ptm_data |> 
    pull("Protein.Group") |> 
    unique()
  prot_data <- qf[,,"proteins"]|>
    longForm(colvars = colnames(colData(qf)), rowvars = "Protein.Group") |>
    data.frame() |> 
    filter(Protein.Group==feature_protein) 
  ptm_protein <- rbind(ptm_data, prot_data)
  ylims <- ptm_protein |> 
  group_by(assay) |> 
  summarise(cent = mean(range(value,na.rm=TRUE)), ampl = diff(range(value,na.rm=TRUE))) |> 
  mutate(lower = cent - max(ampl)/2, 
         upper = cent + max(ampl)/2) |> 
  select(-c(cent, ampl))
  
  comparison_plot <- ptm_protein |>
    ggplot() +
    aes(x = sampleId,
        y = value) +
    geom_line(aes(group = rowname), linewidth = 0.1) +
    geom_point(aes(colour = strain)) +
    facet_wrap(~ assay, scales = "free") +
    labs(
      title = paste0(feat," / ", feature_protein)
    ) +
    theme_minimal() +
    theme(axis.text.x = element_blank()) +
    ggh4x::facetted_pos_scales(
    y = list(
      assay == ylims$assay[1] ~ scale_y_continuous(limits = unlist(ylims[1,c("lower","upper")])),
      assay == ylims$assay[2] ~ scale_y_continuous(limits = unlist(ylims[2,c("lower","upper")]))
    )
    ) 
 print(comparison_plot)
}

We prioritised DA phospho-precursors. However, they might be DA due to the parent proteins on which the PTMs occur that can also change in abundance regardless of the modification, which is clearly illustrated for the top DA phospho-precursor!

Any changes in the abundance of a phospho-peptidoform can thus be confounded with changes in protein abundance.

We therefore first assess differential abundance at the protein level for the non-enriched samples and will then propose an differential usage analysis where the precursor-level log2-FC is corrected for the protein-level log2-FC.

#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 11662788 622.9   17413800 930.0         NA  17413800  930
Vcells 34979495 266.9  102851388 784.7      24576 312075668 2381
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 11662784 622.9   17413800 930.0         NA  17413800  930
Vcells 34979521 266.9  102851388 784.7      24576 312075668 2381

11.7 Data Modeling at protein-level (non-enriched samples)

11.7.1 Model estimation

We can use the same model to model the protein-level data of the non-enriched runs. Indeed, they stem from the same biological samples.

qf <- msqrob(
  qf,
  i = "proteins",
  formula = model,
  robust = TRUE)

We enabled M-estimation (robust = TRUE) for improved robustness against outliers.

#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 11764913 628.4   17413800 930.0         NA  17413800  930
Vcells 35289928 269.3  102851388 784.7      24576 312075668 2381
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 11764915 628.4   17413800 930.0         NA  17413800  930
Vcells 35289964 269.3  102851388 784.7      24576 312075668 2381

11.7.2 Inference

We assess the contrast for each protein.

qf <- hypothesisTest(qf, i = "proteins", contrast = L, overwrite = TRUE)

We extract the results table from the proteins summarised experiment in the qf object.

inferences <- 
  msqrobCollect(qf[["proteins"]], L)
#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 11779016 629.1   17413800 930.0         NA  17413800  930
Vcells 35577742 271.5  102851388 784.7      24576 312075668 2381
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 11779012 629.1   17413800 930.0         NA  17413800  930
Vcells 35577768 271.5  102851388 784.7      24576 312075668 2381

11.7.3 Report results

We report the results using a results table, volcano plots and heatmaps.

Results table

for (j in colnames(L)) {

  inference <- inferences |> 
    dplyr::filter(adjPval < alpha & contrast == j)

  cat("**Median - Contrast:**", j, "= 0 (", nrow(inference),
      "significant proteins)\n\n")

  cat('<div style="max-height:300px; overflow-y:auto;">')

  print(
    kable(
      inference |>
        dplyr::arrange(pval) |>
        dplyr::relocate(feature),
      row.names = FALSE
    )
  )

  cat('</div>')

  cat("\n\n\n---\n\n")
}

Median - Contrast: strainCtrl = 0 ( 748 significant proteins)

feature logFC se df t pval adjPval contrast
Q12068 -1.2515608 0.0409454 16.684352 -30.566594 0.0000000 0.0000000 strainCtrl
P31539 -0.4692805 0.0214118 16.974579 -21.916913 0.0000000 0.0000000 strainCtrl
P53912 -0.7635445 0.0419731 16.446139 -18.191295 0.0000000 0.0000000 strainCtrl
P10591 -0.6394538 0.0325643 15.320763 -19.636640 0.0000000 0.0000000 strainCtrl
Q03148 0.4653748 0.0268753 16.605675 17.316078 0.0000000 0.0000000 strainCtrl
P32644 -0.4277644 0.0257658 16.974579 -16.602039 0.0000000 0.0000000 strainCtrl
P38113 0.5005009 0.0308429 16.575401 16.227403 0.0000000 0.0000000 strainCtrl
P07264 0.4898030 0.0277702 14.986955 17.637712 0.0000000 0.0000000 strainCtrl
P38260 -0.4665672 0.0305727 16.794048 -15.260904 0.0000000 0.0000000 strainCtrl
P38737 -0.3769284 0.0259363 16.647957 -14.532830 0.0000000 0.0000000 strainCtrl
P34227 -0.4477016 0.0304955 16.388726 -14.680893 0.0000000 0.0000000 strainCtrl
Q01217 0.3584061 0.0240049 16.042311 14.930556 0.0000000 0.0000000 strainCtrl
P08432 0.6410670 0.0461286 15.937895 13.897388 0.0000000 0.0000001 strainCtrl
P03965 0.3701687 0.0287237 16.829890 12.887203 0.0000000 0.0000001 strainCtrl
P36007 0.4011821 0.0327505 16.839239 12.249666 0.0000000 0.0000002 strainCtrl
P15705 -0.3278496 0.0252991 15.717892 -12.958933 0.0000000 0.0000002 strainCtrl
P23337 0.6903051 0.0573546 16.974579 12.035735 0.0000000 0.0000003 strainCtrl
Q03102 -0.7064956 0.0513845 14.521020 -13.749185 0.0000000 0.0000003 strainCtrl
P07702 0.2464155 0.0205648 16.751575 11.982381 0.0000000 0.0000003 strainCtrl
P53691 -0.3579545 0.0300233 16.259605 -11.922546 0.0000000 0.0000004 strainCtrl
P33416 -0.3399719 0.0290902 16.485462 -11.686813 0.0000000 0.0000005 strainCtrl
P32643 0.4972365 0.0432695 16.571430 11.491617 0.0000000 0.0000005 strainCtrl
P22134 -0.4817169 0.0441770 16.974579 -10.904256 0.0000000 0.0000009 strainCtrl
P53834 -0.4761132 0.0424268 16.157707 -11.221978 0.0000000 0.0000009 strainCtrl
P11972 0.5694035 0.0538771 16.888043 10.568552 0.0000000 0.0000013 strainCtrl
P47164 0.5217311 0.0491352 16.665067 10.618267 0.0000000 0.0000014 strainCtrl
Q04792 0.4919844 0.0465857 16.560622 10.560855 0.0000000 0.0000015 strainCtrl
P40897 0.7777419 0.0744662 16.828073 10.444232 0.0000000 0.0000015 strainCtrl
P16474 -0.2816371 0.0263727 16.273428 -10.679102 0.0000000 0.0000015 strainCtrl
P10592 -0.4237089 0.0403486 16.606174 -10.501195 0.0000000 0.0000015 strainCtrl
P32642 -0.8119299 0.0748661 15.686945 -10.845097 0.0000000 0.0000016 strainCtrl
P40008 -0.3107781 0.0289843 15.884016 -10.722302 0.0000000 0.0000016 strainCtrl
P53940 -0.3908033 0.0347100 14.837382 -11.259101 0.0000000 0.0000016 strainCtrl
P33734 0.2557564 0.0251440 16.864098 10.171651 0.0000000 0.0000017 strainCtrl
P32775 0.4455859 0.0410519 15.374210 10.854196 0.0000000 0.0000017 strainCtrl
Q12449 -0.4189592 0.0391410 15.665439 -10.703839 0.0000000 0.0000017 strainCtrl
P36152 -0.2644068 0.0256171 16.387672 -10.321508 0.0000000 0.0000017 strainCtrl
P40017 0.2987682 0.0297455 16.397686 10.044137 0.0000000 0.0000025 strainCtrl
P25294 -0.3317738 0.0331396 16.336859 -10.011391 0.0000000 0.0000026 strainCtrl
P27614 -0.2622410 0.0262751 16.336872 -9.980594 0.0000000 0.0000027 strainCtrl
P19097 0.1831380 0.0188461 16.848949 9.717572 0.0000000 0.0000028 strainCtrl
P07258 0.2752772 0.0284994 16.974579 9.659045 0.0000000 0.0000028 strainCtrl
P47169 0.4423025 0.0436344 15.757329 10.136546 0.0000000 0.0000028 strainCtrl
P21954 0.2503838 0.0256402 16.592547 9.765263 0.0000000 0.0000029 strainCtrl
P05694 0.2439711 0.0257028 16.934830 9.491998 0.0000000 0.0000034 strainCtrl
P53044 -0.2603441 0.0270159 16.527721 -9.636707 0.0000000 0.0000034 strainCtrl
P00635 -1.2495505 0.1023388 12.093030 -12.209934 0.0000000 0.0000036 strainCtrl
O14467 -0.4100752 0.0420435 16.030651 -9.753601 0.0000000 0.0000037 strainCtrl
Q04432 -0.4215017 0.0431582 15.867825 -9.766426 0.0000000 0.0000039 strainCtrl
P04076 0.2958434 0.0308973 15.909932 9.575051 0.0000001 0.0000047 strainCtrl
P39692 0.4426534 0.0473760 16.502542 9.343405 0.0000001 0.0000047 strainCtrl
P22202 -0.3812215 0.0373039 14.411886 -10.219354 0.0000001 0.0000047 strainCtrl
P22768 0.2968733 0.0313463 16.097399 9.470758 0.0000001 0.0000047 strainCtrl
P53128 0.2918069 0.0289613 14.667423 10.075751 0.0000001 0.0000047 strainCtrl
P39522 0.2071070 0.0224979 16.759280 9.205596 0.0000001 0.0000049 strainCtrl
P36141 -0.3661856 0.0374150 15.012320 -9.787122 0.0000001 0.0000054 strainCtrl
Q12746 -0.2531209 0.0272464 16.054187 -9.290053 0.0000001 0.0000059 strainCtrl
P26637 0.1819555 0.0195728 15.891880 9.296338 0.0000001 0.0000063 strainCtrl
P33755 -0.2132146 0.0238730 16.901073 -8.931203 0.0000001 0.0000064 strainCtrl
Q06625 0.4811625 0.0500372 14.998485 9.616099 0.0000001 0.0000064 strainCtrl
Q96VH4 -0.6524179 0.0720156 16.364601 -9.059398 0.0000001 0.0000067 strainCtrl
P53241 0.7328647 0.0827235 16.532874 8.859213 0.0000001 0.0000082 strainCtrl
P53078 0.3726470 0.0388904 14.379819 9.581970 0.0000001 0.0000092 strainCtrl
Q08422 -0.5295791 0.0584993 15.608114 -9.052748 0.0000001 0.0000095 strainCtrl
P18544 0.3299091 0.0384280 16.933011 8.585129 0.0000001 0.0000101 strainCtrl
P53090 0.2264840 0.0256731 16.013845 8.821840 0.0000002 0.0000104 strainCtrl
P53549 -0.2012717 0.0231544 16.422492 -8.692588 0.0000002 0.0000104 strainCtrl
P54007 -1.0972010 0.1306766 16.974579 -8.396309 0.0000002 0.0000129 strainCtrl
Q04894 -0.2732325 0.0319611 16.299209 -8.548909 0.0000002 0.0000134 strainCtrl
P06738 0.5035087 0.0585409 16.007799 8.600980 0.0000002 0.0000140 strainCtrl
P23180 0.2750518 0.0323943 16.109446 8.490749 0.0000002 0.0000156 strainCtrl
P07149 0.1805547 0.0205039 15.110728 8.805874 0.0000002 0.0000156 strainCtrl
Q04066 0.2616091 0.0312882 16.258918 8.361258 0.0000003 0.0000174 strainCtrl
P32795 -0.1736590 0.0211298 16.726809 -8.218658 0.0000003 0.0000176 strainCtrl
P38219 -0.2315767 0.0280240 16.413237 -8.263511 0.0000003 0.0000185 strainCtrl
P32496 -0.2354309 0.0282325 16.059662 -8.339004 0.0000003 0.0000190 strainCtrl
P40016 -0.2166511 0.0263586 16.381533 -8.219376 0.0000003 0.0000197 strainCtrl
P05150 0.2954501 0.0363865 16.613910 8.119777 0.0000004 0.0000207 strainCtrl
P02829 -0.5384905 0.0668282 16.758146 -8.057827 0.0000004 0.0000213 strainCtrl
P33299 -0.1760210 0.0214342 15.984244 -8.212172 0.0000004 0.0000228 strainCtrl
P25491 -0.2866627 0.0346959 15.750772 -8.262152 0.0000004 0.0000232 strainCtrl
P38631 0.2435668 0.0292079 15.144861 8.339067 0.0000005 0.0000269 strainCtrl
P09368 -1.0608489 0.1322049 16.198998 -8.024278 0.0000005 0.0000271 strainCtrl
P21243 -0.2038059 0.0245657 15.135678 -8.296354 0.0000005 0.0000282 strainCtrl
P00815 0.2553638 0.0318956 16.110484 8.006249 0.0000005 0.0000283 strainCtrl
P05374 0.3063047 0.0380642 15.630737 8.047055 0.0000006 0.0000323 strainCtrl
P28817 -0.1998959 0.0258685 16.615061 -7.727385 0.0000007 0.0000358 strainCtrl
Q04728 0.2490986 0.0321836 15.955132 7.739921 0.0000009 0.0000452 strainCtrl
P21801 0.3294746 0.0423350 15.693141 7.782555 0.0000009 0.0000465 strainCtrl
P40989 -0.7334250 0.0952160 15.925965 -7.702753 0.0000009 0.0000476 strainCtrl
P43558 -0.3029606 0.0401967 16.552314 -7.536956 0.0000010 0.0000487 strainCtrl
P14843 0.1984880 0.0255577 15.459793 7.766277 0.0000010 0.0000509 strainCtrl
P00899 0.1674339 0.0225056 16.657931 7.439661 0.0000011 0.0000540 strainCtrl
P53915 0.2946943 0.0394385 16.487821 7.472257 0.0000011 0.0000540 strainCtrl
Q04062 -0.2076007 0.0281403 16.827625 -7.377332 0.0000011 0.0000557 strainCtrl
P12866 0.3677210 0.0482995 15.509333 7.613357 0.0000013 0.0000612 strainCtrl
P33297 -0.1926878 0.0262142 16.560136 -7.350501 0.0000013 0.0000630 strainCtrl
P22137 0.1921361 0.0265347 16.974579 7.240938 0.0000014 0.0000653 strainCtrl
P41930 0.5055440 0.0689623 16.410263 7.330728 0.0000015 0.0000675 strainCtrl
P38840 -0.2886393 0.0390299 15.659247 -7.395332 0.0000017 0.0000794 strainCtrl
Q03558 -0.2254940 0.0300564 14.631762 -7.502371 0.0000022 0.0000998 strainCtrl
P47112 -0.3914571 0.0554134 16.277512 -7.064307 0.0000024 0.0001090 strainCtrl
P07172 0.2210763 0.0315580 16.573604 7.005389 0.0000024 0.0001090 strainCtrl
P38162 -0.4071609 0.0584297 16.720403 -6.968388 0.0000025 0.0001099 strainCtrl
P07285 0.2410786 0.0347030 16.691819 6.946918 0.0000026 0.0001142 strainCtrl
Q12179 -0.2457418 0.0351427 16.361866 -6.992687 0.0000027 0.0001164 strainCtrl
P07283 0.2068678 0.0285462 15.093081 7.246777 0.0000027 0.0001181 strainCtrl
P32589 -0.2457046 0.0336307 14.696775 -7.305953 0.0000029 0.0001242 strainCtrl
P32386 0.2367477 0.0345754 16.743227 6.847287 0.0000031 0.0001298 strainCtrl
P38777 -0.3448343 0.0479991 15.008046 -7.184180 0.0000031 0.0001306 strainCtrl
P47988 0.4006811 0.0582293 16.479224 6.881096 0.0000032 0.0001306 strainCtrl
P38279 1.1219377 0.1636369 16.526101 6.856262 0.0000032 0.0001333 strainCtrl
P38764 -0.1611569 0.0236473 16.626977 -6.815012 0.0000034 0.0001379 strainCtrl
P53318 0.2275861 0.0325980 15.661104 6.981603 0.0000035 0.0001405 strainCtrl
Q04693 -0.1918581 0.0282605 16.348995 -6.788921 0.0000039 0.0001553 strainCtrl
P33298 -0.2138363 0.0305478 15.243846 -7.000059 0.0000039 0.0001553 strainCtrl
P53885 -0.2021041 0.0289613 15.126582 -6.978426 0.0000042 0.0001666 strainCtrl
P15108 -0.4015873 0.0587437 15.746940 -6.836258 0.0000044 0.0001691 strainCtrl
P19882 -0.2720423 0.0402919 16.177738 -6.751790 0.0000044 0.0001691 strainCtrl
P38972 0.1523939 0.0227567 16.469961 6.696669 0.0000044 0.0001691 strainCtrl
Q12680 0.1551766 0.0217063 14.265109 7.148909 0.0000044 0.0001691 strainCtrl
P11154 -0.2391994 0.0362801 16.647348 -6.593137 0.0000051 0.0001912 strainCtrl
P15424 -0.1765361 0.0265896 16.314933 -6.639281 0.0000052 0.0001928 strainCtrl
P11075 0.1905059 0.0292096 16.974579 6.522031 0.0000053 0.0001951 strainCtrl
P37012 0.3253588 0.0486046 15.812708 6.693992 0.0000055 0.0002016 strainCtrl
Q06103 -0.1956908 0.0302131 16.974579 -6.477024 0.0000057 0.0002092 strainCtrl
P52489 0.2182713 0.0323925 15.399579 6.738334 0.0000058 0.0002104 strainCtrl
P38891 0.2457319 0.0371004 15.948700 6.623424 0.0000060 0.0002139 strainCtrl
P21826 -0.6740917 0.1042932 16.891935 -6.463430 0.0000060 0.0002147 strainCtrl
P32861 0.1592521 0.0244806 16.521719 6.505225 0.0000062 0.0002194 strainCtrl
Q06078 -0.1630774 0.0235265 14.112332 -6.931646 0.0000067 0.0002343 strainCtrl
P14832 -0.1748067 0.0273546 16.491024 -6.390401 0.0000078 0.0002703 strainCtrl
P05626 0.2212577 0.0340565 15.773417 6.496787 0.0000079 0.0002732 strainCtrl
P38202 -0.4889797 0.0773792 16.834635 -6.319268 0.0000081 0.0002765 strainCtrl
Q04304 -0.3371332 0.0519180 15.499634 -6.493575 0.0000086 0.0002948 strainCtrl
P16547 0.2644025 0.0417353 16.435132 6.335227 0.0000087 0.0002950 strainCtrl
Q05506 0.1424685 0.0215599 14.837979 6.608038 0.0000088 0.0002950 strainCtrl
P39076 -0.1454944 0.0228167 16.005803 -6.376666 0.0000092 0.0003055 strainCtrl
P32379 -0.2606321 0.0416736 16.648592 -6.254123 0.0000096 0.0003178 strainCtrl
P46683 -0.1915317 0.0307565 16.796313 -6.227349 0.0000097 0.0003191 strainCtrl
P30902 0.1892078 0.0289420 14.860257 6.537486 0.0000098 0.0003211 strainCtrl
P32178 -0.1973227 0.0312697 16.099238 -6.310342 0.0000101 0.0003265 strainCtrl
Q06106 -0.1827451 0.0289079 15.940932 -6.321637 0.0000103 0.0003324 strainCtrl
Q06214 -0.1602049 0.0250438 15.412040 -6.396992 0.0000106 0.0003374 strainCtrl
P40215 0.1833810 0.0298549 16.866350 6.142411 0.0000112 0.0003528 strainCtrl
Q07896 -0.1985061 0.0310493 15.221452 -6.393248 0.0000113 0.0003528 strainCtrl
P38627 -0.2189109 0.0356227 16.812354 -6.145270 0.0000113 0.0003528 strainCtrl
P40202 -0.2095329 0.0340686 16.767455 -6.150328 0.0000113 0.0003528 strainCtrl
P43573 -0.2136874 0.0348303 16.739401 -6.135105 0.0000118 0.0003636 strainCtrl
P16550 -0.1590759 0.0250576 15.197339 -6.348416 0.0000123 0.0003772 strainCtrl
P53303 -0.3219146 0.0517486 15.892085 -6.220739 0.0000126 0.0003847 strainCtrl
P27882 0.2173596 0.0339193 14.759516 6.408143 0.0000127 0.0003848 strainCtrl
P32327 0.1935427 0.0313053 16.061552 6.182431 0.0000129 0.0003887 strainCtrl
P40327 -0.1886984 0.0308643 16.444365 -6.113801 0.0000133 0.0003926 strainCtrl
P06634 -0.1694716 0.0275025 16.078566 -6.162040 0.0000134 0.0003926 strainCtrl
Q12100 0.2932671 0.0480704 16.480695 6.100782 0.0000135 0.0003926 strainCtrl
P21147 0.2209821 0.0352406 15.353065 6.270671 0.0000135 0.0003926 strainCtrl
P06105 0.1315999 0.0215172 16.366384 6.116043 0.0000135 0.0003926 strainCtrl
P03962 0.3569324 0.0587379 16.563743 6.076701 0.0000138 0.0003993 strainCtrl
P35817 -0.1781004 0.0285623 15.340926 -6.235506 0.0000144 0.0004145 strainCtrl
P17555 0.1342810 0.0219809 16.128868 6.108975 0.0000146 0.0004163 strainCtrl
P38988 0.4259090 0.0684703 15.259234 6.220351 0.0000152 0.0004310 strainCtrl
P39927 -0.1706572 0.0283807 16.574150 -6.013151 0.0000156 0.0004392 strainCtrl
P42846 -0.1983132 0.0320432 15.345886 -6.188940 0.0000157 0.0004392 strainCtrl
P53133 0.3338704 0.0552720 16.215748 6.040496 0.0000162 0.0004518 strainCtrl
Q06408 -0.2600361 0.0430509 16.158309 -6.040196 0.0000165 0.0004552 strainCtrl
P38230 0.1842080 0.0303423 15.927663 6.070997 0.0000165 0.0004552 strainCtrl
P09232 -0.2904410 0.0482324 16.186528 -6.021700 0.0000169 0.0004635 strainCtrl
P46970 -0.1693895 0.0285798 16.794243 -5.926891 0.0000174 0.0004743 strainCtrl
Q08985 0.2135210 0.0356089 16.076436 5.996282 0.0000183 0.0004948 strainCtrl
P06786 0.1501905 0.0252178 16.300981 5.955734 0.0000186 0.0005015 strainCtrl
P47079 -0.1137715 0.0189880 15.961683 -5.991753 0.0000190 0.0005084 strainCtrl
P25638 -0.3074844 0.0516372 16.176645 -5.954705 0.0000193 0.0005088 strainCtrl
P25335 -0.6672257 0.1135127 16.764304 -5.877981 0.0000193 0.0005088 strainCtrl
P56628 0.6477244 0.1065215 15.279794 6.080689 0.0000194 0.0005088 strainCtrl
P30657 -0.2589372 0.0438265 16.493153 -5.908230 0.0000195 0.0005088 strainCtrl
P50278 -0.2011227 0.0342223 16.633055 -5.876954 0.0000200 0.0005195 strainCtrl
P23724 -0.1710461 0.0285728 15.699256 -5.986330 0.0000206 0.0005321 strainCtrl
Q04373 -0.1456477 0.0249650 16.737622 -5.834088 0.0000212 0.0005449 strainCtrl
P07806 0.1234046 0.0203267 14.960814 6.071073 0.0000216 0.0005533 strainCtrl
P32449 0.1698101 0.0287988 16.028273 5.896425 0.0000224 0.0005689 strainCtrl
P40471 0.2184463 0.0377352 16.796022 5.788925 0.0000229 0.0005779 strainCtrl
P19262 0.1551109 0.0266138 16.418522 5.828220 0.0000232 0.0005815 strainCtrl
P38858 -0.2065472 0.0345178 15.267848 -5.983792 0.0000233 0.0005815 strainCtrl
Q12220 -0.1597542 0.0273987 16.267208 -5.830728 0.0000239 0.0005948 strainCtrl
P00931 0.1448374 0.0236598 14.302086 6.121666 0.0000241 0.0005956 strainCtrl
P12630 0.4609074 0.0788813 16.053146 5.843050 0.0000246 0.0006060 strainCtrl
P48415 0.1439026 0.0248598 16.403655 5.788568 0.0000251 0.0006145 strainCtrl
P38009 -0.1668590 0.0289494 16.432756 -5.763814 0.0000262 0.0006371 strainCtrl
P38707 0.1470156 0.0257271 16.543988 5.714429 0.0000281 0.0006803 strainCtrl
P27809 0.1139456 0.0199296 16.371602 5.717397 0.0000291 0.0007005 strainCtrl
P32471 -0.1995332 0.0351460 16.613065 -5.677265 0.0000298 0.0007131 strainCtrl
Q12451 0.1633944 0.0285811 16.232725 5.716875 0.0000301 0.0007171 strainCtrl
P40487 -0.2082569 0.0366726 16.433883 -5.678821 0.0000309 0.0007332 strainCtrl
P38236 0.3341708 0.0586732 16.138216 5.695458 0.0000321 0.0007566 strainCtrl
P32600 0.2724521 0.0469953 15.263577 5.797429 0.0000328 0.0007678 strainCtrl
Q04773 -0.1692882 0.0294147 15.567355 -5.755234 0.0000329 0.0007678 strainCtrl
P32781 0.7186633 0.1258796 15.780568 5.709133 0.0000340 0.0007910 strainCtrl
Q12428 -0.2651489 0.0473921 16.693684 -5.594790 0.0000344 0.0007938 strainCtrl
P39719 0.2319664 0.0410441 16.189556 5.651636 0.0000345 0.0007938 strainCtrl
Q12230 0.1505427 0.0268333 16.365099 5.610298 0.0000359 0.0008227 strainCtrl
P25584 0.3489211 0.0605309 15.128772 5.764342 0.0000361 0.0008233 strainCtrl
P21242 -0.2177958 0.0389159 16.421736 -5.596577 0.0000365 0.0008263 strainCtrl
P53903 -0.3035071 0.0543868 16.475053 -5.580525 0.0000372 0.0008388 strainCtrl
Q12123 0.3432562 0.0606608 15.634889 5.658620 0.0000388 0.0008715 strainCtrl
P25382 -0.1834605 0.0328008 16.109971 -5.593168 0.0000394 0.0008799 strainCtrl
Q03034 0.1895004 0.0341150 16.328566 5.554749 0.0000404 0.0008988 strainCtrl
P13134 0.2979949 0.0540826 16.585087 5.509996 0.0000418 0.0009178 strainCtrl
P40303 -0.2357288 0.0420231 15.711612 -5.609509 0.0000419 0.0009178 strainCtrl
P13663 0.1896145 0.0333764 15.156127 5.681100 0.0000419 0.0009178 strainCtrl
P42945 -0.1462736 0.0265282 16.487179 -5.513901 0.0000423 0.0009234 strainCtrl
P18963 0.2350675 0.0430768 16.618668 5.456936 0.0000461 0.0010014 strainCtrl
Q12377 -0.1952530 0.0355979 16.266777 -5.484954 0.0000471 0.0010164 strainCtrl
P39721 -0.2441613 0.0446586 16.407472 -5.467290 0.0000473 0.0010164 strainCtrl
P32771 -0.2094435 0.0383704 16.356617 -5.458466 0.0000486 0.0010409 strainCtrl
Q03103 -0.1400757 0.0258895 16.754431 -5.410526 0.0000493 0.0010493 strainCtrl
Q12386 -0.1828147 0.0340288 16.974579 -5.372349 0.0000509 0.0010797 strainCtrl
Q00955 0.1572932 0.0289274 16.038754 5.437518 0.0000543 0.0011462 strainCtrl
P47122 -0.1879674 0.0350413 16.678747 -5.364172 0.0000550 0.0011526 strainCtrl
P53296 -0.3785907 0.0693574 15.785338 -5.458547 0.0000551 0.0011526 strainCtrl
Q03640 0.2315496 0.0427906 15.735354 5.411229 0.0000611 0.0012697 strainCtrl
P48361 0.2076104 0.0391181 16.713336 5.307268 0.0000613 0.0012697 strainCtrl
Q12213 0.6721938 0.1246625 15.859583 5.392110 0.0000617 0.0012736 strainCtrl
P53742 -0.2081199 0.0390779 16.277142 -5.325774 0.0000644 0.0013238 strainCtrl
P08679 -0.1739976 0.0319154 14.915046 -5.451845 0.0000682 0.0013936 strainCtrl
Q86ZR7 0.2395681 0.0451223 16.144041 5.309302 0.0000685 0.0013936 strainCtrl
P02309 0.3008204 0.0570685 16.499181 5.271211 0.0000688 0.0013940 strainCtrl
P53101 0.3806463 0.0725477 16.582022 5.246843 0.0000711 0.0014346 strainCtrl
P53899 -0.3544106 0.0663039 15.551177 -5.345249 0.0000723 0.0014529 strainCtrl
P38822 0.1424907 0.0265566 15.211799 5.365552 0.0000750 0.0014996 strainCtrl
P09440 -0.1066955 0.0201673 15.845912 -5.290507 0.0000756 0.0015054 strainCtrl
Q06678 -0.1569442 0.0297633 15.982110 -5.273073 0.0000761 0.0015083 strainCtrl
P53094 0.1617129 0.0311625 16.691399 5.189344 0.0000783 0.0015457 strainCtrl
Q04697 -0.1791129 0.0338497 15.511238 -5.291422 0.0000810 0.0015922 strainCtrl
P50277 0.5144461 0.1001730 16.762374 5.135579 0.0000863 0.0016890 strainCtrl
P28707 -0.1732783 0.0333814 15.958333 -5.190860 0.0000900 0.0017543 strainCtrl
Q12250 -0.1823546 0.0353969 16.272138 -5.151709 0.0000915 0.0017771 strainCtrl
Q05881 -0.1881873 0.0370074 16.974579 -5.085121 0.0000922 0.0017815 strainCtrl
P08004 0.1890160 0.0371458 16.754098 5.088493 0.0000952 0.0018328 strainCtrl
Q05050 0.1228325 0.0239419 16.180089 5.130448 0.0000973 0.0018602 strainCtrl
P38197 -0.2001267 0.0395446 16.945890 -5.060779 0.0000974 0.0018602 strainCtrl
P40559 0.2726681 0.0535450 16.447021 5.092313 0.0000999 0.0018998 strainCtrl
P43588 -0.2024938 0.0398679 16.454872 -5.079116 0.0001025 0.0019408 strainCtrl
P00924 -0.2457285 0.0482057 16.152893 -5.097498 0.0001045 0.0019701 strainCtrl
Q05902 -0.1597562 0.0314047 16.186833 -5.087024 0.0001060 0.0019832 strainCtrl
P38250 0.2391217 0.0471620 16.369494 5.070219 0.0001060 0.0019832 strainCtrl
P10869 0.1786078 0.0342522 14.874593 5.214487 0.0001077 0.0020061 strainCtrl
P35191 -0.2930244 0.0576370 15.869779 -5.083962 0.0001133 0.0021022 strainCtrl
P40557 0.1790728 0.0353183 15.912245 5.070260 0.0001155 0.0021345 strainCtrl
P32459 -0.6002760 0.1186126 15.982118 -5.060813 0.0001162 0.0021381 strainCtrl
P38712 -0.1451539 0.0287375 16.053067 -5.051023 0.0001169 0.0021413 strainCtrl
Q3E762 0.4203794 0.0840186 16.569314 5.003407 0.0001173 0.0021413 strainCtrl
Q12375 0.2438359 0.0480842 15.729692 5.071021 0.0001195 0.0021700 strainCtrl
P00425 0.3002646 0.0591900 15.679008 5.072891 0.0001202 0.0021700 strainCtrl
P48353 -0.2574706 0.0500065 14.944747 -5.148738 0.0001203 0.0021700 strainCtrl
Q08746 -0.2106328 0.0420885 16.120398 -5.004516 0.0001268 0.0022798 strainCtrl
P25694 -0.1061865 0.0213590 16.453036 -4.971508 0.0001278 0.0022885 strainCtrl
Q12034 -0.1629933 0.0329252 16.480331 -4.950409 0.0001329 0.0023694 strainCtrl
P07342 0.1619382 0.0324253 15.932377 4.994198 0.0001341 0.0023816 strainCtrl
P22855 0.1916990 0.0387163 16.299928 4.951381 0.0001369 0.0024218 strainCtrl
P30656 -0.1989968 0.0404959 16.636858 -4.913997 0.0001394 0.0024583 strainCtrl
P00410 0.2869109 0.0573379 15.576302 5.003861 0.0001406 0.0024658 strainCtrl
D6VTK4 0.3281959 0.0666633 16.462983 4.923189 0.0001409 0.0024658 strainCtrl
P40991 -0.1112550 0.0222287 15.379883 -5.005022 0.0001456 0.0025377 strainCtrl
P34216 0.1433100 0.0286235 15.224465 5.006729 0.0001496 0.0025968 strainCtrl
Q12466 0.2237380 0.0456205 16.293944 4.904331 0.0001509 0.0026093 strainCtrl
P32565 -0.1482036 0.0301248 15.963605 -4.919652 0.0001549 0.0026701 strainCtrl
P38077 0.1602177 0.0327040 16.172457 4.899027 0.0001557 0.0026738 strainCtrl
P24869 0.5158428 0.1026601 14.790560 5.024765 0.0001575 0.0026932 strainCtrl
P21672 0.7935430 0.1320747 9.539988 6.008291 0.0001583 0.0026983 strainCtrl
P32892 -0.1104092 0.0228076 16.726557 -4.840902 0.0001600 0.0027159 strainCtrl
P36159 -0.1394936 0.0284270 15.754047 -4.907080 0.0001650 0.0027910 strainCtrl
P53753 -0.2091871 0.0423421 15.360653 -4.940409 0.0001660 0.0027975 strainCtrl
P40207 -0.4477219 0.0906001 15.232420 -4.941740 0.0001696 0.0028481 strainCtrl
Q05530 -0.3150304 0.0634504 14.858033 -4.964985 0.0001743 0.0029159 strainCtrl
P52892 0.2394289 0.0502051 16.868895 4.769011 0.0001818 0.0030310 strainCtrl
P08638 -0.1271130 0.0259696 15.318736 -4.894681 0.0001831 0.0030413 strainCtrl
Q03533 0.2455704 0.0512200 16.413313 4.794421 0.0001854 0.0030690 strainCtrl
Q04344 -0.1914529 0.0390277 15.091204 -4.905564 0.0001870 0.0030840 strainCtrl
P22141 -0.2620045 0.0538990 15.510099 -4.861026 0.0001890 0.0030976 strainCtrl
Q06629 -0.1123518 0.0234763 16.391051 -4.785763 0.0001895 0.0030976 strainCtrl
P43638 0.1504357 0.0315917 16.688816 4.761877 0.0001899 0.0030976 strainCtrl
P38182 -0.3823833 0.0794961 15.913561 -4.810088 0.0001952 0.0031732 strainCtrl
P15992 0.5182054 0.1081878 16.048625 4.789869 0.0001988 0.0032168 strainCtrl
P38143 0.1914331 0.0401324 16.281205 4.770041 0.0001993 0.0032168 strainCtrl
P38803 -0.1337859 0.0283016 16.658649 -4.727157 0.0002051 0.0033002 strainCtrl
Q12532 -0.1305937 0.0275923 16.403901 -4.732972 0.0002109 0.0033817 strainCtrl
P53920 -0.0986418 0.0208721 16.457481 -4.726003 0.0002122 0.0033902 strainCtrl
Q08818 -0.1612262 0.0343116 16.607682 -4.698882 0.0002194 0.0034926 strainCtrl
P38910 -0.2629233 0.0556257 16.202898 -4.726655 0.0002207 0.0035013 strainCtrl
P20448 -0.1715604 0.0359450 15.595563 -4.772853 0.0002222 0.0035131 strainCtrl
P38784 -0.1640402 0.0346260 15.962907 -4.737491 0.0002244 0.0035143 strainCtrl
P36143 0.5651900 0.1196026 16.098621 4.725566 0.0002249 0.0035143 strainCtrl
Q12458 -0.1579600 0.0330108 15.381113 -4.785096 0.0002250 0.0035143 strainCtrl
Q12118 -0.1574730 0.0331883 15.838174 -4.744834 0.0002257 0.0035143 strainCtrl
Q07716 0.1255127 0.0269512 16.974579 4.657043 0.0002267 0.0035143 strainCtrl
P39006 0.1573427 0.0333742 16.187383 4.714501 0.0002269 0.0035143 strainCtrl
P38342 0.3709663 0.0785877 15.911372 4.720413 0.0002344 0.0036146 strainCtrl
Q12018 -0.0958050 0.0203321 16.002619 -4.712004 0.0002349 0.0036146 strainCtrl
Q04511 -0.2928282 0.0631704 16.953681 -4.635527 0.0002381 0.0036466 strainCtrl
Q07418 -0.1769586 0.0372654 15.458200 -4.748610 0.0002388 0.0036466 strainCtrl
P06208 0.2422871 0.0513508 15.798724 4.718270 0.0002398 0.0036466 strainCtrl
P17065 0.1955500 0.0418878 16.433204 4.668420 0.0002402 0.0036466 strainCtrl
Q00539 0.2288710 0.0493088 16.734051 4.641591 0.0002428 0.0036741 strainCtrl
P38084 0.2336127 0.0491822 15.304349 4.749945 0.0002446 0.0036781 strainCtrl
P36100 -0.1780729 0.0378771 15.867879 -4.701329 0.0002454 0.0036781 strainCtrl
P36145 -0.1608800 0.0342398 15.901142 -4.698621 0.0002454 0.0036781 strainCtrl
P08566 0.1168269 0.0251297 16.410205 4.648949 0.0002510 0.0037492 strainCtrl
P53278 0.1388888 0.0297344 15.887163 4.670977 0.0002603 0.0038753 strainCtrl
P47085 0.3896974 0.0838667 15.824673 4.646626 0.0002763 0.0041005 strainCtrl
P37304 0.1411463 0.0303052 15.610383 4.657498 0.0002797 0.0041317 strainCtrl
P47068 0.1198554 0.0259422 16.082767 4.620095 0.0002802 0.0041317 strainCtrl
P06244 0.2053947 0.0449109 16.496779 4.573386 0.0002902 0.0042618 strainCtrl
P30619 0.1516386 0.0321223 14.651329 4.720661 0.0002909 0.0042618 strainCtrl
P17967 -0.1525842 0.0330269 15.729492 -4.619993 0.0002961 0.0043255 strainCtrl
P53119 -0.1515379 0.0334397 16.796345 -4.531671 0.0003036 0.0044198 strainCtrl
P04821 0.1863482 0.0399485 14.936345 4.664714 0.0003086 0.0044793 strainCtrl
P25605 0.1423773 0.0313608 16.410650 4.539968 0.0003151 0.0045589 strainCtrl
P40048 -0.2311326 0.0499371 15.215177 -4.628476 0.0003164 0.0045589 strainCtrl
P00549 -0.1032979 0.0228807 16.741869 -4.514625 0.0003171 0.0045589 strainCtrl
P53552 -0.1149645 0.0249010 15.324331 -4.616867 0.0003181 0.0045589 strainCtrl
P40078 -0.2508636 0.0547699 15.753530 -4.580315 0.0003199 0.0045708 strainCtrl
Q3E7Z5 -0.4622163 0.1015903 16.102104 -4.549809 0.0003230 0.0046015 strainCtrl
P28737 -0.2008710 0.0445519 16.624079 -4.508693 0.0003265 0.0046361 strainCtrl
Q06150 0.8052630 0.1769287 15.935780 4.551342 0.0003301 0.0046737 strainCtrl
P38999 0.1265176 0.0281478 16.702571 4.494754 0.0003326 0.0046939 strainCtrl
Q03862 -0.1232104 0.0275829 16.974579 -4.466909 0.0003401 0.0047817 strainCtrl
Q03144 0.3450327 0.0747135 14.892368 4.618076 0.0003409 0.0047817 strainCtrl
Q12427 -0.1238023 0.0273312 15.796993 -4.529699 0.0003524 0.0049289 strainCtrl
P38841 -0.2988717 0.0666824 16.390795 -4.482016 0.0003568 0.0049746 strainCtrl
Q12329 -0.2913033 0.0652663 16.653838 -4.463303 0.0003579 0.0049746 strainCtrl
P32356 0.1224001 0.0275249 16.623730 4.446893 0.0003721 0.0051198 strainCtrl
P32331 0.1633178 0.0363434 15.926732 4.493744 0.0003722 0.0051198 strainCtrl
P07278 0.0894524 0.0200366 16.345217 4.464447 0.0003726 0.0051198 strainCtrl
P38820 -0.1535515 0.0337672 15.202450 -4.547350 0.0003729 0.0051198 strainCtrl
Q06108 0.3074698 0.0691621 16.607173 4.445639 0.0003739 0.0051198 strainCtrl
P32770 -0.1560468 0.0347241 15.836414 -4.493899 0.0003771 0.0051486 strainCtrl
Q08096 -0.1695631 0.0381553 16.319899 -4.444024 0.0003903 0.0053124 strainCtrl
P40047 0.1495410 0.0337232 16.339074 4.434360 0.0003972 0.0053908 strainCtrl
P39078 -0.1076430 0.0243346 16.170779 -4.423447 0.0004159 0.0056287 strainCtrl
P40087 -0.1897377 0.0428579 16.033473 -4.427130 0.0004208 0.0056773 strainCtrl
P18562 -0.1099172 0.0249877 16.436239 -4.398848 0.0004224 0.0056820 strainCtrl
P43593 -0.0955964 0.0219510 16.974579 -4.355001 0.0004323 0.0057982 strainCtrl
P11353 0.1432018 0.0327291 16.527989 4.375372 0.0004384 0.0058623 strainCtrl
P36139 -0.2033847 0.0462163 16.098004 -4.400713 0.0004406 0.0058623 strainCtrl
P53258 0.1857920 0.0425605 16.647840 4.365366 0.0004409 0.0058623 strainCtrl
Q00711 0.1766565 0.0404313 16.491744 4.369295 0.0004462 0.0059167 strainCtrl
P22108 -0.1688599 0.0385696 16.307084 -4.378055 0.0004490 0.0059359 strainCtrl
P39960 0.1279545 0.0296102 16.844101 4.321301 0.0004723 0.0062267 strainCtrl
Q9URQ5 -0.1696320 0.0388816 16.024780 -4.362783 0.0004816 0.0063036 strainCtrl
P32860 -0.1246848 0.0288656 16.699956 -4.319498 0.0004828 0.0063036 strainCtrl
Q12359 0.3166999 0.0732154 16.597834 4.325589 0.0004828 0.0063036 strainCtrl
P32773 -0.2274455 0.0525305 16.515556 -4.329781 0.0004836 0.0063036 strainCtrl
P04806 0.2490406 0.0570444 15.919152 4.365734 0.0004856 0.0063038 strainCtrl
Q12523 0.2151040 0.0495331 16.264453 4.342633 0.0004864 0.0063038 strainCtrl
P40054 0.1139408 0.0263847 16.494749 4.318440 0.0004967 0.0064047 strainCtrl
P23585 0.3853903 0.0875452 15.234177 4.402189 0.0004970 0.0064047 strainCtrl
P53622 0.1128314 0.0261971 16.561475 4.307016 0.0005046 0.0064847 strainCtrl
Q04341 -0.3742254 0.0860256 15.795540 -4.350166 0.0005101 0.0065375 strainCtrl
P36521 -0.1702068 0.0392636 15.781024 -4.334981 0.0005274 0.0067405 strainCtrl
P53930 -0.2550592 0.0587613 15.529899 -4.340601 0.0005398 0.0068797 strainCtrl
P07991 -0.3113692 0.0732349 16.896156 -4.251650 0.0005449 0.0069259 strainCtrl
P43590 0.1365485 0.0321628 16.970155 4.245544 0.0005473 0.0069319 strainCtrl
P47117 0.1307997 0.0306041 16.457211 4.273929 0.0005484 0.0069319 strainCtrl
P51601 0.1515830 0.0356201 16.672839 4.255541 0.0005552 0.0069988 strainCtrl
Q07878 0.0923631 0.0216475 16.393022 4.266678 0.0005614 0.0070573 strainCtrl
P09624 0.1047897 0.0242526 15.464243 4.320762 0.0005673 0.0071105 strainCtrl
P38616 -0.2805664 0.0657874 16.322581 -4.264741 0.0005687 0.0071105 strainCtrl
P32179 0.1579457 0.0361991 14.796102 4.363244 0.0005736 0.0071522 strainCtrl
Q06510 0.2751706 0.0650998 16.882060 4.226904 0.0005756 0.0071571 strainCtrl
P37262 -0.1900409 0.0445298 16.158078 -4.267724 0.0005771 0.0071571 strainCtrl
Q12176 -0.1100825 0.0257765 15.979619 -4.270651 0.0005870 0.0072598 strainCtrl
Q12122 0.1587336 0.0371610 15.917270 4.271511 0.0005907 0.0072864 strainCtrl
P40507 -0.2380581 0.0561557 16.381939 -4.239254 0.0005957 0.0073287 strainCtrl
P39106 0.1270811 0.0299834 16.284046 4.238390 0.0006041 0.0074122 strainCtrl
P36006 0.1802144 0.0425022 16.016683 4.240115 0.0006226 0.0076187 strainCtrl
Q06819 -0.2349918 0.0562155 16.974579 -4.180197 0.0006297 0.0076854 strainCtrl
P21182 -0.1927854 0.0456499 16.102300 -4.223127 0.0006382 0.0077550 strainCtrl
P53336 -0.1865632 0.0437497 15.440627 -4.264330 0.0006388 0.0077550 strainCtrl
P14540 -0.1335180 0.0316108 15.979057 -4.223810 0.0006473 0.0078371 strainCtrl
P38883 -0.1254325 0.0291564 14.663730 -4.302055 0.0006607 0.0079727 strainCtrl
P53051 -0.3522885 0.0830143 15.490398 -4.243708 0.0006619 0.0079727 strainCtrl
P53172 -0.1837743 0.0436456 15.896130 -4.210607 0.0006724 0.0080773 strainCtrl
P38274 0.1521798 0.0364841 16.515431 4.171123 0.0006773 0.0080949 strainCtrl
P54005 -0.5740797 0.1368910 16.119709 -4.193701 0.0006774 0.0080949 strainCtrl
P53136 -0.1057726 0.0254433 16.678298 -4.157184 0.0006846 0.0081492 strainCtrl
P54999 -0.3036464 0.0729123 16.511033 -4.164545 0.0006872 0.0081492 strainCtrl
Q04301 -0.2524219 0.0600668 15.856946 -4.202352 0.0006874 0.0081492 strainCtrl
P53315 0.3418543 0.0817433 16.180638 4.182045 0.0006890 0.0081492 strainCtrl
P46959 -0.1549552 0.0371201 16.240136 -4.174423 0.0006951 0.0081999 strainCtrl
P34232 -0.1859284 0.0446658 16.427292 -4.162658 0.0006968 0.0081999 strainCtrl
O13563 -0.2200261 0.0528919 16.416297 -4.159921 0.0007018 0.0082373 strainCtrl
P40579 -0.1769953 0.0427787 16.790811 -4.137465 0.0007050 0.0082539 strainCtrl
P47148 0.2274802 0.0541596 15.631684 4.200182 0.0007107 0.0082993 strainCtrl
Q03337 -0.1090878 0.0257860 15.119286 -4.230502 0.0007149 0.0083278 strainCtrl
P29465 0.2592664 0.0626902 16.678648 4.135679 0.0007168 0.0083285 strainCtrl
P33313 -0.1265416 0.0302243 15.316102 -4.186753 0.0007612 0.0088217 strainCtrl
P53877 -0.1104143 0.0269410 16.789962 -4.098380 0.0007669 0.0088650 strainCtrl
Q12154 -0.1283961 0.0310077 15.969884 -4.140780 0.0007708 0.0088887 strainCtrl
P03874 -0.1581921 0.0376665 14.927747 -4.199810 0.0007808 0.0089599 strainCtrl
Q08004 -0.2232950 0.0543686 16.463866 -4.107060 0.0007809 0.0089599 strainCtrl
P16140 0.1252044 0.0305903 16.630509 4.092947 0.0007897 0.0090388 strainCtrl
P38885 -0.2435326 0.0591091 16.008734 -4.120055 0.0008013 0.0091480 strainCtrl
P40094 -0.1182822 0.0289058 16.367548 -4.091993 0.0008152 0.0092844 strainCtrl
Q05791 -0.1625502 0.0399399 16.654054 -4.069875 0.0008276 0.0094015 strainCtrl
P16664 0.1810012 0.0443202 16.227319 4.083947 0.0008427 0.0095271 strainCtrl
P25349 0.1863991 0.0447681 14.902147 4.163660 0.0008428 0.0095271 strainCtrl
P28272 -0.3193116 0.0781961 16.138012 -4.083472 0.0008523 0.0096109 strainCtrl
P27810 0.1563983 0.0377041 15.002834 4.148047 0.0008582 0.0096541 strainCtrl
P53295 -0.1340132 0.0324272 15.130062 -4.132741 0.0008707 0.0097622 strainCtrl
P00830 0.1514636 0.0372033 16.162700 4.071238 0.0008720 0.0097622 strainCtrl
P08539 0.1768691 0.0437681 16.607021 4.041055 0.0008848 0.0098808 strainCtrl
P38812 -0.2566783 0.0634619 16.408652 -4.044604 0.0008974 0.0099978 strainCtrl
P39730 -0.0995987 0.0242349 15.235423 -4.109717 0.0009003 0.0100054 strainCtrl
P38068 0.1609768 0.0396516 16.030845 4.059782 0.0009070 0.0100555 strainCtrl
Q01939 -0.1613386 0.0398745 16.209191 -4.046157 0.0009146 0.0101159 strainCtrl
P38137 -0.1410613 0.0347106 15.797545 -4.063924 0.0009239 0.0101941 strainCtrl
P53953 0.1107238 0.0275011 16.467262 4.026160 0.0009274 0.0102015 strainCtrl
P13586 0.1350882 0.0337667 16.967803 4.000628 0.0009290 0.0102015 strainCtrl
P32474 0.1466170 0.0364991 16.103617 4.016998 0.0009843 0.0107616 strainCtrl
P53099 0.2943578 0.0716710 14.570552 4.107072 0.0009869 0.0107616 strainCtrl
P38013 -0.1995540 0.0494494 15.738666 -4.035520 0.0009870 0.0107616 strainCtrl
P33310 0.2007220 0.0501601 16.072644 4.001625 0.0010202 0.0110971 strainCtrl
P33307 -0.1001467 0.0253002 16.883706 -3.958333 0.0010268 0.0111422 strainCtrl
Q12108 0.1636138 0.0403899 15.107322 4.050857 0.0010316 0.0111565 strainCtrl
P36009 -0.1399628 0.0352189 16.498151 -3.974086 0.0010330 0.0111565 strainCtrl
P38623 0.1701363 0.0426582 16.170595 3.988358 0.0010379 0.0111585 strainCtrl
P07251 0.1634535 0.0410765 16.348722 3.979250 0.0010380 0.0111585 strainCtrl
P19414 0.0998985 0.0252747 16.868848 3.952515 0.0010413 0.0111684 strainCtrl
P38809 0.1940691 0.0487360 16.156267 3.982053 0.0010535 0.0112473 strainCtrl
P32898 -0.1162842 0.0292243 16.202104 -3.979030 0.0010550 0.0112473 strainCtrl
P41735 0.2938188 0.0726155 14.994781 4.046229 0.0010560 0.0112473 strainCtrl
Q06631 -0.1189453 0.0296566 15.461533 -4.010757 0.0010733 0.0114044 strainCtrl
P38765 0.1873308 0.0476230 16.846267 3.933625 0.0010872 0.0115255 strainCtrl
Q12287 -0.3961779 0.0993311 15.702615 -3.988458 0.0010932 0.0115631 strainCtrl
P05373 -0.1472159 0.0369300 15.560837 -3.986354 0.0011159 0.0117761 strainCtrl
P07275 -0.1488828 0.0378157 16.486876 -3.937065 0.0011193 0.0117800 strainCtrl
Q06648 0.2083329 0.0523785 15.680192 3.977453 0.0011214 0.0117800 strainCtrl
Q12024 -0.1728826 0.0429730 14.856997 -4.023053 0.0011260 0.0118009 strainCtrl
P39929 -0.0989621 0.0249647 15.798402 -3.964084 0.0011380 0.0118996 strainCtrl
P50861 -0.1945405 0.0494578 16.338982 -3.933463 0.0011453 0.0119494 strainCtrl
P38145 0.1578927 0.0399702 15.955391 3.950261 0.0011514 0.0119856 strainCtrl
P38790 0.3189124 0.0808967 16.075171 3.942217 0.0011561 0.0119978 strainCtrl
P53736 -0.3249780 0.0826431 16.258873 -3.932308 0.0011578 0.0119978 strainCtrl
P39676 -0.2481892 0.0626590 15.670214 -3.960948 0.0011619 0.0120136 strainCtrl
P38088 0.0882208 0.0224268 16.072266 3.933718 0.0011773 0.0121456 strainCtrl
P47154 -0.1201144 0.0306327 16.263177 -3.921117 0.0011851 0.0121983 strainCtrl
P38355 -0.1726394 0.0440595 16.141112 -3.918324 0.0012074 0.0124004 strainCtrl
P43597 0.1624574 0.0411640 15.478639 3.946594 0.0012231 0.0125210 strainCtrl
P35184 -0.1748312 0.0444184 15.664814 -3.936009 0.0012246 0.0125210 strainCtrl
P38112 -0.1337556 0.0344679 16.739561 -3.880580 0.0012318 0.0125670 strainCtrl
P47170 0.1906261 0.0485208 15.727890 3.928750 0.0012347 0.0125683 strainCtrl
P00927 0.0951490 0.0241899 15.546351 3.933413 0.0012475 0.0126706 strainCtrl
P32836 0.3466233 0.0858418 13.653531 4.037931 0.0012814 0.0129703 strainCtrl
P53960 0.2069752 0.0536105 16.764101 3.860720 0.0012827 0.0129703 strainCtrl
P38326 -0.2068184 0.0529434 15.596438 -3.906402 0.0013123 0.0132406 strainCtrl
P24000 0.3095659 0.0801806 16.472644 3.860858 0.0013192 0.0132811 strainCtrl
P32799 0.2789952 0.0723149 16.448815 3.858061 0.0013302 0.0133343 strainCtrl
P32788 0.3223294 0.0830710 15.984640 3.880170 0.0013302 0.0133343 strainCtrl
Q99296 0.3767259 0.0977546 16.515072 3.853793 0.0013337 0.0133398 strainCtrl
P54964 -0.2031575 0.0526346 16.313068 -3.859769 0.0013433 0.0134068 strainCtrl
Q05948 -0.1471544 0.0382433 16.475766 -3.847850 0.0013560 0.0135038 strainCtrl
Q01477 -0.0979197 0.0255913 16.922085 -3.826287 0.0013613 0.0135274 strainCtrl
P12709 -0.0909415 0.0234794 15.856858 -3.873244 0.0013678 0.0135633 strainCtrl
P39081 -0.1567010 0.0406526 16.183297 -3.854633 0.0013758 0.0136130 strainCtrl
Q08202 -0.2387176 0.0612273 15.261893 -3.898873 0.0013830 0.0136547 strainCtrl
P24279 0.0992686 0.0259499 16.631489 3.825398 0.0014016 0.0137714 strainCtrl
Q02892 -0.1544527 0.0400594 15.963167 -3.855586 0.0014040 0.0137714 strainCtrl
P04807 -0.1153663 0.0300199 16.217083 -3.843001 0.0014054 0.0137714 strainCtrl
P38719 -0.1231887 0.0318229 15.633531 -3.871077 0.0014068 0.0137714 strainCtrl
Q08157 0.2218299 0.0571850 15.421789 3.879162 0.0014152 0.0138247 strainCtrl
P07255 0.2611809 0.0676522 15.671109 3.860641 0.0014320 0.0139591 strainCtrl
P25297 -0.8376066 0.2174310 15.760928 -3.852287 0.0014436 0.0140423 strainCtrl
P36775 -0.1030232 0.0267630 15.797514 -3.849467 0.0014467 0.0140423 strainCtrl
P39004 0.6160355 0.1622788 16.858328 3.796154 0.0014616 0.0141572 strainCtrl
P39678 -0.1686952 0.0438036 15.638566 -3.851169 0.0014656 0.0141664 strainCtrl
P14180 0.2290377 0.0604358 16.933557 3.789766 0.0014718 0.0141783 strainCtrl
P20486 -0.1846923 0.0487155 16.889522 -3.791240 0.0014730 0.0141783 strainCtrl
Q08968 -0.1595010 0.0420415 16.778626 -3.793898 0.0014795 0.0142111 strainCtrl
P36160 -0.3058253 0.0791122 15.175271 -3.865716 0.0014948 0.0143285 strainCtrl
P32487 0.2310060 0.0596470 14.937518 3.872888 0.0015127 0.0144696 strainCtrl
Q00055 0.1013379 0.0263187 15.307847 3.850415 0.0015205 0.0144704 strainCtrl
P47083 -0.1563002 0.0411873 16.460754 -3.794867 0.0015208 0.0144704 strainCtrl
P53281 -0.2073400 0.0541195 15.664960 -3.831149 0.0015239 0.0144704 strainCtrl
P53010 0.1441147 0.0366904 13.953386 3.927862 0.0015254 0.0144704 strainCtrl
P53076 0.1372361 0.0361197 16.304050 3.799479 0.0015286 0.0144712 strainCtrl
P40360 0.1598824 0.0421420 16.178029 3.793896 0.0015657 0.0147861 strainCtrl
P54115 -0.0990572 0.0257605 15.119828 -3.845309 0.0015683 0.0147861 strainCtrl
P37299 0.2395274 0.0637527 16.949133 3.757134 0.0015775 0.0148425 strainCtrl
Q06406 -0.1281901 0.0340830 16.743740 -3.761110 0.0015930 0.0149577 strainCtrl
P12688 0.1160180 0.0308345 16.641675 3.762602 0.0016026 0.0150177 strainCtrl
P40555 -0.1825952 0.0485193 16.509675 -3.763356 0.0016195 0.0151452 strainCtrl
P38886 -0.1628260 0.0435030 16.832012 -3.742865 0.0016439 0.0153423 strainCtrl
P28778 -0.3587224 0.0949491 15.999514 -3.778049 0.0016474 0.0153432 strainCtrl
P25555 0.1175587 0.0310753 15.860348 3.783023 0.0016526 0.0153605 strainCtrl
P32486 0.1517922 0.0406820 16.974579 3.731187 0.0016651 0.0154458 strainCtrl
P54000 -0.0918850 0.0245420 16.603135 -3.743993 0.0016739 0.0154938 strainCtrl
P23201 0.1194498 0.0315382 15.620113 3.787466 0.0016770 0.0154938 strainCtrl
Q06389 0.1590275 0.0424057 16.358231 3.750140 0.0016894 0.0155770 strainCtrl
P13574 0.1259956 0.0330485 15.030371 3.812449 0.0016939 0.0155868 strainCtrl
P08153 0.1749393 0.0464203 15.802949 3.768592 0.0017131 0.0157322 strainCtrl
P31382 0.1294888 0.0346819 16.523919 3.733610 0.0017239 0.0157998 strainCtrl
Q06010 0.0917728 0.0243759 15.788022 3.764897 0.0017289 0.0158147 strainCtrl
Q05946 -0.0867741 0.0231455 15.979886 -3.749073 0.0017545 0.0160140 strainCtrl
P40825 0.0832400 0.0222186 16.020189 3.746412 0.0017577 0.0160140 strainCtrl
P50276 0.3478144 0.0937743 16.835425 3.709059 0.0017680 0.0160766 strainCtrl
Q06696 0.1867900 0.0505368 16.900868 3.696117 0.0018081 0.0164080 strainCtrl
P43586 -0.1359463 0.0364161 15.840515 -3.733136 0.0018388 0.0166376 strainCtrl
Q12331 -0.1837907 0.0495231 16.328653 -3.711214 0.0018406 0.0166376 strainCtrl
P31787 -0.2508799 0.0670581 15.429237 -3.741233 0.0018820 0.0169704 strainCtrl
Q06632 -0.0815883 0.0216870 14.995140 -3.762077 0.0018848 0.0169704 strainCtrl
P23639 -0.1508071 0.0409236 16.592689 -3.685092 0.0019014 0.0170862 strainCtrl
P14680 0.1478889 0.0392581 14.749457 3.767089 0.0019150 0.0171754 strainCtrl
P16120 0.0820491 0.0222745 16.438353 3.683545 0.0019336 0.0173083 strainCtrl
P40361 0.2852052 0.0771216 16.048007 3.698122 0.0019415 0.0173452 strainCtrl
P15442 0.1319380 0.0353360 15.173672 3.733812 0.0019609 0.0174281 strainCtrl
P53313 -0.1401742 0.0382344 16.674378 -3.666181 0.0019664 0.0174281 strainCtrl
P50077 0.1825698 0.0495941 16.299485 3.681284 0.0019669 0.0174281 strainCtrl
Q02196 0.2070410 0.0564937 16.699222 3.664850 0.0019679 0.0174281 strainCtrl
Q08492 -0.1633309 0.0438657 15.329126 -3.723434 0.0019723 0.0174281 strainCtrl
P40010 -0.1022232 0.0279351 16.806910 -3.659312 0.0019735 0.0174281 strainCtrl
Q12482 0.2266943 0.0619573 16.667167 3.658877 0.0019988 0.0176175 strainCtrl
Q01080 -0.0922366 0.0250937 16.097790 -3.675693 0.0020267 0.0178293 strainCtrl
P33338 0.1093582 0.0297772 16.021972 3.672549 0.0020542 0.0180371 strainCtrl
Q05040 0.1266023 0.0344183 15.753877 3.678347 0.0020798 0.0181949 strainCtrl
P32332 0.1643585 0.0445944 15.589932 3.685635 0.0020801 0.0181949 strainCtrl
P39708 -0.6986417 0.1910544 16.169369 -3.656769 0.0020962 0.0183012 strainCtrl
P07143 0.2377748 0.0653042 16.457686 3.641035 0.0021141 0.0183949 strainCtrl
P38928 0.2075488 0.0567440 16.048593 3.657637 0.0021150 0.0183949 strainCtrl
P46951 -0.2052018 0.0564028 16.436719 -3.638146 0.0021310 0.0184998 strainCtrl
Q03212 0.2319572 0.0637204 16.333873 3.640233 0.0021403 0.0185456 strainCtrl
P33336 0.3167041 0.0865631 15.843576 3.658651 0.0021498 0.0185926 strainCtrl
P25375 -0.0905723 0.0249120 16.319954 -3.635686 0.0021638 0.0186783 strainCtrl
P38169 -0.1758411 0.0472297 14.414534 -3.723107 0.0021697 0.0186947 strainCtrl
P43636 0.1773679 0.0482418 15.221906 3.676646 0.0021955 0.0188813 strainCtrl
P31688 0.1481870 0.0398669 14.373235 3.717046 0.0022061 0.0189371 strainCtrl
Q06147 -0.1335677 0.0367834 16.131812 -3.631197 0.0022204 0.0190243 strainCtrl
P40414 -0.1362375 0.0373533 15.509347 -3.647272 0.0022704 0.0194163 strainCtrl
Q08965 -0.1003229 0.0279155 16.781651 -3.593810 0.0022780 0.0194456 strainCtrl
P47019 -0.1761555 0.0482758 15.412946 -3.648940 0.0022830 0.0194519 strainCtrl
P13090 -0.3779532 0.1046996 16.230950 -3.609884 0.0023034 0.0195899 strainCtrl
Q12031 -0.3769945 0.1035018 15.367146 -3.642395 0.0023242 0.0197297 strainCtrl
Q12099 -0.2041044 0.0566353 16.091966 -3.603835 0.0023611 0.0200061 strainCtrl
P47039 0.1586411 0.0438485 15.639031 3.617936 0.0023852 0.0201438 strainCtrl
Q06001 -0.3408402 0.0954565 16.828058 -3.570636 0.0023861 0.0201438 strainCtrl
Q05778 -0.1508410 0.0423577 16.877530 -3.561123 0.0024262 0.0204454 strainCtrl
P53276 -0.1090880 0.0306812 16.827859 -3.555536 0.0024652 0.0207359 strainCtrl
P53755 0.3646574 0.0918112 10.313770 3.971817 0.0024809 0.0208300 strainCtrl
Q12463 -0.1613744 0.0454054 16.608739 -3.554076 0.0025159 0.0210816 strainCtrl
Q03768 -0.1513582 0.0423187 16.002671 -3.576628 0.0025201 0.0210816 strainCtrl
Q08235 -0.1192646 0.0334263 16.195632 -3.567986 0.0025254 0.0210881 strainCtrl
P33331 -0.1952632 0.0550694 16.405106 -3.545764 0.0026030 0.0216965 strainCtrl
Q08723 -0.2586420 0.0725370 15.857345 -3.565658 0.0026111 0.0217248 strainCtrl
P15274 0.0890518 0.0241960 13.443879 3.680441 0.0026303 0.0218448 strainCtrl
P47046 0.5095122 0.1381423 13.267304 3.688313 0.0026444 0.0219225 strainCtrl
Q12461 -0.1601476 0.0454227 16.678876 -3.525718 0.0026594 0.0219709 strainCtrl
Q08224 -0.1975993 0.0558025 16.242339 -3.541046 0.0026640 0.0219709 strainCtrl
Q12754 -0.1003509 0.0283399 16.226177 -3.540978 0.0026679 0.0219709 strainCtrl
Q06543 -0.1264789 0.0354873 15.614611 -3.564058 0.0026753 0.0219709 strainCtrl
P40106 -0.1828021 0.0508408 14.889049 -3.595575 0.0026775 0.0219709 strainCtrl
P52893 -0.1021271 0.0287506 15.881779 -3.552178 0.0026807 0.0219709 strainCtrl
P35691 -0.1632032 0.0463013 16.580606 -3.524806 0.0026850 0.0219709 strainCtrl
P40302 -0.1637262 0.0464448 16.553772 -3.525181 0.0026885 0.0219709 strainCtrl
P26364 -0.6215081 0.1740827 15.342444 -3.570189 0.0027056 0.0220716 strainCtrl
P17076 0.2504495 0.0710888 16.505095 3.523049 0.0027110 0.0220770 strainCtrl
P49957 -0.1380257 0.0392922 16.741891 -3.512798 0.0027213 0.0221211 strainCtrl
P21951 0.0801405 0.0226335 15.953359 3.540799 0.0027294 0.0221479 strainCtrl
P33411 -0.2568820 0.0715725 14.789765 -3.589115 0.0027388 0.0221855 strainCtrl
P37898 0.0735614 0.0209592 16.457214 3.509743 0.0027998 0.0226393 strainCtrl
P47095 -0.1586087 0.0454678 16.974301 -3.488377 0.0028194 0.0227577 strainCtrl
P32324 0.0813601 0.0233240 16.865879 3.488262 0.0028426 0.0229054 strainCtrl
P34253 -0.1226409 0.0351417 16.674397 -3.489896 0.0028734 0.0231126 strainCtrl
P32354 -0.4234770 0.1207859 16.012708 -3.506015 0.0029231 0.0234643 strainCtrl
P53925 0.1202463 0.0344394 16.365956 3.491535 0.0029315 0.0234643 strainCtrl
Q06688 -0.1995061 0.0570201 16.162442 -3.498872 0.0029324 0.0234643 strainCtrl
P40099 -0.1366667 0.0392284 16.552209 -3.483873 0.0029377 0.0234661 strainCtrl
P10962 -0.1308425 0.0372005 15.624088 -3.517227 0.0029479 0.0235068 strainCtrl
P36126 0.2635889 0.0761162 16.732211 3.462979 0.0030316 0.0241324 strainCtrl
Q12156 0.1402913 0.0403436 16.291370 3.477412 0.0030385 0.0241450 strainCtrl
Q05031 0.1660427 0.0482542 16.798193 3.441004 0.0031634 0.0250943 strainCtrl
P40024 -0.0846295 0.0245752 16.626151 -3.443698 0.0031845 0.0252185 strainCtrl
P32578 -0.1538076 0.0447499 16.722178 -3.437053 0.0032079 0.0253599 strainCtrl
P28273 0.1214266 0.0349662 15.695920 3.472683 0.0032167 0.0253862 strainCtrl
P40476 0.3606880 0.1042613 15.771471 3.459460 0.0032871 0.0258631 strainCtrl
Q07844 -0.0921278 0.0267970 16.356128 -3.437992 0.0032884 0.0258631 strainCtrl
P40413 -0.0883799 0.0257532 16.477781 -3.431801 0.0033023 0.0259284 strainCtrl
Q3E798 -0.5027695 0.1468207 16.644221 -3.424377 0.0033150 0.0259835 strainCtrl
P23638 -0.1277941 0.0369105 15.438136 -3.462270 0.0033573 0.0262371 strainCtrl
P38853 0.0932912 0.0272206 16.380141 3.427225 0.0033588 0.0262371 strainCtrl
P48510 -0.1385947 0.0405894 16.708210 -3.414552 0.0033703 0.0262824 strainCtrl
P42842 -0.0912432 0.0263300 15.256598 -3.465369 0.0033864 0.0263637 strainCtrl
P38636 -0.2291813 0.0671881 16.710650 -3.411038 0.0033952 0.0263689 strainCtrl
P09457 0.0979161 0.0286850 16.618130 3.413495 0.0033996 0.0263689 strainCtrl
Q12259 -0.2107007 0.0619021 16.896402 -3.403770 0.0034043 0.0263689 strainCtrl
P09032 -0.1017057 0.0295796 15.790446 -3.438373 0.0034307 0.0265290 strainCtrl
Q04372 -0.1217991 0.0355605 16.060834 -3.425125 0.0034552 0.0266721 strainCtrl
P00942 -0.1601636 0.0469170 16.363149 -3.413765 0.0034608 0.0266721 strainCtrl
P53111 -0.1219638 0.0355728 15.805860 -3.428564 0.0034979 0.0269127 strainCtrl
Q08446 -0.1263712 0.0372729 16.612356 -3.390428 0.0035735 0.0274482 strainCtrl
Q02754 -0.1795627 0.0530272 16.595473 -3.386239 0.0036100 0.0276823 strainCtrl
P46670 0.3046390 0.0894641 15.885686 3.405154 0.0036519 0.0279573 strainCtrl
P39521 -0.1035727 0.0307157 16.705464 -3.371976 0.0036938 0.0282173 strainCtrl
P47120 -0.1401626 0.0414413 16.370320 -3.382197 0.0036997 0.0282173 strainCtrl
P22515 -0.0775114 0.0227711 15.732379 -3.403939 0.0037042 0.0282173 strainCtrl
P43606 -0.3072837 0.0907026 16.050751 -3.387815 0.0037414 0.0284535 strainCtrl
P43574 -0.2012211 0.0597140 16.534740 -3.369745 0.0037556 0.0285137 strainCtrl
P00925 -0.2198152 0.0653172 16.559793 -3.365350 0.0037844 0.0286857 strainCtrl
P38323 0.1153140 0.0339788 15.614129 3.393705 0.0038189 0.0288995 strainCtrl
P38196 0.1961917 0.0577582 15.422946 3.396775 0.0038514 0.0290366 strainCtrl
Q08268 0.3375041 0.1009378 16.974579 3.343682 0.0038556 0.0290366 strainCtrl
P53970 -1.1120219 0.2846889 8.667795 -3.906096 0.0038560 0.0290366 strainCtrl
Q04660 -0.1034512 0.0309647 16.974579 -3.340942 0.0038785 0.0291416 strainCtrl
Q99288 -0.0999894 0.0294632 15.401357 -3.393706 0.0038826 0.0291416 strainCtrl
P24031 0.1632012 0.0489090 16.974579 3.336836 0.0039131 0.0293225 strainCtrl
P38074 -0.1100612 0.0325173 15.446228 -3.384701 0.0039421 0.0294917 strainCtrl
P53045 -0.2115793 0.0627591 15.740448 -3.371291 0.0039640 0.0295549 strainCtrl
P32504 -0.1412926 0.0422376 16.511698 -3.345183 0.0039643 0.0295549 strainCtrl
Q03920 -0.2255135 0.0673180 16.343758 -3.349971 0.0039698 0.0295549 strainCtrl
P54072 0.4567468 0.1370108 16.719318 3.333655 0.0040068 0.0297823 strainCtrl
Q08726 -0.1778944 0.0529399 15.881491 -3.360309 0.0040143 0.0297902 strainCtrl
P39516 0.2901105 0.0856098 15.006999 3.388754 0.0040479 0.0299908 strainCtrl
P43587 -0.2091096 0.0627734 16.582726 -3.331179 0.0040651 0.0300045 strainCtrl
Q3E747 -0.4615568 0.1377977 16.013137 -3.349524 0.0040675 0.0300045 strainCtrl
Q06179 0.2029995 0.0605420 15.904680 3.353037 0.0040693 0.0300045 strainCtrl
P00401 0.2889215 0.0863114 16.042406 3.347431 0.0040770 0.0300131 strainCtrl
P41277 -0.1419036 0.0420919 15.329001 -3.371279 0.0040904 0.0300641 strainCtrl
P38797 0.1237108 0.0368515 15.632460 3.357013 0.0041173 0.0302132 strainCtrl
P25502 -0.2842910 0.0859613 16.974579 -3.307198 0.0041716 0.0305631 strainCtrl
P49367 0.0899280 0.0270979 16.486342 3.318636 0.0042026 0.0307413 strainCtrl
P40007 -0.1674241 0.0505964 16.755675 -3.309015 0.0042143 0.0307781 strainCtrl
Q12205 0.1222823 0.0369602 16.651768 3.308481 0.0042479 0.0309741 strainCtrl
P36015 -0.0927678 0.0282119 16.937778 -3.288255 0.0043557 0.0317098 strainCtrl
Q03655 0.1141753 0.0346948 16.587738 3.290850 0.0044297 0.0321977 strainCtrl
P04802 0.0822471 0.0249016 16.170485 3.302889 0.0044395 0.0322181 strainCtrl
Q92331 -0.0842218 0.0256461 16.479447 -3.284002 0.0045268 0.0327703 strainCtrl
Q06493 -0.1277109 0.0389208 16.557607 -3.281300 0.0045299 0.0327703 strainCtrl
P06787 -0.1192880 0.0364716 16.795470 -3.270711 0.0045639 0.0329647 strainCtrl
P08678 0.1045998 0.0320794 16.706137 3.260654 0.0046897 0.0338199 strainCtrl
P21264 -0.0772283 0.0234134 15.448672 -3.298471 0.0047145 0.0339350 strainCtrl
Q08909 -0.2609497 0.0799796 16.534231 -3.262702 0.0047204 0.0339350 strainCtrl
Q06689 0.1267280 0.0387222 16.131132 3.272748 0.0047442 0.0340534 strainCtrl
P32863 -0.2790031 0.0857390 16.680611 -3.254097 0.0047636 0.0341265 strainCtrl
Q12186 -0.0910641 0.0277582 15.810552 -3.280620 0.0047693 0.0341265 strainCtrl
Q08971 -0.1094924 0.0336415 16.610823 -3.254686 0.0047785 0.0341397 strainCtrl
Q08162 -0.0730727 0.0222888 15.771602 -3.278446 0.0048040 0.0342684 strainCtrl
P36051 0.1867928 0.0561278 14.308560 3.327991 0.0048495 0.0345091 strainCtrl
P24783 -0.1093067 0.0333116 15.541922 -3.281341 0.0048527 0.0345091 strainCtrl
Q02770 -0.1217212 0.0370328 15.346655 -3.286853 0.0048654 0.0345456 strainCtrl
Q03690 0.0620065 0.0190881 16.433135 3.248442 0.0048975 0.0347199 strainCtrl
Q12515 -0.1443249 0.0444092 16.282319 -3.249889 0.0049300 0.0348969 strainCtrl
P18961 0.2427225 0.0749208 16.538002 3.239720 0.0049563 0.0350258 strainCtrl
P38152 -0.1713688 0.0528595 16.439284 -3.241966 0.0049634 0.0350258 strainCtrl
Q12251 -0.2508684 0.0775306 16.619996 -3.235735 0.0049731 0.0350398 strainCtrl
P38624 -0.1799972 0.0553510 16.026187 -3.251926 0.0049920 0.0350655 strainCtrl
P40165 0.2363687 0.0720902 15.204955 3.278789 0.0049985 0.0350655 strainCtrl
P25655 -0.0633948 0.0195632 16.373712 -3.240517 0.0049996 0.0350655 strainCtrl
P38793 -0.0886778 0.0274519 16.584246 -3.230293 0.0050423 0.0353117 strainCtrl
P33775 0.1195278 0.0368816 16.139753 3.240854 0.0050719 0.0354646 strainCtrl
P07703 -0.0952619 0.0296512 16.974579 -3.212750 0.0051132 0.0356992 strainCtrl
Q02931 -0.0726282 0.0218694 13.777694 -3.320989 0.0051445 0.0358534 strainCtrl
P33401 0.1304275 0.0398625 14.989028 3.271936 0.0051509 0.0358534 strainCtrl
P12612 -0.0851275 0.0263134 15.995583 -3.235137 0.0051820 0.0359244 strainCtrl
P22470 -0.1364038 0.0414163 14.341299 -3.293478 0.0051840 0.0359244 strainCtrl
Q06346 0.2242381 0.0687503 15.172655 3.261630 0.0051906 0.0359244 strainCtrl
P32500 -0.1623166 0.0505631 16.809141 -3.210180 0.0051923 0.0359244 strainCtrl
Q12460 -0.0792651 0.0241464 14.532479 -3.282688 0.0052181 0.0360489 strainCtrl
P38879 -0.0969579 0.0302184 16.641388 -3.208571 0.0052631 0.0363051 strainCtrl
Q02354 -0.1076801 0.0336404 16.841287 -3.200915 0.0052863 0.0364107 strainCtrl
P28625 0.1514124 0.0472386 16.574574 3.205269 0.0053218 0.0364976 strainCtrl
Q04149 -0.2010285 0.0620700 15.481891 -3.238741 0.0053243 0.0364976 strainCtrl
P00724 0.2494836 0.0778017 16.506892 3.206659 0.0053281 0.0364976 strainCtrl
Q07897 -0.1370636 0.0426898 16.360550 -3.210688 0.0053307 0.0364976 strainCtrl
P32900 0.1968344 0.0602148 14.545330 3.268870 0.0053607 0.0366148 strainCtrl
O74700 -0.1901226 0.0592808 16.381853 -3.207152 0.0053637 0.0366148 strainCtrl
P17709 0.1216801 0.0377188 15.470168 3.225984 0.0054715 0.0372035 strainCtrl
Q02979 0.1222393 0.0378252 15.293811 3.231691 0.0054737 0.0372035 strainCtrl
Q04958 0.1735572 0.0539113 15.668069 3.219311 0.0054742 0.0372035 strainCtrl
P25451 -0.1243264 0.0381065 14.371141 -3.262602 0.0055031 0.0373077 strainCtrl
P54885 0.1212032 0.0376904 15.688114 3.215759 0.0055075 0.0373077 strainCtrl
Q06682 -0.1495001 0.0467921 16.352434 -3.194987 0.0055139 0.0373077 strainCtrl
P47167 -0.4811461 0.1501046 15.855183 -3.205406 0.0055665 0.0376086 strainCtrl
P32660 0.1388725 0.0437967 16.974579 3.170846 0.0055952 0.0377470 strainCtrl
P48239 0.6805390 0.2023686 12.055936 3.362869 0.0056101 0.0377923 strainCtrl
P50106 -0.1318556 0.0415846 16.879464 -3.170779 0.0056266 0.0378277 strainCtrl
P32377 -0.1064231 0.0334694 16.538165 -3.179714 0.0056318 0.0378277 strainCtrl
P39109 -0.1130073 0.0356130 16.586489 -3.173201 0.0056940 0.0381899 strainCtrl
P39011 -0.1484003 0.0460739 14.971637 -3.220919 0.0057254 0.0383441 strainCtrl
P38237 0.0784970 0.0246274 15.959357 3.187386 0.0057423 0.0384014 strainCtrl
Q04336 0.1404379 0.0438888 15.415742 3.199856 0.0057974 0.0387139 strainCtrl
P53317 -0.1476178 0.0467127 16.561365 -3.160121 0.0058634 0.0390540 strainCtrl
Q08001 -0.1326810 0.0416250 15.625631 -3.187528 0.0058653 0.0390540 strainCtrl
P40030 -0.2726051 0.0858672 15.908938 -3.174729 0.0059155 0.0393315 strainCtrl
Q03697 0.2410072 0.0757584 15.586114 3.181258 0.0059577 0.0395545 strainCtrl
P38699 -0.2079040 0.0661974 16.887937 -3.140667 0.0059986 0.0397690 strainCtrl
P19955 0.2096220 0.0664918 16.259533 3.152600 0.0060653 0.0401340 strainCtrl
P38070 0.1591689 0.0503289 15.887571 3.162574 0.0060762 0.0401340 strainCtrl
P12684 0.1790267 0.0571323 16.902911 3.133544 0.0060857 0.0401340 strainCtrl
P54730 -0.1548273 0.0492320 16.471906 -3.144850 0.0060886 0.0401340 strainCtrl
Q08208 -0.1311987 0.0415482 15.934854 -3.157750 0.0061199 0.0402825 strainCtrl
P53900 -0.1201527 0.0383041 16.529125 -3.136809 0.0061729 0.0405330 strainCtrl
P29469 0.0835747 0.0263863 15.471942 3.167353 0.0061780 0.0405330 strainCtrl
P48445 0.1060173 0.0337599 16.369038 3.140328 0.0061843 0.0405330 strainCtrl
Q12383 0.2336360 0.0739870 15.704511 3.157798 0.0062083 0.0406268 strainCtrl
P10127 -0.2594723 0.0821350 15.641723 -3.159095 0.0062163 0.0406268 strainCtrl
P38604 0.1340877 0.0425623 15.648943 3.150388 0.0063270 0.0412918 strainCtrl
Q08634 -0.1885244 0.0605108 16.678347 -3.115550 0.0064038 0.0417336 strainCtrl
P25351 0.4291997 0.1354468 14.821794 3.168771 0.0064362 0.0418854 strainCtrl
P17255 0.0741255 0.0238218 16.652148 3.111668 0.0064664 0.0420224 strainCtrl
P25642 -0.1965166 0.0624604 15.222778 -3.146257 0.0065593 0.0425658 strainCtrl
P53298 -0.1670597 0.0531033 15.177387 -3.145940 0.0065832 0.0426610 strainCtrl
P32790 0.0721082 0.0232506 16.490816 3.101351 0.0066696 0.0431601 strainCtrl
P38427 0.1167088 0.0374223 15.797564 3.118701 0.0066967 0.0432744 strainCtrl
P40368 -0.1032783 0.0333846 16.446867 -3.093592 0.0067968 0.0438013 strainCtrl
P47102 0.0971603 0.0315412 16.960568 3.080420 0.0067972 0.0438013 strainCtrl
P07270 -0.2225699 0.0711881 15.275566 -3.126503 0.0068080 0.0438093 strainCtrl
Q3E7A3 0.1405469 0.0447346 14.725279 3.141792 0.0068446 0.0439834 strainCtrl
Q07915 -0.1903358 0.0617010 16.594846 -3.084810 0.0068679 0.0440715 strainCtrl
P06778 -0.1885912 0.0612822 16.826738 -3.077422 0.0068897 0.0441499 strainCtrl
Q02890 0.1679222 0.0546108 16.783528 3.074891 0.0069430 0.0444294 strainCtrl
P01094 -0.4327864 0.1402562 16.326567 -3.085685 0.0069582 0.0444647 strainCtrl
P35194 -0.0759201 0.0245021 15.800179 -3.098513 0.0069835 0.0445314 strainCtrl
Q04370 0.1836262 0.0591939 15.665188 3.102113 0.0069880 0.0445314 strainCtrl
P14904 0.0891881 0.0286819 15.308280 3.109565 0.0070350 0.0447690 strainCtrl
O13516 0.3840712 0.1242389 15.890304 3.091392 0.0070502 0.0448040 strainCtrl
P22276 -0.1259325 0.0408458 16.044501 -3.083118 0.0071091 0.0451160 strainCtrl
P04786 -0.1249371 0.0408229 16.870182 -3.060465 0.0071270 0.0451674 strainCtrl
P33314 0.1885699 0.0614196 16.230471 3.070193 0.0072279 0.0457436 strainCtrl
P37267 0.1674280 0.0541529 15.333588 3.091765 0.0072861 0.0460488 strainCtrl
P38081 0.1492489 0.0486483 16.136678 3.067914 0.0073010 0.0460794 strainCtrl
Q03677 -0.1942176 0.0636987 16.839779 -3.049005 0.0073149 0.0461038 strainCtrl
P32628 -0.1235876 0.0405658 16.694879 -3.046594 0.0074084 0.0465796 strainCtrl
P06103 -0.0709744 0.0232102 16.246356 -3.057903 0.0074106 0.0465796 strainCtrl
P52918 -0.0944767 0.0310140 16.600616 -3.046257 0.0074507 0.0467308 strainCtrl
P39079 -0.0819513 0.0269464 16.791631 -3.041267 0.0074550 0.0467308 strainCtrl
P32525 -0.1647596 0.0539265 16.208833 -3.055261 0.0074674 0.0467450 strainCtrl
P32623 0.1528900 0.0501804 16.309565 3.046810 0.0075593 0.0472562 strainCtrl
P40066 0.1274788 0.0412420 14.729538 3.090996 0.0075853 0.0473543 strainCtrl
P28274 -0.0831367 0.0271013 15.401215 -3.067629 0.0076260 0.0475439 strainCtrl
P53123 0.4166139 0.1362666 15.673930 3.057345 0.0076647 0.0477204 strainCtrl
P40081 0.1590709 0.0522344 16.007255 3.045329 0.0077106 0.0479410 strainCtrl
P52593 -0.1097509 0.0363451 16.974579 -3.019690 0.0077332 0.0480169 strainCtrl
P20051 -0.2103868 0.0692666 16.173280 -3.037347 0.0077688 0.0481729 strainCtrl
P25651 -0.2353746 0.0778678 16.572094 -3.022744 0.0078427 0.0485126 strainCtrl
Q12265 -0.0773850 0.0256100 16.610785 -3.021676 0.0078447 0.0485126 strainCtrl
Q03151 -0.2869476 0.0951207 16.473635 -3.016669 0.0079849 0.0493136 strainCtrl
P36519 -0.2082651 0.0691950 16.683069 -3.009831 0.0080141 0.0494177 strainCtrl
P45818 -0.1975684 0.0653487 16.122302 -3.023297 0.0080233 0.0494177 strainCtrl
Q12321 -0.0825797 0.0272807 15.822107 -3.027034 0.0080939 0.0497864 strainCtrl

Median - Contrast: strainProAla = 0 ( 323 significant proteins)

feature logFC se df t pval adjPval contrast
Q12068 -0.6062905 0.0404348 16.684352 -14.994282 0.0000000 0.0000002 strainProAla
P22202 0.5052529 0.0373647 14.411886 13.522203 0.0000000 0.0000032 strainProAla
P31539 0.2251810 0.0214118 16.974579 10.516677 0.0000000 0.0000102 strainProAla
P27614 -0.2782490 0.0260608 16.336872 -10.676917 0.0000000 0.0000102 strainProAla
Q12428 -0.4858774 0.0479705 16.693684 -10.128671 0.0000000 0.0000124 strainProAla
P33416 0.2996359 0.0294477 16.485462 10.175203 0.0000000 0.0000124 strainProAla
Q05902 -0.3200986 0.0323217 16.186833 -9.903519 0.0000000 0.0000181 strainProAla
P24784 0.3506211 0.0357892 16.263583 9.796828 0.0000000 0.0000181 strainProAla
P53912 -0.3890510 0.0416019 16.446139 -9.351758 0.0000001 0.0000279 strainProAla
P10591 0.3257236 0.0337939 15.320763 9.638544 0.0000001 0.0000309 strainProAla
P22855 0.3372982 0.0398078 16.299928 8.473165 0.0000002 0.0000949 strainProAla
P11972 0.4276327 0.0540739 16.888043 7.908303 0.0000004 0.0001590 strainProAla
P19414 -0.1986600 0.0251621 16.868848 -7.895214 0.0000005 0.0001590 strainProAla
Q03148 0.2130749 0.0268753 16.605675 7.928280 0.0000005 0.0001590 strainProAla
P80210 -0.2697796 0.0345201 16.177203 -7.815141 0.0000007 0.0002014 strainProAla
Q04304 -0.4361670 0.0545936 15.499634 -7.989338 0.0000007 0.0002014 strainProAla
P07702 0.1521140 0.0203692 16.751575 7.467849 0.0000010 0.0002647 strainProAla
P38169 -0.3671649 0.0457194 14.414534 -8.030837 0.0000011 0.0002647 strainProAla
P40008 -0.2233701 0.0293318 15.884016 -7.615284 0.0000011 0.0002647 strainProAla
P32590 0.2413426 0.0313412 15.342120 7.700495 0.0000012 0.0002731 strainProAla
P32644 -0.1866593 0.0257658 16.974579 -7.244467 0.0000014 0.0003028 strainProAla
Q04432 -0.3161305 0.0424410 15.867825 -7.448699 0.0000015 0.0003040 strainProAla
P38822 0.2022331 0.0267457 15.211799 7.561344 0.0000016 0.0003118 strainProAla
P32642 -0.5674360 0.0764370 15.686945 -7.423580 0.0000016 0.0003118 strainProAla
P00635 -0.7596796 0.0884986 12.093030 -8.584083 0.0000017 0.0003131 strainProAla
P40579 -0.3068165 0.0430898 16.790811 -7.120398 0.0000018 0.0003131 strainProAla
P32528 -0.2201520 0.0304481 16.174718 -7.230391 0.0000019 0.0003131 strainProAla
P32643 0.3036725 0.0425107 16.571430 7.143430 0.0000019 0.0003131 strainProAla
P39976 -0.2025747 0.0285208 16.042356 -7.102704 0.0000025 0.0003910 strainProAla
Q12256 -0.4892919 0.0734607 16.807217 -6.660596 0.0000043 0.0006526 strainProAla
P23180 0.2191251 0.0325170 16.109446 6.738792 0.0000046 0.0006810 strainProAla
P19262 0.1744549 0.0261995 16.418522 6.658700 0.0000048 0.0006919 strainProAla
Q06494 0.2517947 0.0383699 16.559109 6.562298 0.0000055 0.0007634 strainProAla
Q12179 -0.2375596 0.0360943 16.361866 -6.581632 0.0000056 0.0007634 strainProAla
P05626 0.2367037 0.0355714 15.773417 6.654322 0.0000060 0.0007732 strainProAla
Q00402 0.1361472 0.0209191 16.513338 6.508274 0.0000062 0.0007732 strainProAla
P36141 -0.2648830 0.0390958 15.012320 -6.775230 0.0000062 0.0007732 strainProAla
P54007 -0.8338733 0.1306766 16.974579 -6.381200 0.0000069 0.0008208 strainProAla
P07278 0.1332074 0.0205858 16.345217 6.470835 0.0000070 0.0008208 strainProAla
P32454 0.1418497 0.0223705 16.849249 6.340934 0.0000077 0.0008844 strainProAla
P08432 0.2881544 0.0447134 15.937895 6.444471 0.0000083 0.0009258 strainProAla
P19145 -0.2575778 0.0410721 16.852219 -6.271360 0.0000088 0.0009617 strainProAla
P56628 0.6995774 0.1075761 15.279794 6.503090 0.0000091 0.0009747 strainProAla
P10127 -0.5016794 0.0785726 15.641723 -6.384915 0.0000101 0.0010511 strainProAla
P00410 0.3755426 0.0589379 15.576302 6.371840 0.0000105 0.0010734 strainProAla
P38634 0.5397833 0.0877857 16.573486 6.148876 0.0000120 0.0011975 strainProAla
P38858 -0.2234567 0.0355052 15.267848 -6.293628 0.0000133 0.0012589 strainProAla
P33734 0.1527268 0.0252292 16.864098 6.053578 0.0000134 0.0012589 strainProAla
P53318 0.2016971 0.0324090 15.661104 6.223480 0.0000134 0.0012589 strainProAla
P40850 0.2333107 0.0379197 15.904146 6.152749 0.0000143 0.0012710 strainProAla
Q08199 0.1416590 0.0234521 16.691406 6.040352 0.0000143 0.0012710 strainProAla
P14540 -0.1969161 0.0320827 15.979057 -6.137764 0.0000144 0.0012710 strainProAla
P54838 0.1509711 0.0243012 15.292646 6.212500 0.0000152 0.0013219 strainProAla
Q05948 -0.2280952 0.0382433 16.475766 -5.964320 0.0000175 0.0014926 strainProAla
P00924 -0.2768730 0.0464002 16.152893 -5.967070 0.0000189 0.0015507 strainProAla
Q12289 -0.6927120 0.1173293 16.604597 -5.903997 0.0000191 0.0015507 strainProAla
P53278 0.1799356 0.0300092 15.887163 5.996014 0.0000192 0.0015507 strainProAla
P15424 -0.1551975 0.0261790 16.314933 -5.928311 0.0000196 0.0015516 strainProAla
P53099 0.4426762 0.0717447 14.570552 6.170156 0.0000204 0.0015594 strainProAla
P22209 -0.3609981 0.0610889 16.269705 -5.909387 0.0000205 0.0015594 strainProAla
P33302 -0.2823698 0.0472199 15.724957 -5.979892 0.0000207 0.0015594 strainProAla
P53742 -0.2348879 0.0403424 16.277142 -5.822363 0.0000242 0.0017978 strainProAla
P36007 0.1879510 0.0328991 16.839239 5.712952 0.0000263 0.0019209 strainProAla
Q12001 -0.2104680 0.0352061 14.671184 -5.978162 0.0000278 0.0019948 strainProAla
P53090 0.1452483 0.0255339 16.013845 5.688458 0.0000335 0.0023679 strainProAla
P32775 0.2511653 0.0439516 15.374210 5.714585 0.0000372 0.0025759 strainProAla
P38231 0.8316284 0.1497840 16.688986 5.552184 0.0000375 0.0025759 strainProAla
P25335 -0.6220850 0.1124959 16.764304 -5.529846 0.0000386 0.0026116 strainProAla
P38616 -0.3576108 0.0649397 16.322581 -5.506809 0.0000445 0.0029658 strainProAla
P38928 0.3228974 0.0586869 16.048593 5.502030 0.0000477 0.0031187 strainProAla
P21826 -0.5653502 0.1046567 16.891935 -5.401949 0.0000487 0.0031187 strainProAla
P32562 -0.3936767 0.0692815 14.550179 -5.682278 0.0000488 0.0031187 strainProAla
P40472 0.4310526 0.0791320 16.095854 5.447261 0.0000526 0.0033022 strainProAla
P38853 0.1466280 0.0270960 16.380141 5.411420 0.0000532 0.0033022 strainProAla
P16547 0.2249031 0.0417470 16.435132 5.387286 0.0000551 0.0033802 strainProAla
P26637 0.1046317 0.0193860 15.891880 5.397292 0.0000607 0.0036701 strainProAla
P30902 0.1641306 0.0299011 14.860257 5.489118 0.0000644 0.0038467 strainProAla
Q12123 0.3219571 0.0598979 15.634889 5.375100 0.0000670 0.0039300 strainProAla
Q12746 -0.1450394 0.0272351 16.054187 -5.325452 0.0000675 0.0039300 strainProAla
P15705 0.1412802 0.0266429 15.717892 5.302734 0.0000758 0.0042596 strainProAla
P48415 0.1333450 0.0255050 16.403655 5.228193 0.0000765 0.0042596 strainProAla
P53322 -0.3421913 0.0615170 13.613754 -5.562550 0.0000775 0.0042596 strainProAla
Q03529 -0.2889948 0.0558220 16.714785 -5.177077 0.0000799 0.0042596 strainProAla
Q03102 -0.2799206 0.0516775 14.521020 -5.416679 0.0000800 0.0042596 strainProAla
P40054 -0.1378484 0.0265259 16.494749 -5.196743 0.0000801 0.0042596 strainProAla
Q12100 0.2444345 0.0470274 16.480695 5.197703 0.0000801 0.0042596 strainProAla
P47169 0.2282584 0.0433364 15.757329 5.267134 0.0000806 0.0042596 strainProAla
P03965 0.1470920 0.0287237 16.829890 5.120922 0.0000878 0.0045876 strainProAla
P10962 -0.1880982 0.0361006 15.624088 -5.210386 0.0000926 0.0047850 strainProAla
P47912 0.1642798 0.0315475 15.584549 5.207380 0.0000939 0.0047987 strainProAla
P53111 -0.1872744 0.0364764 15.805860 -5.134121 0.0001038 0.0052448 strainProAla
A5Z2X5 0.3427790 0.0681684 16.613569 5.028419 0.0001105 0.0055223 strainProAla
P23254 -0.1390143 0.0273965 15.877604 -5.074169 0.0001154 0.0056950 strainProAla
Q03254 -0.1718575 0.0341804 16.328249 -5.027956 0.0001165 0.0056950 strainProAla
P24783 -0.1708504 0.0335897 15.541922 -5.086387 0.0001202 0.0057167 strainProAla
P38715 0.2003528 0.0400487 16.420011 5.002730 0.0001206 0.0057167 strainProAla
Q06151 0.1222366 0.0236672 14.763825 5.164815 0.0001212 0.0057167 strainProAla
P47988 0.2923457 0.0585570 16.479224 4.992500 0.0001219 0.0057167 strainProAla
P40559 0.2677820 0.0536976 16.447021 4.986855 0.0001240 0.0057577 strainProAla
P26364 0.8632370 0.1698329 15.342444 5.082862 0.0001259 0.0057882 strainProAla
P41819 -0.2065000 0.0418053 16.328348 -4.939563 0.0001395 0.0063497 strainProAla
Q04066 0.1506410 0.0305254 16.258918 4.934944 0.0001426 0.0064249 strainProAla
Q12482 0.3012611 0.0619573 16.667167 4.862395 0.0001545 0.0068933 strainProAla
P27514 -0.1943242 0.0398224 16.181253 -4.879768 0.0001617 0.0070823 strainProAla
P21801 0.2099440 0.0426586 15.693141 4.921496 0.0001621 0.0070823 strainProAla
P53177 -0.1732659 0.0354385 16.015549 -4.889194 0.0001633 0.0070823 strainProAla
P41930 0.3409384 0.0706691 16.410263 4.824435 0.0001744 0.0074908 strainProAla
P22768 0.1524596 0.0314913 16.097399 4.841331 0.0001775 0.0075550 strainProAla
Q04894 -0.1539056 0.0319611 16.299209 -4.815405 0.0001809 0.0076308 strainProAla
Q03508 -0.3326351 0.0688597 15.861527 -4.830623 0.0001889 0.0078940 strainProAla
P38697 -0.4340760 0.0906125 15.534756 -4.790465 0.0002167 0.0088987 strainProAla
P47164 0.2333661 0.0496765 16.665067 4.697712 0.0002180 0.0088987 strainProAla
P35817 -0.1432805 0.0298587 15.340926 -4.798625 0.0002206 0.0088987 strainProAla
Q08986 -0.3661478 0.0781123 16.725925 -4.687455 0.0002207 0.0088987 strainProAla
P38719 -0.1490894 0.0312942 15.633531 -4.764116 0.0002247 0.0089810 strainProAla
P32179 0.1777519 0.0368736 14.796102 4.820568 0.0002333 0.0092445 strainProAla
P38355 -0.2133323 0.0455173 16.141112 -4.686838 0.0002419 0.0095058 strainProAla
Q07896 -0.1572179 0.0330934 15.221452 -4.750731 0.0002478 0.0096530 strainProAla
Q12031 0.4788478 0.1011670 15.367146 4.733240 0.0002502 0.0096640 strainProAla
P00401 0.4030703 0.0863114 16.042406 4.669953 0.0002544 0.0097126 strainProAla
P32861 0.1133422 0.0244806 16.521719 4.629867 0.0002568 0.0097126 strainProAla
P53076 0.1658852 0.0357209 16.304050 4.643931 0.0002578 0.0097126 strainProAla
P40078 -0.2547372 0.0544973 15.753530 -4.674312 0.0002641 0.0098715 strainProAla
Q03834 0.1106258 0.0237497 15.865821 4.657984 0.0002682 0.0099421 strainProAla
Q12348 -1.3138735 0.2811711 15.425834 -4.672861 0.0002795 0.0102804 strainProAla
P53317 -0.2139357 0.0467127 16.561365 -4.579817 0.0002836 0.0103461 strainProAla
P14843 0.1201074 0.0257931 15.459793 4.656573 0.0002872 0.0103968 strainProAla
P32795 -0.0952997 0.0209059 16.726809 -4.558502 0.0002896 0.0104013 strainProAla
Q03862 -0.1248550 0.0275829 16.974579 -4.526533 0.0002994 0.0106689 strainProAla
P38113 0.1415106 0.0311722 16.575401 4.539635 0.0003080 0.0108901 strainProAla
P53960 0.2401745 0.0531298 16.764101 4.520520 0.0003122 0.0109280 strainProAla
Q03323 -0.1384120 0.0301970 15.834179 -4.583626 0.0003138 0.0109280 strainProAla
P08153 -0.2038413 0.0445231 15.802949 -4.578323 0.0003187 0.0110172 strainProAla
Q01476 0.1014145 0.0218561 14.971150 4.640104 0.0003221 0.0110484 strainProAla
Q04773 -0.1283259 0.0280129 15.567355 -4.580953 0.0003289 0.0111997 strainProAla
P38329 -0.3602940 0.0800609 16.429824 -4.500247 0.0003415 0.0115449 strainProAla
P00549 -0.1032553 0.0231104 16.741869 -4.467919 0.0003502 0.0117497 strainProAla
P17649 -0.1617324 0.0359816 16.277215 -4.494865 0.0003530 0.0117590 strainProAla
P18963 0.1945239 0.0437507 16.618668 4.446193 0.0003729 0.0123313 strainProAla
P12709 -0.1064813 0.0237016 15.856858 -4.492586 0.0003770 0.0123786 strainProAla
P39692 0.2143771 0.0482398 16.502542 4.443988 0.0003806 0.0124081 strainProAla
P47095 -0.2004977 0.0454678 16.974301 -4.409668 0.0003844 0.0124453 strainProAla
P00931 0.1082028 0.0235026 14.302086 4.603873 0.0003880 0.0124726 strainProAla
P00128 0.1955145 0.0442589 16.284247 4.417521 0.0004146 0.0132349 strainProAla
P38132 -0.1593273 0.0359359 15.760713 -4.433648 0.0004316 0.0136489 strainProAla
P47143 -0.1616430 0.0358622 14.760617 -4.507331 0.0004335 0.0136489 strainProAla
P04076 0.1418722 0.0321997 15.909932 4.406010 0.0004473 0.0139881 strainProAla
Q04178 -0.4042891 0.0932781 16.528229 -4.334232 0.0004783 0.0148565 strainProAla
P43638 0.1373493 0.0318541 16.688816 4.311827 0.0004915 0.0151626 strainProAla
P04806 0.2430893 0.0559694 15.919152 4.343250 0.0005088 0.0155262 strainProAla
P38197 -0.1692383 0.0395446 16.945890 -4.279678 0.0005100 0.0155262 strainProAla
Q03957 -0.1642140 0.0382449 16.591718 -4.293752 0.0005170 0.0155739 strainProAla
P38934 0.1138303 0.0265315 16.555564 4.290383 0.0005231 0.0155739 strainProAla
P36145 -0.1529606 0.0353195 15.901142 -4.330774 0.0005234 0.0155739 strainProAla
P36100 -0.1657078 0.0382576 15.867879 -4.331367 0.0005251 0.0155739 strainProAla
P52893 -0.1275282 0.0294771 15.881779 -4.326344 0.0005296 0.0156066 strainProAla
Q12451 0.1225004 0.0285811 16.232725 4.286069 0.0005500 0.0161045 strainProAla
P32353 0.2124366 0.0495199 16.023316 4.289929 0.0005606 0.0162592 strainProAla
Q07915 -0.2664362 0.0626316 16.594846 -4.254023 0.0005624 0.0162592 strainProAla
P25638 -0.2259029 0.0528750 16.176645 -4.272394 0.0005701 0.0163805 strainProAla
P07283 0.1231738 0.0284141 15.093081 4.334952 0.0005810 0.0165181 strainProAla
P53312 0.1060125 0.0250151 16.592846 4.237935 0.0005821 0.0165181 strainProAla
Q05498 -0.3326473 0.0787890 16.819573 -4.222000 0.0005861 0.0165285 strainProAla
P37898 0.0892863 0.0210842 16.457214 4.234741 0.0005959 0.0167028 strainProAla
P38797 0.1551074 0.0362276 15.632460 4.281470 0.0006009 0.0167427 strainProAla
P46974 -0.2363221 0.0555575 15.915818 -4.253651 0.0006132 0.0169103 strainProAla
P32561 -0.1262125 0.0301102 16.974579 -4.191682 0.0006143 0.0169103 strainProAla
P38691 0.2389286 0.0568798 16.725541 4.200589 0.0006204 0.0169774 strainProAla
P16474 0.1125190 0.0266535 16.273428 4.221554 0.0006268 0.0170492 strainProAla
P47172 -0.6884667 0.1561079 13.607902 -4.410199 0.0006333 0.0171109 strainProAla
P38067 0.1949262 0.0466054 16.839169 4.182481 0.0006365 0.0171109 strainProAla
P25584 0.2643780 0.0617162 15.128772 4.283772 0.0006410 0.0171323 strainProAla
P39516 0.3798671 0.0886587 15.006999 4.284600 0.0006510 0.0172997 strainProAla
P32459 -0.4821031 0.1144988 15.982118 -4.210552 0.0006652 0.0174743 strainProAla
P14065 -0.2509942 0.0602412 16.754418 -4.166486 0.0006652 0.0174743 strainProAla
P33413 -0.5985348 0.1420443 15.709419 -4.213720 0.0006842 0.0178072 strainProAla
P36013 -0.1066135 0.0255142 16.280737 -4.178593 0.0006856 0.0178072 strainProAla
P32799 0.3064031 0.0738159 16.448815 4.150910 0.0007126 0.0183426 strainProAla
P38972 0.0957094 0.0230731 16.469961 4.148098 0.0007151 0.0183426 strainProAla
Q12680 -0.0897609 0.0209247 14.265109 -4.289701 0.0007185 0.0183426 strainProAla
P38279 0.6910688 0.1669091 16.526101 4.140391 0.0007222 0.0183426 strainProAla
Q00711 0.1664828 0.0402650 16.491744 4.134680 0.0007340 0.0185064 strainProAla
Q05779 0.2185771 0.0532138 16.974579 4.107528 0.0007367 0.0185064 strainProAla
P25087 0.1195851 0.0289988 16.574544 4.123796 0.0007441 0.0185894 strainProAla
P22134 -0.1806860 0.0441770 16.974579 -4.090049 0.0007651 0.0189204 strainProAla
P38862 0.2011375 0.0483181 15.655208 4.162778 0.0007655 0.0189204 strainProAla
P43586 -0.1517039 0.0366706 15.840515 -4.136932 0.0007894 0.0193030 strainProAla
Q04458 0.1573907 0.0384781 16.683165 4.090392 0.0007894 0.0193030 strainProAla
P38809 0.2035164 0.0497874 16.156267 4.087705 0.0008429 0.0205018 strainProAla
P23285 0.4396063 0.1074781 16.004222 4.090196 0.0008535 0.0206505 strainProAla
Q04301 -0.2497271 0.0610193 15.856946 -4.092594 0.0008642 0.0207987 strainProAla
Q07824 -0.4121344 0.1016635 16.230586 -4.053909 0.0008976 0.0214123 strainProAla
P32178 -0.1251190 0.0308214 16.099238 -4.059488 0.0009004 0.0214123 strainProAla
P53903 -0.2214178 0.0548344 16.475053 -4.037935 0.0009036 0.0214123 strainProAla
P39005 -0.2595556 0.0639703 15.822427 -4.057440 0.0009338 0.0220041 strainProAla
Q12513 0.2515648 0.0620121 15.795350 4.056703 0.0009382 0.0220041 strainProAla
P36159 -0.1170757 0.0288681 15.754047 -4.055533 0.0009450 0.0220525 strainProAla
Q03973 0.1611067 0.0402942 16.765370 3.998266 0.0009536 0.0221405 strainProAla
P06634 -0.1109828 0.0276086 16.078566 -4.019865 0.0009811 0.0226351 strainProAla
P38988 0.2832555 0.0696915 15.259234 4.064418 0.0009848 0.0226351 strainProAla
Q02883 -0.2695372 0.0663784 15.199032 -4.060614 0.0009999 0.0228667 strainProAla
P25294 0.1339119 0.0335218 16.336859 3.994774 0.0010056 0.0228667 strainProAla
P38162 -0.2296646 0.0577941 16.720403 -3.973844 0.0010098 0.0228667 strainProAla
P24279 -0.1028099 0.0258761 16.631489 -3.973161 0.0010206 0.0229995 strainProAla
P52867 0.3383893 0.0841014 15.571263 4.023585 0.0010318 0.0231374 strainProAla
P34227 -0.1204417 0.0303974 16.388726 -3.962232 0.0010717 0.0239157 strainProAla
Q12198 -0.2914505 0.0725609 15.168028 -4.016634 0.0010981 0.0242737 strainProAla
P00899 0.0898465 0.0228169 16.657931 3.937714 0.0010983 0.0242737 strainProAla
P07884 -0.1703830 0.0430108 16.117377 -3.961396 0.0011052 0.0243083 strainProAla
P08638 -0.1032472 0.0258596 15.318736 -3.992603 0.0011330 0.0247236 strainProAla
P29340 -0.1490897 0.0374458 15.448248 -3.981483 0.0011419 0.0247236 strainProAla
P48015 0.1393636 0.0354217 16.331305 3.934418 0.0011439 0.0247236 strainProAla
P38072 0.1692625 0.0431185 16.501221 3.925519 0.0011456 0.0247236 strainProAla
Q12213 0.4787596 0.1211667 15.859583 3.951247 0.0011611 0.0249420 strainProAla
Q06688 -0.2219967 0.0564991 16.162442 -3.929209 0.0011773 0.0251723 strainProAla
P15992 0.4443964 0.1130158 16.048625 3.932161 0.0011842 0.0252023 strainProAla
P38796 0.2686257 0.0688775 16.241606 3.900052 0.0012421 0.0261844 strainProAla
P47176 -0.1349203 0.0340957 15.142147 -3.957100 0.0012441 0.0261844 strainProAla
Q03178 0.2565081 0.0660860 16.592963 3.881431 0.0012474 0.0261844 strainProAla
P10566 -0.6059120 0.1561342 16.393875 -3.880712 0.0012744 0.0265553 strainProAla
P43597 0.1671969 0.0425996 15.478639 3.924843 0.0012795 0.0265553 strainProAla
P36110 0.4646203 0.1197812 16.369367 3.878907 0.0012824 0.0265553 strainProAla
P11154 -0.1421306 0.0367995 16.647348 -3.862292 0.0012928 0.0266509 strainProAla
P38626 -0.1109889 0.0282978 15.379347 -3.922171 0.0013009 0.0266980 strainProAla
P40085 -1.1271116 0.2046433 6.241479 -5.507688 0.0013207 0.0269827 strainProAla
P23287 0.0909831 0.0237057 16.622734 3.838021 0.0013653 0.0277317 strainProAla
Q12415 -0.1171605 0.0304800 16.432039 -3.843851 0.0013734 0.0277317 strainProAla
P19097 0.0719055 0.0188005 16.848949 3.824650 0.0013754 0.0277317 strainProAla
P53112 0.1263595 0.0329877 16.606283 3.830497 0.0013897 0.0278969 strainProAla
Q12280 -0.3067899 0.0800022 16.368101 -3.834770 0.0014091 0.0281636 strainProAla
Q12204 0.1962974 0.0511333 16.083900 3.838938 0.0014365 0.0285878 strainProAla
P29496 -0.1243558 0.0318004 14.645903 -3.910512 0.0014499 0.0287284 strainProAla
Q03103 0.0983241 0.0258895 16.754431 3.797839 0.0014702 0.0290073 strainProAla
P36112 0.0930567 0.0242837 15.810005 3.832059 0.0014985 0.0294382 strainProAla
P40487 -0.1425428 0.0375696 16.433883 -3.794099 0.0015272 0.0298746 strainProAla
P40094 -0.1086458 0.0286862 16.367548 -3.787385 0.0015590 0.0303677 strainProAla
P53241 0.3121144 0.0827235 16.532874 3.772985 0.0015831 0.0305618 strainProAla
Q04728 0.1265551 0.0333403 15.955132 3.795865 0.0015935 0.0305618 strainProAla
P38840 -0.1578524 0.0414396 15.659247 -3.809216 0.0015962 0.0305618 strainProAla
P10869 0.1310886 0.0340518 14.874593 3.849679 0.0015971 0.0305618 strainProAla
P12630 0.3005366 0.0793419 16.053146 3.787867 0.0016052 0.0305618 strainProAla
Q02785 -0.2871849 0.0757595 15.967462 -3.790747 0.0016089 0.0305618 strainProAla
P41834 0.2019432 0.0533406 15.840860 3.785920 0.0016457 0.0311330 strainProAla
P53313 -0.1416148 0.0378012 16.674378 -3.746301 0.0016549 0.0311789 strainProAla
Q06689 0.1501168 0.0398671 16.131132 3.765433 0.0016706 0.0313462 strainProAla
P13134 0.2017673 0.0540722 16.585087 3.731441 0.0017224 0.0321863 strainProAla
Q03208 -0.1785997 0.0471563 15.316071 -3.787398 0.0017303 0.0322023 strainProAla
Q3E762 0.3176216 0.0853022 16.569314 3.723487 0.0017545 0.0325224 strainProAla
P38786 -0.2059635 0.0555476 16.666162 -3.707876 0.0017989 0.0332110 strainProAla
P50106 -0.1534012 0.0415846 16.879464 -3.688893 0.0018399 0.0338322 strainProAla
P09734 -0.1144206 0.0309206 16.504273 -3.700461 0.0018540 0.0338894 strainProAla
P32288 -0.1239873 0.0332981 15.944528 -3.723559 0.0018578 0.0338894 strainProAla
Q06679 -0.1477501 0.0401966 16.972423 -3.675681 0.0018786 0.0339665 strainProAla
P31116 -0.0851825 0.0229651 16.097525 -3.709213 0.0018878 0.0339665 strainProAla
P22943 -0.2782826 0.0753841 16.509843 -3.691530 0.0018889 0.0339665 strainProAla
P22213 0.1165475 0.0315537 16.443328 3.693619 0.0018915 0.0339665 strainProAla
Q04991 -0.1824209 0.0495633 16.709129 -3.680566 0.0019008 0.0339991 strainProAla
P47771 0.1202158 0.0325561 16.198300 3.692574 0.0019378 0.0345265 strainProAla
P06738 0.2234612 0.0605305 16.007799 3.691715 0.0019752 0.0350586 strainProAla
P02829 0.2463593 0.0674506 16.758146 3.652442 0.0020112 0.0355593 strainProAla
P53940 0.1220323 0.0326811 14.837382 3.734028 0.0020291 0.0356111 strainProAla
P47027 -0.5991087 0.1609894 15.084063 -3.721416 0.0020299 0.0356111 strainProAla
Q07688 -0.1266631 0.0347853 16.892991 -3.641279 0.0020374 0.0356111 strainProAla
P08466 -0.1422395 0.0390533 16.664337 -3.642190 0.0020723 0.0359714 strainProAla
P38202 -0.2812998 0.0773792 16.834635 -3.635343 0.0020736 0.0359714 strainProAla
P39960 0.1065221 0.0294470 16.844101 3.617421 0.0021539 0.0372230 strainProAla
P02309 0.2069078 0.0571781 16.499181 3.618654 0.0022101 0.0380270 strainProAla
P29055 -0.1947356 0.0534639 15.882251 -3.642378 0.0022169 0.0380270 strainProAla
Q00539 0.1772119 0.0493088 16.734051 3.593925 0.0022862 0.0390345 strainProAla
P28273 0.1288622 0.0354585 15.695920 3.634174 0.0022937 0.0390345 strainProAla
P53946 -0.1204087 0.0330510 15.457555 -3.643118 0.0023011 0.0390345 strainProAla
P38332 -0.2235128 0.0617173 15.785470 -3.621561 0.0023363 0.0394844 strainProAla
Q03690 0.0668005 0.0186316 16.433135 3.585323 0.0023866 0.0399824 strainProAla
P27809 -0.0720735 0.0200947 16.371602 -3.586698 0.0023917 0.0399824 strainProAla
P53336 -0.1621329 0.0447228 15.440627 -3.625281 0.0023918 0.0399824 strainProAla
P00925 -0.2377344 0.0665189 16.559793 -3.573940 0.0024204 0.0403131 strainProAla
P07255 0.2592396 0.0718710 15.671109 3.607011 0.0024333 0.0403823 strainProAla
P46992 -0.2916781 0.0812631 15.905259 -3.589305 0.0024741 0.0408186 strainProAla
Q01080 -0.0905417 0.0252846 16.097790 -3.580907 0.0024774 0.0408186 strainProAla
Q04660 -0.1097716 0.0309647 16.974579 -3.545058 0.0024934 0.0408995 strainProAla
P38705 -0.1735518 0.0482016 15.519898 -3.600539 0.0025001 0.0408995 strainProAla
P47149 0.1523741 0.0426528 16.098359 3.572425 0.0025221 0.0411145 strainProAla
P47019 -0.1777056 0.0494365 15.412946 -3.594622 0.0025556 0.0415122 strainProAla
P00950 -0.1426513 0.0403568 16.628987 -3.534750 0.0026184 0.0421726 strainProAla
P07259 -0.1010931 0.0284707 16.197015 -3.550774 0.0026192 0.0421726 strainProAla
Q3E7A8 1.1137919 0.3115590 15.578071 3.574899 0.0026237 0.0421726 strainProAla
P40462 0.1003106 0.0283678 16.285313 3.536077 0.0026830 0.0428460 strainProAla
P38244 -0.1739448 0.0493687 16.579902 -3.523379 0.0026934 0.0428460 strainProAla
P11075 0.1025090 0.0292096 16.974579 3.509428 0.0026936 0.0428460 strainProAla
P50623 -0.1848375 0.0524776 16.290366 -3.522220 0.0027622 0.0436373 strainProAla
Q12421 0.3562014 0.0987979 14.326474 3.605354 0.0027736 0.0436373 strainProAla
Q06337 -0.1689193 0.0477750 15.837866 -3.535729 0.0027854 0.0436373 strainProAla
P27466 0.1257572 0.0358332 16.517834 3.509514 0.0027880 0.0436373 strainProAla
Q02931 -0.0975531 0.0268662 13.777694 -3.631065 0.0027908 0.0436373 strainProAla
P16521 -0.0920120 0.0256868 14.702479 -3.582068 0.0028017 0.0436584 strainProAla
P40991 -0.0753270 0.0212340 15.379883 -3.547473 0.0028267 0.0438552 strainProAla
P41735 0.2712650 0.0761314 14.994781 3.563115 0.0028334 0.0438552 strainProAla
P39111 -0.1220553 0.0344962 15.515781 -3.538224 0.0028477 0.0439291 strainProAla
Q05040 0.1194261 0.0338717 15.753877 3.525834 0.0028639 0.0440315 strainProAla
P36150 0.2474681 0.0701705 15.597671 3.526669 0.0028968 0.0443887 strainProAla
Q04599 -0.1780465 0.0512043 16.801986 -3.477182 0.0029252 0.0446751 strainProAla
P46681 0.1007388 0.0290430 16.853900 3.468605 0.0029685 0.0451866 strainProAla
P00498 -0.1668960 0.0481195 16.747964 -3.468365 0.0029932 0.0454118 strainProAla
P30619 0.1134176 0.0319518 14.651329 3.549643 0.0030069 0.0454256 strainProAla
P22138 -0.0738984 0.0213193 16.585969 -3.466271 0.0030430 0.0454256 strainProAla
P43592 0.2825483 0.0808104 15.733714 3.496434 0.0030511 0.0454256 strainProAla
P32589 0.1237721 0.0349624 14.696775 3.540150 0.0030524 0.0454256 strainProAla
Q04373 -0.0872413 0.0252203 16.737622 -3.459174 0.0030553 0.0454256 strainProAla
P40554 -0.4454285 0.1275149 15.759554 -3.493150 0.0030657 0.0454256 strainProAla
P53860 -0.2186750 0.0629989 16.320507 -3.471092 0.0030727 0.0454256 strainProAla
P21243 -0.0836897 0.0237929 15.135678 -3.517426 0.0030732 0.0454256 strainProAla
P36107 -0.2027025 0.0573371 14.613486 -3.535276 0.0031068 0.0457757 strainProAla
Q08471 0.3746336 0.1080879 16.242522 3.466007 0.0031248 0.0458934 strainProAla
Q05827 0.4995659 0.1446448 16.357497 3.453743 0.0031795 0.0465485 strainProAla
Q12263 0.1115588 0.0321154 15.773518 3.473682 0.0031899 0.0465530 strainProAla
Q04964 0.2053919 0.0593941 16.048258 3.458122 0.0032254 0.0469220 strainProAla
Q3E776 0.5154254 0.1501664 16.636824 3.432361 0.0032604 0.0472811 strainProAla
P38342 0.2725311 0.0789228 15.911372 3.453134 0.0032945 0.0476258 strainProAla
P32449 0.1031372 0.0299340 16.028273 3.445488 0.0033179 0.0477693 strainProAla
P40553 0.1127119 0.0327799 16.194594 3.438446 0.0033252 0.0477693 strainProAla
Q05900 -0.2725815 0.0792082 15.949807 -3.441331 0.0033674 0.0482244 strainProAla
Q08004 -0.1898543 0.0555165 16.463866 -3.419781 0.0033917 0.0484213 strainProAla
P50861 -0.1675049 0.0489918 16.338982 -3.419037 0.0034282 0.0487914 strainProAla

Median - Contrast: strainProAla - strainCtrl = 0 ( 479 significant proteins)

feature logFC se df t pval adjPval contrast
P31539 0.6944615 0.0214118 16.97458 32.433590 0.0000000 0.0000000 strainProAla - strainCtrl
P10591 0.9651774 0.0326527 15.32076 29.558884 0.0000000 0.0000000 strainProAla - strainCtrl
P33416 0.6396078 0.0292010 16.48546 21.903636 0.0000000 0.0000000 strainProAla - strainCtrl
P22202 0.8864744 0.0371130 14.41189 23.885797 0.0000000 0.0000000 strainProAla - strainCtrl
P15705 0.4691298 0.0265893 15.71789 17.643545 0.0000000 0.0000000 strainProAla - strainCtrl
Q12068 0.6452703 0.0409454 16.68435 15.759294 0.0000000 0.0000000 strainProAla - strainCtrl
P38260 0.4818940 0.0308089 16.79405 15.641389 0.0000000 0.0000000 strainProAla - strainCtrl
P16474 0.3941562 0.0261457 16.27343 15.075385 0.0000000 0.0000000 strainProAla - strainCtrl
P53691 0.4463356 0.0303459 16.25961 14.708273 0.0000000 0.0000000 strainProAla - strainCtrl
P53940 0.5128356 0.0335372 14.83738 15.291522 0.0000000 0.0000001 strainProAla - strainCtrl
P25294 0.4656857 0.0337872 16.33686 13.782903 0.0000000 0.0000001 strainProAla - strainCtrl
P07264 -0.4220768 0.0283544 14.98695 -14.885736 0.0000000 0.0000001 strainProAla - strainCtrl
Q01217 -0.3287772 0.0238277 16.04231 -13.798112 0.0000000 0.0000001 strainProAla - strainCtrl
Q12449 0.4933104 0.0387162 15.66544 12.741703 0.0000000 0.0000004 strainProAla - strainCtrl
P38737 0.3175363 0.0263070 16.64796 12.070417 0.0000000 0.0000004 strainProAla - strainCtrl
P19414 -0.2985585 0.0252747 16.86885 -11.812560 0.0000000 0.0000004 strainProAla - strainCtrl
P02829 0.7848498 0.0674506 16.75815 11.635926 0.0000000 0.0000005 strainProAla - strainCtrl
P38113 -0.3589904 0.0309796 16.57540 -11.587964 0.0000000 0.0000006 strainProAla - strainCtrl
P53128 -0.3411177 0.0275259 14.66742 -12.392597 0.0000000 0.0000009 strainProAla - strainCtrl
P10592 0.4438504 0.0403323 16.60617 11.004838 0.0000000 0.0000011 strainProAla - strainCtrl
P39522 -0.2445336 0.0224979 16.75928 -10.869150 0.0000000 0.0000011 strainProAla - strainCtrl
Q12680 -0.2449375 0.0198771 14.26511 -12.322607 0.0000000 0.0000011 strainProAla - strainCtrl
P34227 0.3272599 0.0308254 16.38873 10.616573 0.0000000 0.0000019 strainProAla - strainCtrl
P53044 0.2774489 0.0264883 16.52772 10.474410 0.0000000 0.0000020 strainProAla - strainCtrl
P40017 -0.3161885 0.0300690 16.39769 -10.515417 0.0000000 0.0000020 strainProAla - strainCtrl
P40897 -0.7431552 0.0740815 16.82807 -10.031590 0.0000000 0.0000029 strainProAla - strainCtrl
P05694 -0.2554191 0.0257456 16.93483 -9.920871 0.0000000 0.0000031 strainProAla - strainCtrl
P32528 -0.3080539 0.0304375 16.17472 -10.120857 0.0000000 0.0000034 strainProAla - strainCtrl
P00815 -0.3154036 0.0315794 16.11048 -9.987642 0.0000000 0.0000040 strainProAla - strainCtrl
P23337 -0.5534137 0.0573546 16.97458 -9.648981 0.0000000 0.0000040 strainProAla - strainCtrl
O14467 0.4083865 0.0413644 16.03065 9.872895 0.0000000 0.0000047 strainProAla - strainCtrl
Q04792 -0.4583027 0.0474409 16.56062 -9.660502 0.0000000 0.0000047 strainProAla - strainCtrl
P32589 0.3694767 0.0353877 14.69678 10.440831 0.0000000 0.0000047 strainProAla - strainCtrl
P40054 -0.2517891 0.0261288 16.49475 -9.636454 0.0000000 0.0000047 strainProAla - strainCtrl
Q03148 -0.2522999 0.0264457 16.60568 -9.540312 0.0000000 0.0000050 strainProAla - strainCtrl
Q08422 0.6005348 0.0606259 15.60811 9.905587 0.0000000 0.0000050 strainProAla - strainCtrl
P32644 0.2411051 0.0257658 16.97458 9.357572 0.0000000 0.0000051 strainProAla - strainCtrl
Q03103 0.2383997 0.0256464 16.75443 9.295635 0.0000001 0.0000061 strainProAla - strainCtrl
P27809 -0.1860191 0.0197482 16.37160 -9.419568 0.0000001 0.0000061 strainProAla - strainCtrl
P53834 0.4113542 0.0433883 16.15771 9.480771 0.0000001 0.0000061 strainProAla - strainCtrl
P53912 0.3744936 0.0414145 16.44614 9.042564 0.0000001 0.0000098 strainProAla - strainCtrl
P33755 0.2112282 0.0237993 16.90107 8.875390 0.0000001 0.0000099 strainProAla - strainCtrl
P38634 0.7477929 0.0880628 16.57349 8.491588 0.0000002 0.0000208 strainProAla - strainCtrl
P21954 -0.2114155 0.0252339 16.59255 -8.378222 0.0000002 0.0000242 strainProAla - strainCtrl
P09368 1.1227743 0.1332838 16.19900 8.423939 0.0000003 0.0000263 strainProAla - strainCtrl
P26364 1.4847451 0.1714772 15.34244 8.658556 0.0000003 0.0000270 strainProAla - strainCtrl
P36152 0.2127143 0.0256171 16.38767 8.303614 0.0000003 0.0000278 strainProAla - strainCtrl
P38631 -0.2750359 0.0316976 15.14486 -8.676862 0.0000003 0.0000278 strainProAla - strainCtrl
P48361 -0.3098287 0.0386804 16.71334 -8.009966 0.0000004 0.0000379 strainProAla - strainCtrl
P08153 -0.3787806 0.0466920 15.80295 -8.112325 0.0000005 0.0000458 strainProAla - strainCtrl
Q03102 0.4265751 0.0501404 14.52102 8.507608 0.0000005 0.0000458 strainProAla - strainCtrl
P16550 0.2077443 0.0251403 15.19734 8.263399 0.0000005 0.0000464 strainProAla - strainCtrl
P03965 -0.2230767 0.0285479 16.82989 -7.814112 0.0000005 0.0000466 strainProAla - strainCtrl
P25491 0.2777836 0.0344271 15.75077 8.068754 0.0000006 0.0000471 strainProAla - strainCtrl
Q12031 0.8558424 0.1056404 15.36715 8.101467 0.0000006 0.0000521 strainProAla - strainCtrl
Q06494 0.3036095 0.0390770 16.55911 7.769515 0.0000006 0.0000529 strainProAla - strainCtrl
P24279 -0.2020785 0.0261004 16.63149 -7.742339 0.0000007 0.0000529 strainProAla - strainCtrl
P19882 0.3166402 0.0404941 16.17774 7.819411 0.0000007 0.0000548 strainProAla - strainCtrl
P07258 -0.2167297 0.0284994 16.97458 -7.604705 0.0000007 0.0000562 strainProAla - strainCtrl
P24784 0.2689487 0.0346439 16.26358 7.763236 0.0000007 0.0000562 strainProAla - strainCtrl
Q12001 -0.2883457 0.0352207 14.67118 -8.186828 0.0000008 0.0000569 strainProAla - strainCtrl
P08432 -0.3529126 0.0455017 15.93789 -7.756026 0.0000008 0.0000629 strainProAla - strainCtrl
P39106 -0.2245712 0.0294169 16.28405 -7.634095 0.0000009 0.0000660 strainProAla - strainCtrl
Q08199 0.1764858 0.0234521 16.69141 7.525370 0.0000009 0.0000669 strainProAla - strainCtrl
P28817 0.1911521 0.0254659 16.61506 7.506202 0.0000010 0.0000701 strainProAla - strainCtrl
Q06625 -0.4119062 0.0523794 14.99848 -7.863900 0.0000011 0.0000741 strainProAla - strainCtrl
P40048 0.3863189 0.0506978 15.21518 7.620027 0.0000014 0.0000978 strainProAla - strainCtrl
P38891 -0.2679486 0.0369009 15.94870 -7.261304 0.0000019 0.0001311 strainProAla - strainCtrl
Q12118 0.2449960 0.0338773 15.83817 7.231856 0.0000021 0.0001396 strainProAla - strainCtrl
P14832 0.1915512 0.0269863 16.49102 7.098087 0.0000021 0.0001396 strainProAla - strainCtrl
Q12256 -0.5150736 0.0734607 16.80722 -7.011554 0.0000022 0.0001444 strainProAla - strainCtrl
Q12329 0.4515668 0.0647203 16.65384 6.977206 0.0000025 0.0001585 strainProAla - strainCtrl
P38132 -0.2418849 0.0338535 15.76071 -7.145050 0.0000025 0.0001585 strainProAla - strainCtrl
P22209 -0.4440213 0.0630892 16.26971 -7.037994 0.0000026 0.0001585 strainProAla - strainCtrl
Q08986 -0.5415807 0.0781123 16.72592 -6.933362 0.0000026 0.0001619 strainProAla - strainCtrl
Q96VH4 0.4974323 0.0718531 16.36460 6.922904 0.0000030 0.0001813 strainProAla - strainCtrl
P22134 0.3010310 0.0441770 16.97458 6.814207 0.0000030 0.0001813 strainProAla - strainCtrl
P53549 0.1624952 0.0236807 16.42249 6.861924 0.0000033 0.0001958 strainProAla - strainCtrl
P40989 0.6870733 0.0991935 15.92596 6.926595 0.0000035 0.0002034 strainProAla - strainCtrl
P24869 -0.7350214 0.1038969 14.79056 -7.074528 0.0000041 0.0002350 strainProAla - strainCtrl
P38219 0.1902094 0.0282615 16.41324 6.730344 0.0000042 0.0002401 strainProAla - strainCtrl
P32561 -0.1988666 0.0301102 16.97458 -6.604618 0.0000045 0.0002503 strainProAla - strainCtrl
P15108 0.4175304 0.0612669 15.74694 6.814939 0.0000045 0.0002503 strainProAla - strainCtrl
P53885 0.1976656 0.0285772 15.12658 6.916903 0.0000047 0.0002572 strainProAla - strainCtrl
P07275 0.2565570 0.0385841 16.48688 6.649296 0.0000048 0.0002594 strainProAla - strainCtrl
Q08446 0.2442964 0.0369415 16.61236 6.613054 0.0000049 0.0002638 strainProAla - strainCtrl
P32562 -0.4783435 0.0684064 14.55018 -6.992667 0.0000051 0.0002705 strainProAla - strainCtrl
P32324 -0.1519830 0.0232171 16.86588 -6.546163 0.0000052 0.0002708 strainProAla - strainCtrl
P18544 -0.2513739 0.0384949 16.93301 -6.530050 0.0000052 0.0002708 strainProAla - strainCtrl
P39976 -0.1907041 0.0287050 16.04236 -6.643588 0.0000056 0.0002797 strainProAla - strainCtrl
P80210 -0.2247292 0.0339465 16.17720 -6.620092 0.0000056 0.0002797 strainProAla - strainCtrl
P39676 0.4362017 0.0650278 15.67021 6.707931 0.0000056 0.0002797 strainProAla - strainCtrl
P36007 -0.2132311 0.0329185 16.83924 -6.477552 0.0000060 0.0002916 strainProAla - strainCtrl
P53078 -0.2823613 0.0406962 14.37982 -6.938266 0.0000060 0.0002916 strainProAla - strainCtrl
P16664 -0.2904115 0.0445570 16.22732 -6.517746 0.0000066 0.0003201 strainProAla - strainCtrl
P32496 0.1871959 0.0286860 16.05966 6.525681 0.0000069 0.0003281 strainProAla - strainCtrl
P05150 -0.2372094 0.0368814 16.61391 -6.431686 0.0000069 0.0003281 strainProAla - strainCtrl
P50278 0.2164860 0.0337173 16.63306 6.420620 0.0000070 0.0003298 strainProAla - strainCtrl
Q04062 0.1769228 0.0279963 16.82763 6.319510 0.0000081 0.0003745 strainProAla - strainCtrl
P22515 0.1433797 0.0221494 15.73238 6.473312 0.0000083 0.0003834 strainProAla - strainCtrl
P06786 -0.1544224 0.0244564 16.30098 -6.314183 0.0000094 0.0004274 strainProAla - strainCtrl
P47112 0.3536867 0.0560039 16.27751 6.315393 0.0000095 0.0004274 strainProAla - strainCtrl
P47117 -0.1881689 0.0300615 16.45721 -6.259474 0.0000100 0.0004471 strainProAla - strainCtrl
P40016 0.1655874 0.0264516 16.38153 6.260003 0.0000102 0.0004517 strainProAla - strainCtrl
P33299 0.1382740 0.0220758 15.98424 6.263590 0.0000114 0.0004972 strainProAla - strainCtrl
P14180 -0.3671655 0.0604358 16.93356 -6.075295 0.0000126 0.0005454 strainProAla - strainCtrl
P19145 -0.2503674 0.0412853 16.85222 -6.064324 0.0000131 0.0005634 strainProAla - strainCtrl
P38143 -0.2408456 0.0392618 16.28120 -6.134348 0.0000133 0.0005634 strainProAla - strainCtrl
P32623 -0.2983912 0.0486861 16.30957 -6.128881 0.0000134 0.0005634 strainProAla - strainCtrl
P32590 0.1917527 0.0306789 15.34212 6.250305 0.0000140 0.0005862 strainProAla - strainCtrl
P48015 0.2128097 0.0351091 16.33130 6.061388 0.0000151 0.0006201 strainProAla - strainCtrl
P38777 0.3074192 0.0490855 15.00805 6.262937 0.0000152 0.0006201 strainProAla - strainCtrl
P38699 0.3946163 0.0659562 16.88794 5.983001 0.0000152 0.0006201 strainProAla - strainCtrl
Q08873 -0.2423911 0.0396007 15.70760 -6.120873 0.0000160 0.0006442 strainProAla - strainCtrl
Q00402 0.1248618 0.0208046 16.51334 6.001630 0.0000162 0.0006442 strainProAla - strainCtrl
P35191 0.3648728 0.0599334 15.86978 6.087974 0.0000163 0.0006442 strainProAla - strainCtrl
P19097 -0.1112325 0.0187928 16.84895 -5.918889 0.0000175 0.0006831 strainProAla - strainCtrl
P53946 -0.2047839 0.0335218 15.45755 -6.108975 0.0000175 0.0006831 strainProAla - strainCtrl
P07149 -0.1249593 0.0203507 15.11073 -6.140304 0.0000183 0.0007069 strainProAla - strainCtrl
P29469 -0.1622613 0.0267188 15.47194 -6.072917 0.0000187 0.0007147 strainProAla - strainCtrl
P33336 -0.5054022 0.0846315 15.84358 -5.971800 0.0000204 0.0007694 strainProAla - strainCtrl
Q12250 0.2130859 0.0360434 16.27214 5.911922 0.0000204 0.0007694 strainProAla - strainCtrl
P52489 -0.2013442 0.0334964 15.39958 -6.010913 0.0000213 0.0007875 strainProAla - strainCtrl
P24031 -0.2837961 0.0489090 16.97458 -5.802537 0.0000213 0.0007875 strainProAla - strainCtrl
P10964 -0.1553797 0.0256188 15.03374 -6.065069 0.0000214 0.0007875 strainProAla - strainCtrl
P17123 -0.6192858 0.1055387 16.39083 -5.867858 0.0000216 0.0007875 strainProAla - strainCtrl
P47164 -0.2883650 0.0495669 16.66507 -5.817692 0.0000223 0.0008062 strainProAla - strainCtrl
P32353 0.3020397 0.0514450 16.02332 5.871120 0.0000235 0.0008444 strainProAla - strainCtrl
P53947 -0.6787194 0.1176254 16.35108 -5.770179 0.0000264 0.0009391 strainProAla - strainCtrl
P46367 0.2232490 0.0388407 16.48346 5.747811 0.0000267 0.0009426 strainProAla - strainCtrl
P05374 -0.2382935 0.0407073 15.63074 -5.853823 0.0000269 0.0009426 strainProAla - strainCtrl
P29496 -0.1814917 0.0303028 14.64590 -5.989277 0.0000274 0.0009549 strainProAla - strainCtrl
Q06103 0.1705376 0.0302131 16.97458 5.644497 0.0000293 0.0010123 strainProAla - strainCtrl
P0CS90 0.2067602 0.0365409 16.77453 5.658321 0.0000298 0.0010218 strainProAla - strainCtrl
P36013 -0.1451405 0.0256196 16.28074 -5.665210 0.0000329 0.0011200 strainProAla - strainCtrl
P43558 0.2249463 0.0401192 16.55231 5.606954 0.0000347 0.0011722 strainProAla - strainCtrl
P36775 0.1523163 0.0267605 15.79751 5.691821 0.0000350 0.0011755 strainProAla - strainCtrl
P33298 0.1791168 0.0311464 15.24385 5.750802 0.0000360 0.0011983 strainProAla - strainCtrl
P43588 0.2247334 0.0402261 16.45487 5.586754 0.0000369 0.0012201 strainProAla - strainCtrl
Q12498 1.0614532 0.1902650 16.42633 5.578816 0.0000377 0.0012384 strainProAla - strainCtrl
Q06214 0.1381314 0.0246167 15.41204 5.611286 0.0000448 0.0014615 strainProAla - strainCtrl
Q08968 0.2288290 0.0420415 16.77863 5.442936 0.0000459 0.0014856 strainProAla - strainCtrl
P07806 -0.1255799 0.0222751 14.96081 -5.637692 0.0000477 0.0015329 strainProAla - strainCtrl
P32476 0.2051875 0.0369738 15.55629 5.549532 0.0000487 0.0015553 strainProAla - strainCtrl
P43573 0.1903151 0.0351837 16.73940 5.409183 0.0000495 0.0015705 strainProAla - strainCtrl
P07285 -0.1888630 0.0349118 16.69182 -5.409714 0.0000500 0.0015734 strainProAla - strainCtrl
P53199 0.2109605 0.0388712 16.00788 5.427167 0.0000558 0.0017445 strainProAla - strainCtrl
P37012 -0.2757301 0.0507023 15.81271 -5.438212 0.0000570 0.0017698 strainProAla - strainCtrl
P22138 -0.1135666 0.0213193 16.58597 -5.326944 0.0000604 0.0018510 strainProAla - strainCtrl
P06101 0.1351554 0.0250168 15.86417 5.402595 0.0000604 0.0018510 strainProAla - strainCtrl
Q02785 -0.4108612 0.0764792 15.96746 -5.372196 0.0000627 0.0019089 strainProAla - strainCtrl
P16521 -0.1312389 0.0238756 14.70248 -5.496772 0.0000660 0.0019956 strainProAla - strainCtrl
P40087 0.2242445 0.0420719 16.03347 5.330025 0.0000672 0.0020192 strainProAla - strainCtrl
P33302 -0.2459670 0.0462743 15.72496 -5.315416 0.0000738 0.0022034 strainProAla - strainCtrl
P33297 0.1367379 0.0261615 16.56014 5.226689 0.0000744 0.0022055 strainProAla - strainCtrl
P29029 0.5166371 0.1000628 16.83193 5.163126 0.0000805 0.0023614 strainProAla - strainCtrl
P53241 -0.4207503 0.0811274 16.53287 -5.186291 0.0000812 0.0023614 strainProAla - strainCtrl
P38326 0.2750928 0.0520929 15.59644 5.280812 0.0000812 0.0023614 strainProAla - strainCtrl
Q12280 -0.4209008 0.0811850 16.36810 -5.184464 0.0000841 0.0024311 strainProAla - strainCtrl
Q12458 0.1753495 0.0333560 15.38111 5.256907 0.0000890 0.0025572 strainProAla - strainCtrl
P38910 0.2969557 0.0576417 16.20290 5.151755 0.0000928 0.0026125 strainProAla - strainCtrl
Q12447 0.1440430 0.0267317 14.11084 5.388462 0.0000930 0.0026125 strainProAla - strainCtrl
P03962 -0.3016415 0.0589890 16.56374 -5.113522 0.0000936 0.0026125 strainProAla - strainCtrl
Q06510 -0.3297426 0.0648464 16.88206 -5.084978 0.0000937 0.0026125 strainProAla - strainCtrl
P05375 -0.4683425 0.0906070 15.96973 -5.168945 0.0000938 0.0026125 strainProAla - strainCtrl
P53322 -0.3237917 0.0596205 13.61375 -5.430875 0.0000977 0.0027050 strainProAla - strainCtrl
P39721 0.2246896 0.0440694 16.40747 5.098539 0.0000994 0.0027353 strainProAla - strainCtrl
Q03323 -0.1591829 0.0309869 15.83418 -5.137105 0.0001026 0.0028078 strainProAla - strainCtrl
Q08202 0.3404473 0.0657755 15.26189 5.175897 0.0001068 0.0029044 strainProAla - strainCtrl
P53303 0.2669674 0.0523342 15.89208 5.101203 0.0001090 0.0029471 strainProAla - strainCtrl
P40202 0.1692659 0.0337681 16.76745 5.012604 0.0001111 0.0029779 strainProAla - strainCtrl
P53008 -0.1860526 0.0367835 16.23445 -5.058042 0.0001114 0.0029779 strainProAla - strainCtrl
P32771 0.1960009 0.0389746 16.35662 5.028935 0.0001156 0.0030551 strainProAla - strainCtrl
P32288 -0.1757582 0.0346898 15.94453 -5.066564 0.0001157 0.0030551 strainProAla - strainCtrl
Q06150 -0.8523383 0.1683363 15.93578 -5.063308 0.0001166 0.0030627 strainProAla - strainCtrl
P21243 0.1201162 0.0234074 15.13568 5.131550 0.0001195 0.0031193 strainProAla - strainCtrl
Q03973 0.2014628 0.0405055 16.76537 4.973721 0.0001205 0.0031292 strainProAla - strainCtrl
P27882 -0.1738687 0.0336777 14.75952 -5.162726 0.0001218 0.0031452 strainProAla - strainCtrl
P47176 -0.1729326 0.0339132 15.14215 -5.099279 0.0001270 0.0032604 strainProAla - strainCtrl
Q05902 -0.1603424 0.0324269 16.18683 -4.944736 0.0001415 0.0036136 strainProAla - strainCtrl
P53296 0.3451326 0.0697840 15.78534 4.945725 0.0001518 0.0038377 strainProAla - strainCtrl
Q02606 -0.3289409 0.0670533 16.23558 -4.905662 0.0001520 0.0038377 strainProAla - strainCtrl
P49956 -0.2188049 0.0437274 14.93135 -5.003840 0.0001594 0.0039897 strainProAla - strainCtrl
Q04934 0.1789938 0.0366689 16.23545 4.881356 0.0001597 0.0039897 strainProAla - strainCtrl
P32486 -0.1956229 0.0406820 16.97458 -4.808585 0.0001645 0.0040872 strainProAla - strainCtrl
P17255 -0.1163894 0.0241089 16.65215 -4.827655 0.0001665 0.0041130 strainProAla - strainCtrl
P49367 -0.1312393 0.0271972 16.48634 -4.825471 0.0001718 0.0042227 strainProAla - strainCtrl
P32565 0.1464828 0.0301687 15.96361 4.855458 0.0001765 0.0042922 strainProAla - strainCtrl
P38274 -0.1758017 0.0365478 16.51543 -4.810181 0.0001765 0.0042922 strainProAla - strainCtrl
P22108 0.1803670 0.0374165 16.30708 4.820522 0.0001788 0.0043252 strainProAla - strainCtrl
P34162 -0.1803935 0.0373882 15.97185 -4.824878 0.0001875 0.0045123 strainProAla - strainCtrl
P04076 -0.1539712 0.0319830 15.90993 -4.814152 0.0001937 0.0046365 strainProAla - strainCtrl
P53133 -0.2717055 0.0568875 16.21575 -4.776188 0.0001989 0.0047348 strainProAla - strainCtrl
Q03212 -0.3125348 0.0655972 16.33387 -4.764451 0.0001999 0.0047348 strainProAla - strainCtrl
P38764 0.1123518 0.0237439 16.62698 4.731819 0.0002042 0.0048117 strainProAla - strainCtrl
P47169 -0.2140441 0.0446340 15.75733 -4.795539 0.0002065 0.0048411 strainProAla - strainCtrl
P39692 -0.2282763 0.0483019 16.50254 -4.726031 0.0002107 0.0049157 strainProAla - strainCtrl
P17106 0.1733230 0.0359956 15.36619 4.815119 0.0002125 0.0049335 strainProAla - strainCtrl
Q03178 0.3153442 0.0669232 16.59296 4.712030 0.0002139 0.0049404 strainProAla - strainCtrl
P40207 0.4439001 0.0925326 15.23242 4.797228 0.0002255 0.0051827 strainProAla - strainCtrl
P38332 -0.2929918 0.0617503 15.78547 -4.744784 0.0002277 0.0052067 strainProAla - strainCtrl
P53899 0.3249281 0.0682423 15.55118 4.761391 0.0002291 0.0052128 strainProAla - strainCtrl
P39719 -0.1990661 0.0423308 16.18956 -4.702636 0.0002324 0.0052614 strainProAla - strainCtrl
P13663 -0.1629123 0.0340443 15.15613 -4.785297 0.0002341 0.0052736 strainProAla - strainCtrl
P21147 -0.1655499 0.0347565 15.35306 -4.763135 0.0002363 0.0052968 strainProAla - strainCtrl
P29465 -0.2914016 0.0626253 16.67865 -4.653095 0.0002389 0.0053231 strainProAla - strainCtrl
Q12532 0.1297427 0.0277817 16.40390 4.670077 0.0002404 0.0053231 strainProAla - strainCtrl
P12383 0.1875699 0.0405246 16.97458 4.628539 0.0002409 0.0053231 strainProAla - strainCtrl
P40557 -0.1581955 0.0337043 15.91224 -4.693637 0.0002475 0.0054185 strainProAla - strainCtrl
P47149 0.1927977 0.0412055 16.09836 4.678928 0.0002476 0.0054185 strainProAla - strainCtrl
Q06344 -0.3182134 0.0687535 16.59952 -4.628324 0.0002547 0.0055472 strainProAla - strainCtrl
Q12428 -0.2207285 0.0479705 16.69368 -4.601337 0.0002658 0.0057631 strainProAla - strainCtrl
P38841 0.3072373 0.0665636 16.39079 4.615698 0.0002698 0.0058213 strainProAla - strainCtrl
P07702 -0.0943015 0.0205648 16.75158 -4.585574 0.0002725 0.0058531 strainProAla - strainCtrl
Q06451 -0.3623702 0.0784714 16.23967 -4.617865 0.0002748 0.0058593 strainProAla - strainCtrl
Q00772 -0.2442065 0.0521896 15.41785 -4.679219 0.0002764 0.0058593 strainProAla - strainCtrl
Q03020 0.2752388 0.0603122 16.97458 4.563568 0.0002766 0.0058593 strainProAla - strainCtrl
P38182 0.3636993 0.0788358 15.91356 4.613379 0.0002916 0.0061120 strainProAla - strainCtrl
P46683 0.1399134 0.0307481 16.79631 4.550315 0.0002918 0.0061120 strainProAla - strainCtrl
P06738 -0.2800475 0.0608405 16.00780 -4.602980 0.0002936 0.0061120 strainProAla - strainCtrl
P32857 -0.2367251 0.0517258 16.34652 -4.576539 0.0002947 0.0061120 strainProAla - strainCtrl
P00927 -0.1169471 0.0252332 15.54635 -4.634657 0.0002960 0.0061120 strainProAla - strainCtrl
P22768 -0.1444137 0.0314525 16.09740 -4.591484 0.0002966 0.0061120 strainProAla - strainCtrl
P54838 0.1168087 0.0251255 15.29265 4.649013 0.0002998 0.0061315 strainProAla - strainCtrl
P38196 -0.2674132 0.0576611 15.42295 -4.637673 0.0003002 0.0061315 strainProAla - strainCtrl
Q03558 0.1390961 0.0296382 14.63176 4.693133 0.0003079 0.0062618 strainProAla - strainCtrl
Q12204 0.2251284 0.0492683 16.08390 4.569439 0.0003110 0.0062971 strainProAla - strainCtrl
P40472 0.3514451 0.0778088 16.09585 4.516780 0.0003462 0.0069793 strainProAla - strainCtrl
P23639 0.1816882 0.0405695 16.59269 4.478447 0.0003495 0.0070150 strainProAla - strainCtrl
P32643 -0.1935640 0.0432695 16.57143 -4.473451 0.0003543 0.0070793 strainProAla - strainCtrl
Q12523 -0.2265142 0.0506221 16.26445 -4.474610 0.0003689 0.0073402 strainProAla - strainCtrl
Q07824 -0.4542413 0.1016635 16.23059 -4.468089 0.0003758 0.0074443 strainProAla - strainCtrl
P47771 0.1478147 0.0330850 16.19830 4.467725 0.0003778 0.0074460 strainProAla - strainCtrl
P32617 -0.3380811 0.0761330 16.58258 -4.440664 0.0003791 0.0074460 strainProAla - strainCtrl
P53094 -0.1397541 0.0315460 16.69140 -4.430163 0.0003820 0.0074706 strainProAla - strainCtrl
P32327 -0.1411794 0.0316275 16.06155 -4.463813 0.0003884 0.0075633 strainProAla - strainCtrl
P17967 0.1523886 0.0339964 15.72949 4.482490 0.0003922 0.0076057 strainProAla - strainCtrl
P32860 0.1288864 0.0292097 16.69996 4.412457 0.0003962 0.0076503 strainProAla - strainCtrl
Q12375 -0.2235219 0.0500762 15.72969 -4.463633 0.0004076 0.0078391 strainProAla - strainCtrl
Q03104 -0.3083939 0.0691791 15.47501 -4.457907 0.0004283 0.0082016 strainProAla - strainCtrl
P32386 -0.1495453 0.0342339 16.74323 -4.368344 0.0004327 0.0082181 strainProAla - strainCtrl
P53915 -0.1742232 0.0397399 16.48782 -4.384086 0.0004327 0.0082181 strainProAla - strainCtrl
P07172 -0.1403229 0.0321181 16.57360 -4.368972 0.0004418 0.0083551 strainProAla - strainCtrl
P00635 0.4898709 0.1027858 12.09303 4.765939 0.0004498 0.0084536 strainProAla - strainCtrl
P35201 0.5073927 0.1157557 16.19805 4.383306 0.0004506 0.0084536 strainProAla - strainCtrl
Q03254 -0.1457298 0.0333328 16.32825 -4.371960 0.0004535 0.0084720 strainProAla - strainCtrl
P53315 -0.3661305 0.0836106 16.18064 -4.378996 0.0004558 0.0084811 strainProAla - strainCtrl
P22204 -0.1558935 0.0361996 16.97458 -4.306504 0.0004797 0.0088905 strainProAla - strainCtrl
P15274 -0.1128666 0.0246901 13.44388 -4.571335 0.0004820 0.0088923 strainProAla - strainCtrl
P32775 -0.1944206 0.0441328 15.37421 -4.405354 0.0004837 0.0088923 strainProAla - strainCtrl
P22137 -0.1134648 0.0265347 16.97458 -4.276092 0.0005122 0.0093781 strainProAla - strainCtrl
Q12348 -1.1744115 0.2686720 15.42583 -4.371172 0.0005147 0.0093863 strainProAla - strainCtrl
P47057 0.1463381 0.0338802 16.15498 4.319284 0.0005182 0.0093873 strainProAla - strainCtrl
P52910 -0.1098914 0.0256685 16.77951 -4.281186 0.0005188 0.0093873 strainProAla - strainCtrl
P46970 0.1231749 0.0288004 16.79424 4.276848 0.0005227 0.0094206 strainProAla - strainCtrl
A5Z2X5 0.2882241 0.0672776 16.61357 4.284099 0.0005263 0.0094267 strainProAla - strainCtrl
P16140 -0.1296715 0.0302804 16.63051 -4.282360 0.0005271 0.0094267 strainProAla - strainCtrl
P39974 -0.6093082 0.1416899 16.19969 -4.300293 0.0005361 0.0095503 strainProAla - strainCtrl
Q99359 0.8149379 0.1891977 16.05525 4.307336 0.0005384 0.0095533 strainProAla - strainCtrl
P38295 -0.1380997 0.0317986 15.25014 -4.342955 0.0005589 0.0098801 strainProAla - strainCtrl
P32379 0.1784193 0.0419761 16.64859 4.250500 0.0005629 0.0099120 strainProAla - strainCtrl
P38803 0.1183501 0.0279163 16.65865 4.239459 0.0005756 0.0100970 strainProAla - strainCtrl
P53930 0.2537757 0.0591086 15.52990 4.293382 0.0005946 0.0103912 strainProAla - strainCtrl
Q04693 0.1195461 0.0281985 16.34899 4.239448 0.0005979 0.0104092 strainProAla - strainCtrl
P28707 0.1407690 0.0330506 15.95833 4.259193 0.0006028 0.0104549 strainProAla - strainCtrl
P40030 0.3631349 0.0854819 15.90894 4.248092 0.0006209 0.0107276 strainProAla - strainCtrl
P39005 -0.2682304 0.0631406 15.82243 -4.248146 0.0006278 0.0108069 strainProAla - strainCtrl
P12866 -0.2092810 0.0492131 15.50933 -4.252543 0.0006484 0.0110569 strainProAla - strainCtrl
P09232 0.2064066 0.0490275 16.18653 4.210019 0.0006491 0.0110569 strainProAla - strainCtrl
P23542 -0.1082685 0.0256943 16.11882 -4.213724 0.0006496 0.0110569 strainProAla - strainCtrl
P50107 -0.1855884 0.0441905 16.27607 -4.199738 0.0006561 0.0110890 strainProAla - strainCtrl
Q3E7A8 1.3840590 0.3262579 15.57807 4.242224 0.0006563 0.0110890 strainProAla - strainCtrl
P38230 -0.1273885 0.0302676 15.92766 -4.208741 0.0006723 0.0113184 strainProAla - strainCtrl
Q04511 0.2613809 0.0631153 16.95368 4.141326 0.0006864 0.0114982 strainProAla - strainCtrl
P38627 0.1487280 0.0358693 16.81235 4.146389 0.0006899 0.0114982 strainProAla - strainCtrl
P30656 0.1707684 0.0410953 16.63686 4.155423 0.0006905 0.0114982 strainProAla - strainCtrl
Q07716 -0.1113684 0.0269512 16.97458 -4.132231 0.0006984 0.0115484 strainProAla - strainCtrl
P50077 -0.2108851 0.0505948 16.29948 -4.168120 0.0006994 0.0115484 strainProAla - strainCtrl
P36107 -0.2486465 0.0581505 14.61349 -4.275914 0.0007010 0.0115484 strainProAla - strainCtrl
P39006 -0.1363875 0.0327196 16.18738 -4.168369 0.0007085 0.0116301 strainProAla - strainCtrl
Q08932 0.2144356 0.0514866 16.09946 4.164877 0.0007214 0.0117640 strainProAla - strainCtrl
P53312 0.1040691 0.0251555 16.59285 4.137033 0.0007218 0.0117640 strainProAla - strainCtrl
P14904 -0.1275968 0.0303285 15.30828 -4.207159 0.0007309 0.0118694 strainProAla - strainCtrl
Q04341 0.3565664 0.0855704 15.79554 4.166936 0.0007457 0.0120682 strainProAla - strainCtrl
Q9URQ5 0.1595306 0.0384754 16.02478 4.146305 0.0007569 0.0122062 strainProAla - strainCtrl
P33775 -0.1522745 0.0368672 16.13975 -4.130354 0.0007720 0.0124055 strainProAla - strainCtrl
P33734 -0.1030296 0.0252451 16.86410 -4.081171 0.0007893 0.0126043 strainProAla - strainCtrl
P21242 0.1637124 0.0398911 16.42174 4.103985 0.0007898 0.0126043 strainProAla - strainCtrl
Q03151 0.3846986 0.0940215 16.47363 4.091604 0.0008061 0.0128198 strainProAla - strainCtrl
P23724 0.1221607 0.0295560 15.69926 4.133197 0.0008095 0.0128287 strainProAla - strainCtrl
P38169 -0.1913238 0.0453884 14.41453 -4.215256 0.0008136 0.0128500 strainProAla - strainCtrl
P32332 -0.1934257 0.0468898 15.58993 -4.125116 0.0008343 0.0131323 strainProAla - strainCtrl
P26637 -0.0773238 0.0188350 15.89188 -4.105328 0.0008380 0.0131446 strainProAla - strainCtrl
P07342 -0.1375576 0.0336407 15.93238 -4.089021 0.0008629 0.0134845 strainProAla - strainCtrl
P00912 -0.2069800 0.0504551 15.67662 -4.102264 0.0008655 0.0134845 strainProAla - strainCtrl
Q08096 0.1507859 0.0371317 16.31990 4.060840 0.0008756 0.0135962 strainProAla - strainCtrl
Q06682 0.1926519 0.0475005 16.35243 4.055787 0.0008819 0.0136466 strainProAla - strainCtrl
P35999 0.1604359 0.0398236 16.74683 4.028668 0.0008950 0.0138036 strainProAla - strainCtrl
P38236 -0.2366209 0.0583220 16.13822 -4.057148 0.0009009 0.0138475 strainProAla - strainCtrl
P32639 -0.1128163 0.0276795 15.64276 -4.075804 0.0009181 0.0139943 strainProAla - strainCtrl
Q06109 0.6311057 0.1565377 16.43070 4.031652 0.0009203 0.0139943 strainProAla - strainCtrl
P46974 -0.2264777 0.0558033 15.91582 -4.058496 0.0009216 0.0139943 strainProAla - strainCtrl
Q04964 0.2369942 0.0585068 16.04826 4.050710 0.0009226 0.0139943 strainProAla - strainCtrl
P11353 -0.1289313 0.0320903 16.52799 -4.017769 0.0009379 0.0141803 strainProAla - strainCtrl
P40471 -0.1512317 0.0378471 16.79602 -3.995855 0.0009555 0.0143986 strainProAla - strainCtrl
D6VTK4 -0.2688198 0.0670750 16.46298 -4.007753 0.0009650 0.0144933 strainProAla - strainCtrl
Q12044 0.1196905 0.0300316 16.67655 3.985482 0.0009893 0.0148112 strainProAla - strainCtrl
P18961 -0.3031153 0.0759623 16.53800 -3.990338 0.0009935 0.0148252 strainProAla - strainCtrl
P47018 0.0881611 0.0219661 16.04827 4.013510 0.0009977 0.0148397 strainProAla - strainCtrl
P25297 0.8691644 0.2161327 15.76093 4.021439 0.0010138 0.0150307 strainProAla - strainCtrl
Q92331 0.1006816 0.0253028 16.47945 3.979073 0.0010240 0.0151334 strainProAla - strainCtrl
P40327 0.1232866 0.0311701 16.44436 3.955281 0.0010814 0.0159292 strainProAla - strainCtrl
P14065 -0.2354501 0.0600327 16.75442 -3.922034 0.0011250 0.0164758 strainProAla - strainCtrl
Q05791 0.1574930 0.0401107 16.65405 3.926455 0.0011256 0.0164758 strainProAla - strainCtrl
P25694 0.0858768 0.0218614 16.45304 3.928233 0.0011446 0.0166999 strainProAla - strainCtrl
P25378 -0.1704012 0.0433786 16.29957 -3.928232 0.0011629 0.0169138 strainProAla - strainCtrl
Q12377 0.1390736 0.0354351 16.26678 3.924746 0.0011756 0.0170438 strainProAla - strainCtrl
P52892 -0.1955177 0.0502051 16.86890 -3.894376 0.0011807 0.0170616 strainProAla - strainCtrl
Q06151 0.0951898 0.0237756 14.76383 4.003673 0.0011846 0.0170616 strainProAla - strainCtrl
P54000 0.0973373 0.0249436 16.60313 3.902297 0.0011916 0.0170616 strainProAla - strainCtrl
Q03780 0.2190869 0.0556633 15.91628 3.935930 0.0011916 0.0170616 strainProAla - strainCtrl
Q12746 0.1080815 0.0275307 16.05419 3.925850 0.0011993 0.0170780 strainProAla - strainCtrl
Q07950 -0.3291809 0.0831108 15.38773 -3.960749 0.0012002 0.0170780 strainProAla - strainCtrl
P30605 -0.3000037 0.0760870 15.62172 -3.942906 0.0012129 0.0171983 strainProAla - strainCtrl
Q12156 -0.1579452 0.0404204 16.29137 -3.907565 0.0012162 0.0171983 strainProAla - strainCtrl
P54072 -0.5378196 0.1385244 16.71932 -3.882489 0.0012292 0.0173297 strainProAla - strainCtrl
P47093 0.2616654 0.0665261 15.62987 3.933276 0.0012364 0.0173771 strainProAla - strainCtrl
Q03786 0.1304598 0.0336380 16.65900 3.878341 0.0012476 0.0174814 strainProAla - strainCtrl
Q06147 0.1415444 0.0362862 16.13181 3.900777 0.0012543 0.0175221 strainProAla - strainCtrl
P40986 -0.1015529 0.0263061 16.79629 -3.860429 0.0012795 0.0178200 strainProAla - strainCtrl
P31382 -0.1363322 0.0352957 16.52392 -3.862577 0.0013077 0.0181578 strainProAla - strainCtrl
Q12220 0.1073148 0.0278463 16.26721 3.853827 0.0013666 0.0189187 strainProAla - strainCtrl
Q04894 0.1193269 0.0309934 16.29921 3.850072 0.0013732 0.0189290 strainProAla - strainCtrl
Q01939 0.1591730 0.0413064 16.20919 3.853472 0.0013756 0.0189290 strainProAla - strainCtrl
Q03533 -0.1988934 0.0518699 16.41331 -3.834465 0.0014038 0.0192595 strainProAla - strainCtrl
P38084 -0.2015467 0.0518487 15.30435 -3.887206 0.0014099 0.0192860 strainProAla - strainCtrl
P38697 -0.3344881 0.0864385 15.53476 -3.869667 0.0014259 0.0194458 strainProAla - strainCtrl
Q07418 0.1423294 0.0368014 15.45820 3.867498 0.0014441 0.0196366 strainProAla - strainCtrl
P39945 0.1221601 0.0320137 16.35818 3.815875 0.0014684 0.0199083 strainProAla - strainCtrl
Q06408 0.1674613 0.0438193 16.15831 3.821632 0.0014792 0.0199946 strainProAla - strainCtrl
P38811 0.1031194 0.0271220 16.31269 3.802056 0.0015190 0.0204171 strainProAla - strainCtrl
Q03529 -0.2132697 0.0563563 16.71478 -3.784309 0.0015193 0.0204171 strainProAla - strainCtrl
P40850 0.1425228 0.0373263 15.90415 3.818297 0.0015278 0.0204713 strainProAla - strainCtrl
P38784 0.1329836 0.0350291 15.96291 3.796375 0.0015906 0.0212512 strainProAla - strainCtrl
P25655 0.0741137 0.0196367 16.37371 3.774249 0.0016024 0.0213466 strainProAla - strainCtrl
P38244 -0.1851465 0.0491916 16.57990 -3.763780 0.0016076 0.0213546 strainProAla - strainCtrl
P35182 0.1610017 0.0427066 16.38900 3.769951 0.0016148 0.0213885 strainProAla - strainCtrl
P42839 -0.2782682 0.0742122 16.66361 -3.749627 0.0016447 0.0217215 strainProAla - strainCtrl
P04786 0.1532213 0.0410032 16.87018 3.736809 0.0016600 0.0218608 strainProAla - strainCtrl
P39998 -0.1843730 0.0490786 16.19081 -3.756690 0.0016923 0.0222220 strainProAla - strainCtrl
P39717 -0.1907637 0.0498292 14.62318 -3.828352 0.0017155 0.0224593 strainProAla - strainCtrl
Q06213 0.1976299 0.0528287 16.37527 3.740957 0.0017201 0.0224593 strainProAla - strainCtrl
Q12166 -0.1245078 0.0326227 14.66800 -3.816606 0.0017479 0.0227239 strainProAla - strainCtrl
P40303 0.1625486 0.0432008 15.71161 3.762626 0.0017503 0.0227239 strainProAla - strainCtrl
P53208 0.3439459 0.0922005 16.34914 3.730412 0.0017635 0.0228308 strainProAla - strainCtrl
P38875 -0.1514324 0.0407426 16.55760 -3.716807 0.0017817 0.0229429 strainProAla - strainCtrl
Q12096 -0.2208059 0.0594408 16.57659 -3.714719 0.0017867 0.0229429 strainProAla - strainCtrl
P32795 0.0783593 0.0211298 16.72681 3.708465 0.0017871 0.0229429 strainProAla - strainCtrl
P38715 0.1485477 0.0399376 16.42001 3.719495 0.0017935 0.0229605 strainProAla - strainCtrl
P47065 0.4650928 0.1173224 12.21370 3.964227 0.0018175 0.0232028 strainProAla - strainCtrl
P38843 -0.3706867 0.1002766 16.62375 -3.696641 0.0018497 0.0235497 strainProAla - strainCtrl
P17555 -0.0846209 0.0227850 16.12887 -3.713888 0.0018638 0.0236514 strainProAla - strainCtrl
P32471 0.1297766 0.0351460 16.61307 3.692499 0.0018680 0.0236514 strainProAla - strainCtrl
Q03796 -0.4058693 0.1102596 16.86568 -3.681032 0.0018737 0.0236576 strainProAla - strainCtrl
Q05933 -0.2111998 0.0574827 16.94279 -3.674147 0.0018895 0.0237534 strainProAla - strainCtrl
P25605 -0.1164839 0.0315251 16.41065 -3.694964 0.0018916 0.0237534 strainProAla - strainCtrl
P17442 0.1575994 0.0424986 15.97961 3.708348 0.0019120 0.0239448 strainProAla - strainCtrl
Q08230 0.1365181 0.0371008 16.62771 3.679649 0.0019179 0.0239525 strainProAla - strainCtrl
P43633 -0.2780918 0.0745684 15.44757 -3.729350 0.0019255 0.0239525 strainProAla - strainCtrl
P53911 0.4677461 0.1263898 16.05961 3.700823 0.0019284 0.0239525 strainProAla - strainCtrl
P48445 -0.1254409 0.0340277 16.36904 -3.686431 0.0019335 0.0239525 strainProAla - strainCtrl
P53070 -0.2105463 0.0574468 16.75746 -3.665063 0.0019573 0.0241238 strainProAla - strainCtrl
P43601 0.1246446 0.0336489 15.81850 3.704265 0.0019578 0.0241238 strainProAla - strainCtrl
Q03208 -0.1853129 0.0497844 15.31607 -3.722307 0.0019795 0.0243250 strainProAla - strainCtrl
P33413 -0.5182896 0.1400552 15.70942 -3.700610 0.0019933 0.0244300 strainProAla - strainCtrl
P39521 0.1123384 0.0307157 16.70546 3.657360 0.0019988 0.0244324 strainProAla - strainCtrl
Q06106 0.1059575 0.0287470 15.94093 3.685864 0.0020121 0.0245294 strainProAla - strainCtrl
P08004 -0.1342849 0.0367965 16.75410 -3.649393 0.0020251 0.0246232 strainProAla - strainCtrl
P22855 0.1455992 0.0397190 16.29993 3.665730 0.0020331 0.0246550 strainProAla - strainCtrl
Q05924 -0.1440358 0.0393370 16.28396 -3.661590 0.0020540 0.0247890 strainProAla - strainCtrl
P32465 -0.3268493 0.0897687 16.79570 -3.641015 0.0020550 0.0247890 strainProAla - strainCtrl
P06168 -0.1523494 0.0413175 15.60283 -3.687282 0.0020704 0.0249102 strainProAla - strainCtrl
Q06538 -0.2342018 0.0639517 15.99122 -3.662168 0.0021056 0.0252672 strainProAla - strainCtrl
P32600 -0.1754047 0.0475529 15.26358 -3.688626 0.0021332 0.0255051 strainProAla - strainCtrl
P41819 -0.1477992 0.0405982 16.32835 -3.640540 0.0021400 0.0255051 strainProAla - strainCtrl
Q04728 -0.1225435 0.0335224 15.95513 -3.655572 0.0021421 0.0255051 strainProAla - strainCtrl
P38707 -0.0914732 0.0252438 16.54399 -3.623594 0.0021787 0.0258502 strainProAla - strainCtrl
P04821 -0.1588090 0.0430023 14.93635 -3.693034 0.0021838 0.0258502 strainProAla - strainCtrl
Q02883 -0.2505216 0.0680876 15.19903 -3.679400 0.0021879 0.0258502 strainProAla - strainCtrl
Q12308 -0.2333730 0.0647798 16.90671 -3.602561 0.0022130 0.0260799 strainProAla - strainCtrl
P53334 0.3266534 0.0896854 15.77794 3.642213 0.0022386 0.0262979 strainProAla - strainCtrl
P53183 -0.1451155 0.0396870 15.43398 -3.656498 0.0022430 0.0262979 strainProAla - strainCtrl
P53630 -0.3533321 0.0980994 16.61030 -3.601777 0.0022706 0.0265541 strainProAla - strainCtrl
Q06053 -0.1446666 0.0398613 15.68683 -3.629254 0.0023193 0.0270550 strainProAla - strainCtrl
Q12421 0.4015368 0.1088221 14.32647 3.689846 0.0023414 0.0272434 strainProAla - strainCtrl
P00724 -0.2845391 0.0794290 16.50689 -3.582308 0.0023876 0.0277101 strainProAla - strainCtrl
Q08224 0.1977896 0.0551627 16.24234 3.585567 0.0024234 0.0279888 strainProAla - strainCtrl
P22140 -0.2140333 0.0592802 15.63264 -3.610539 0.0024237 0.0279888 strainProAla - strainCtrl
Q03629 -0.0896707 0.0251289 16.62861 -3.568432 0.0024357 0.0280559 strainProAla - strainCtrl
Q04066 -0.1109681 0.0310896 16.25892 -3.569294 0.0025053 0.0287856 strainProAla - strainCtrl
P53893 0.0832596 0.0234725 16.63220 3.547111 0.0025491 0.0291922 strainProAla - strainCtrl
Q03034 -0.1201876 0.0337825 16.32857 -3.557687 0.0025534 0.0291922 strainProAla - strainCtrl
P32656 -0.2151699 0.0603889 16.07259 -3.563069 0.0025782 0.0294027 strainProAla - strainCtrl
P40456 -0.2734198 0.0765996 15.87455 -3.569469 0.0025865 0.0294243 strainProAla - strainCtrl
P40215 -0.1048859 0.0297187 16.86635 -3.529287 0.0026014 0.0294856 strainProAla - strainCtrl
P38149 -0.1408038 0.0389823 14.80844 -3.611994 0.0026094 0.0294856 strainProAla - strainCtrl
P14306 -0.2039095 0.0575087 16.36776 -3.545716 0.0026111 0.0294856 strainProAla - strainCtrl
P08417 -0.0763753 0.0215783 16.45510 -3.539449 0.0026279 0.0296024 strainProAla - strainCtrl
P28778 0.3417449 0.0961774 15.99951 3.553278 0.0026482 0.0297584 strainProAla - strainCtrl
Q06629 0.0808680 0.0228884 16.39105 3.533145 0.0026771 0.0299619 strainProAla - strainCtrl
Q3E841 -0.3865776 0.1090201 16.04576 -3.545928 0.0026794 0.0299619 strainProAla - strainCtrl
P25555 -0.1121691 0.0316535 15.86035 -3.543661 0.0027341 0.0305001 strainProAla - strainCtrl
P32621 -0.0926786 0.0262207 15.75261 -3.534559 0.0028123 0.0312959 strainProAla - strainCtrl
Q05979 -0.1971015 0.0561053 16.25660 -3.513067 0.0028241 0.0313460 strainProAla - strainCtrl
P38009 0.0990549 0.0282567 16.43276 3.505541 0.0028304 0.0313460 strainProAla - strainCtrl
P21951 -0.0769535 0.0218506 15.95336 -3.521809 0.0028409 0.0313870 strainProAla - strainCtrl
Q05031 -0.1693948 0.0486182 16.79819 -3.484188 0.0028822 0.0317659 strainProAla - strainCtrl
Q08561 0.1657867 0.0473310 16.06564 3.502709 0.0029311 0.0322286 strainProAla - strainCtrl
P30657 0.1502597 0.0431276 16.49315 3.484077 0.0029496 0.0323544 strainProAla - strainCtrl
P43592 0.2966718 0.0844904 15.73371 3.511309 0.0029575 0.0323631 strainProAla - strainCtrl
Q06651 0.2647485 0.0757810 16.13103 3.493599 0.0029727 0.0324531 strainProAla - strainCtrl
P32454 0.0771226 0.0222521 16.84925 3.465857 0.0029872 0.0325337 strainProAla - strainCtrl
P40917 -0.3036404 0.0870396 16.15508 -3.488533 0.0029992 0.0325865 strainProAla - strainCtrl
P21182 0.1633555 0.0468282 16.10230 3.488403 0.0030125 0.0326542 strainProAla - strainCtrl
Q12018 0.0731816 0.0209778 16.00262 3.488519 0.0030357 0.0328279 strainProAla - strainCtrl
P06208 -0.1751738 0.0502131 15.79872 -3.488608 0.0030853 0.0332321 strainProAla - strainCtrl
P36521 0.1388045 0.0397841 15.78102 3.488948 0.0030875 0.0332321 strainProAla - strainCtrl
Q12168 -0.1013165 0.0288978 15.27686 -3.506022 0.0031080 0.0333742 strainProAla - strainCtrl
P27515 -0.1738544 0.0503524 16.65799 -3.452754 0.0031159 0.0333818 strainProAla - strainCtrl
P32875 -0.1037271 0.0298835 16.03581 -3.471046 0.0031416 0.0335782 strainProAla - strainCtrl
Q04951 0.3465430 0.0996033 15.66403 3.479231 0.0031812 0.0339226 strainProAla - strainCtrl
P23776 0.1453471 0.0420581 16.06389 3.455861 0.0032370 0.0344379 strainProAla - strainCtrl
Q12122 -0.1321107 0.0382585 15.91727 -3.453105 0.0032932 0.0349553 strainProAla - strainCtrl
P36143 -0.4178032 0.1212944 16.09862 -3.444539 0.0033066 0.0350166 strainProAla - strainCtrl
P49955 0.1157592 0.0337363 16.35357 3.431297 0.0033363 0.0352033 strainProAla - strainCtrl
P32898 0.1028956 0.0299531 16.20210 3.435229 0.0033461 0.0352033 strainProAla - strainCtrl
P47172 -0.5237749 0.1476408 13.60790 -3.547630 0.0033472 0.0352033 strainProAla - strainCtrl
P37020 -0.1757786 0.0509742 15.64350 -3.448387 0.0033988 0.0356638 strainProAla - strainCtrl
P54999 0.2539092 0.0744228 16.51103 3.411713 0.0034389 0.0360032 strainProAla - strainCtrl
P25587 -0.4008800 0.1163220 15.51039 -3.446296 0.0034503 0.0360403 strainProAla - strainCtrl
P00899 -0.0775875 0.0228169 16.65793 -3.400438 0.0034864 0.0363341 strainProAla - strainCtrl
P33330 -0.1729700 0.0501881 15.03764 -3.446438 0.0035866 0.0372943 strainProAla - strainCtrl
P47085 -0.2863272 0.0839957 15.82467 -3.408831 0.0036406 0.0377704 strainProAla - strainCtrl
Q12415 -0.1015658 0.0300195 16.43204 -3.383326 0.0036746 0.0379602 strainProAla - strainCtrl
P00498 -0.1607346 0.0476542 16.74796 -3.372940 0.0036754 0.0379602 strainProAla - strainCtrl
P40157 0.0717960 0.0211659 16.01407 3.392061 0.0037181 0.0383149 strainProAla - strainCtrl
Q99296 -0.3298520 0.0977714 16.51507 -3.373707 0.0037290 0.0383410 strainProAla - strainCtrl
Q04052 0.4957747 0.1421473 13.66963 3.487753 0.0037410 0.0383784 strainProAla - strainCtrl
P14742 -0.1273400 0.0374084 15.57229 -3.404051 0.0037495 0.0383800 strainProAla - strainCtrl
P33310 -0.1699235 0.0502560 16.07264 -3.381161 0.0037883 0.0386915 strainProAla - strainCtrl
Q08723 0.2459156 0.0726142 15.85735 3.386606 0.0038052 0.0387067 strainProAla - strainCtrl
P53104 0.1966843 0.0584074 16.41120 3.367458 0.0038067 0.0387067 strainProAla - strainCtrl
P47143 -0.1175537 0.0342963 14.76062 -3.427597 0.0038163 0.0387190 strainProAla - strainCtrl
Q04119 -0.1185744 0.0349171 15.42617 -3.395883 0.0038576 0.0390515 strainProAla - strainCtrl
Q12143 0.1708050 0.0511082 16.96757 3.342025 0.0038712 0.0391037 strainProAla - strainCtrl
Q12230 -0.0898606 0.0268015 16.36510 -3.352813 0.0039400 0.0397108 strainProAla - strainCtrl
P46947 0.2098357 0.0626638 16.02986 3.348593 0.0040706 0.0409380 strainProAla - strainCtrl
Q04174 -0.3165087 0.0945694 15.77304 -3.346842 0.0041623 0.0417688 strainProAla - strainCtrl
P80428 -0.0973637 0.0286961 14.44982 -3.392922 0.0042047 0.0421022 strainProAla - strainCtrl
P36135 0.2290964 0.0691687 16.50025 3.312137 0.0042573 0.0425118 strainProAla - strainCtrl
P38934 0.0878105 0.0265315 16.55556 3.309668 0.0042641 0.0425118 strainProAla - strainCtrl
P25340 -0.1561526 0.0473629 16.71146 -3.296937 0.0043374 0.0430112 strainProAla - strainCtrl
P00045 -0.4046305 0.1227071 16.68203 -3.297530 0.0043402 0.0430112 strainProAla - strainCtrl
P23059 -0.3428738 0.1035195 16.20707 -3.312167 0.0043423 0.0430112 strainProAla - strainCtrl
Q12339 0.1451584 0.0439932 16.50835 3.299560 0.0043708 0.0432002 strainProAla - strainCtrl
Q04311 -0.1391719 0.0423923 16.62420 -3.282954 0.0044945 0.0443277 strainProAla - strainCtrl
P22353 0.1685393 0.0508862 15.58602 3.312082 0.0045374 0.0446146 strainProAla - strainCtrl
P10961 0.1694003 0.0513904 16.03590 3.296344 0.0045430 0.0446146 strainProAla - strainCtrl
P53080 -0.2529140 0.0770047 16.11817 -3.284396 0.0046330 0.0453770 strainProAla - strainCtrl
Q12461 0.1502788 0.0460076 16.67888 3.266392 0.0046404 0.0453770 strainProAla - strainCtrl
P14680 -0.1324641 0.0398272 14.74946 -3.325971 0.0046983 0.0458455 strainProAla - strainCtrl
P32642 0.2444940 0.0745175 15.68695 3.281029 0.0048064 0.0467960 strainProAla - strainCtrl
Q99278 0.1324404 0.0398738 14.55358 3.321491 0.0048160 0.0467960 strainProAla - strainCtrl
Q08651 -0.3390716 0.1038086 16.02641 -3.266314 0.0048429 0.0469160 strainProAla - strainCtrl
P16861 -0.0872631 0.0264004 14.88362 -3.305367 0.0048488 0.0469160 strainProAla - strainCtrl
Q04697 0.1081717 0.0331156 15.51124 3.266488 0.0050158 0.0484302 strainProAla - strainCtrl
P48813 -0.1622348 0.0501217 16.16758 -3.236822 0.0051060 0.0491977 strainProAla - strainCtrl
P06105 -0.0704031 0.0218048 16.36638 -3.228795 0.0051279 0.0493051 strainProAla - strainCtrl
P53920 0.0677631 0.0210345 16.45748 3.221522 0.0051781 0.0496834 strainProAla - strainCtrl

Volcanoplots

plotVolcano(inferences) + 
  facet_wrap(~contrast) + 
  labs(title = "Non-enriched")

inferences |> 
  filter(adjPval < alpha) |> 
  mutate(DA = sign(logFC) |> as.factor() |> recode("-1"= "down","1" = "up")) |>
  group_by(contrast, DA) |> 
  ggplot(aes(x = contrast)) +
  geom_bar(aes(fill = factor(DA)),
           colour = "black") +
  theme_minimal() + 
  theme(axis.text.x = element_text(angle = 90))

We notice that many proteins are DA at the nominal 5% FDR-level.

Heatmaps

lapply(colnames(L),
                   function(contrast, se, alpha)
                   {
                     sig <- rowData(se)[[contrast]] |> 
                       filter(adjPval < alpha) |> 
                       rownames()
                     if (length(sig) > 2)
                     {
                     quants <- t(scale(t(assay(se[sig,]))))
                     colnames(quants) <- se$sampleId #specific to this dataset to get short colnames
                     rowclushlp <- quants
                     rowclushlp[is.na(rowclushlp)] <- min(quants,na.rm=TRUE) - 2
                     rowclus <- hclust(dist(rowclushlp))
                     annotations <- columnAnnotation(
                       group = se$strain
                       ) #3.
                     set.seed(1234) ## annotation colours are randomly generated by default
                     return(
                       Heatmap(show_row_names = FALSE,
                       quants, 
                       name = "log2 intensity",
                       top_annotation = annotations, 
                       column_title = paste0(contrast, " = 0"),
                       cluster_rows = rowclus
                       )
                     )
                     } else return(ggplot() + theme_minimal() + ggtitle(paste0(contrast, " = 0")))
                   },
                   se = getWithColData(qf, "proteins"),
                   alpha = alpha)
[[1]]


[[2]]


[[3]]

Detail plots

We can explore the data for a protein to validate the statistical inference results. For example, let’s explore the normalised precursor and the summarised protein intensities for the protein with the most significant log2 fold change.

(target_feature <- inferences |> 
   dplyr::slice(which.min(pval)) |> 
   pull(feature)
)
[1] "P31539"
inferences |> 
  filter(feature == target_feature)
                                      logFC        se       df         t
strainCtrl.P31539                -0.4692805 0.0214118 16.97458 -21.91691
strainProAla.P31539               0.2251810 0.0214118 16.97458  10.51668
strainProAla - strainCtrl.P31539  0.6944615 0.0214118 16.97458  32.43359
                                         pval      adjPval
strainCtrl.P31539                6.884499e-14 1.583779e-10
strainProAla.P31539              7.475097e-09 1.018281e-05
strainProAla - strainCtrl.P31539 1.032542e-16 4.745561e-13
                                                  contrast feature
strainCtrl.P31539                               strainCtrl  P31539
strainProAla.P31539                           strainProAla  P31539
strainProAla - strainCtrl.P31539 strainProAla - strainCtrl  P31539

To obtain the required data, we perform a little data manipulation pipeline:

  • We use the QFeatures subsetting functionality to retrieve all data related to and focusing on the precursors_log and proteins sets that contains the peptide ion data used for model fitting.
  • We then convert the data with longForm() for plotting.
  • Finally, we plot the log2 normalised intensities for each sample at the protein and at the peptide level. Since multiple peptides are recorded for the protein, we link peptides across samples using a grey line. Samples are colored according to strain.
qf[target_feature, , c("precursors_log","precursors_norm", "proteins")] |> #1
  longForm(colvars = colnames(colData(qf))) |> #2
  data.frame() |> 
  ggplot() +
  aes(x = sampleId,
      y = value) +
  geom_line(aes(group = rowname), linewidth = 0.1) +
  geom_point(aes(colour = strain)) +
  facet_wrap(~ assay, scales = "free") +
  ggtitle(target_feature) +
  theme_minimal() +
  theme(axis.text.x = element_blank())
Warning: 'experiments' dropped; see 'drops()'
harmonizing input:
  removing 72 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'
Warning: Removed 12 rows containing missing values or values outside the scale range
(`geom_line()`).
Warning: Removed 86 rows containing missing values or values outside the scale range
(`geom_point()`).

qf[target_feature, , c("precursors_log","precursors_norm", "proteins")] |> #1
  longForm(colvars = colnames(colData(qf))) |> #2
  data.frame() |>
  filter(!is.na(value)) %>% 
  {
  ggplot(.) +
  aes(x = strain,
      y = value) +
  geom_boxplot(aes(colour = strain)) +
  facet_wrap(~ assay, scales = "free") +
  geom_jitter(aes(shape = rowname)) +
  scale_shape_manual(values = seq_len(dplyr::n_distinct(.$rowname))) +
  ggtitle(target_feature) +
  theme_minimal() +
  theme(axis.text.x = element_blank()) +
  guides(shape = "none")
  }
harmonizing input:
  removing 72 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'

Compare phospo-precursor level intensities to protein level intensities

We compare the intensities for the top 5 DA phospo-precursors for the first contrast to these of their corresponding protein in the non-enriched assay.

contr = colnames(L)[1]
top5 <- inferencesPTM |> 
  filter(contrast == contr) |> 
  arrange(pval) |> 
  head(n = 5) |> 
  pull(feature)

for (feat in top5)
{
  ptm_data <- qf[,,c("precursorsPTM_norm")] |> 
    longForm(colvars = colnames(colData(qf)), rowvars = "Protein.Group") |>
    data.frame() |> 
    filter(rowname==feat)
  feature_protein <- ptm_data |> 
    pull("Protein.Group") |> 
    unique()
  prot_data <- qf[,,"proteins"]|>
    longForm(colvars = colnames(colData(qf)), rowvars = "Protein.Group") |>
    data.frame() |> 
    filter(Protein.Group==feature_protein) 
  ptm_protein <- rbind(ptm_data, prot_data)
  ylims <- ptm_protein |> 
  group_by(assay) |> 
  summarise(cent = mean(range(value,na.rm=TRUE)), ampl = diff(range(value,na.rm=TRUE))) |> 
  mutate(lower = cent - max(ampl)/2, 
         upper = cent + max(ampl)/2) |> 
  select(-c(cent, ampl))
  
  comparison_plot <- ptm_protein |>
    ggplot() +
    aes(x = sampleId,
        y = value) +
    geom_line(aes(group = rowname), linewidth = 0.1) +
    geom_point(aes(colour = strain)) +
    facet_wrap(~ assay, scales = "free") +
    labs(
      title = paste0(feat," / ", feature_protein),
      subtitle = paste("padj PTM =", 
                       inferencesPTM |> 
                         filter(feature == feat & contrast == contr) |> 
                         pull(adjPval) |> 
                         round(digits = 3))
    ) +
    theme_minimal() +
    theme(axis.text.x = element_blank()) +
    ggh4x::facetted_pos_scales(
    y = list(
      assay == ylims$assay[1] ~ scale_y_continuous(limits = unlist(ylims[1,c("lower","upper")])),
      assay == ylims$assay[2] ~ scale_y_continuous(limits = unlist(ylims[2,c("lower","upper")])),
      assay == ylims$assay[3] ~ scale_y_continuous(limits = unlist(ylims[3,c("lower","upper")]))
    )
    ) 
 print(comparison_plot)
}

#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 11780626 629.2   17413800 930.0         NA  17413800  930
Vcells 35601283 271.7  102851388 784.7      24576 312075668 2381
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 11780619 629.2   17413800 930.0         NA  17413800  930
Vcells 35601304 271.7  102851388 784.7      24576 312075668 2381

We see for multiple top DA phospho-precursors, that the reason for DA seems to be associated with the similar changes in overall protein abundance. Interestingly for other phospho-precursors the abundance of the precursor changes between strains while the abundances at the protein-level remains stable between strains. Hence, there is a stron need to correct the phospho-precursor level fold changes/ abundances for corresponding changes at the protein level.

11.8 Data Modeling of phospho-peptidoform usages

11.8.1 Background

  • Differentially abundant PTMs can arise either from changes in PTM regulation or simply from changes in the abundance of the underlying protein.

  • To distinguish PTM-specific regulation from protein-level changes, we extend the concept of differential usage (DU) to PTMs:

\[ \log_2 DU = \log_2 FC^\text{PTM} - \log_2 FC^\text{protein}, \]

where \(log_2 FC^\text{PTM}\) is the fold change of the modified precursor/PTM and \(log_2 FC^\text{protein}\) is the fold change of the corresponding protein.

  • In other words, differential usage represents the differential abundance (DA) of a PTM after correcting for changes in protein abundance.

  • This metric highlights PTMs whose abundance changes cannot be explained solely by changes in the total protein level, thereby prioritising PTMs that may be under specific regulatory control.

Two experimental designs are commonly used to quantify precursor-level (PTM-level) and protein-level abundances:

  • Paired design: PTM and protein abundances are measured in the same biological replicate (sample).

  • Unpaired design: PTM and protein abundances are measured in independent biological replicates (different samples).

Paired samples

  1. Perform regular data processing at the protein-level:

    • log2-transformation,
    • normalisation and
    • summarisation

  2. Calculate relative log2 transformed abundances at peptidoform level \[y^\text{pep,rel}_i = y^\text{pep}_i - y^\text{prot}_i\]

  3. Perform conventional differential msqrob2 analysis on the relative peptidoform level. \(\rightarrow\) Immediately gives us diferential usages!

  4. Optionally

  1. aggregate relative log2 transformed abundances at peptidoform level to PTM-level
  2. perform a differential msqrob2 analysis at PTM-level
  1. The paired design has the advantage that both metrics are estimated on the same biorepeat/sample, which enables a better estimation of the standard error on the usages.

Unpaired PTM-level and protein samples

This is the default MSstatsTMT approach, which they also use for paired designs?!

  1. Perform regular msqrob2 differential analysis at the protein-level
  2. Perform regular msqrob2 differential analysis at the peptidoform (PTM-level)
  3. Calculate usages

\[ \begin{array}{ccc} \log_2 \widehat{DU} & =& \log_2 \widehat{FC}^\text{PTM} - log_2 \widehat{FC}^\text{protein}\\ SE_\widehat{DU} &=& \sqrt{(SE_\widehat{FC}^{PTM})^2 + (SE_\widehat{FC}^{protein})^2} \end{array} \]

Our study

For this dataset we have phospho-enriched and non-enriched runs on the same biological samples. So we have a paired design!

11.8.2 Paired samples: calculate usages

We can calculate the usages for every precursor ion by subtracting the corresponding log-transformed protein level abundance values from the log2 transformed and normalized precursor ion intensities.

We first develop a function that will extract the corresponding protein level abundance values.

It has following inputs:

  • se: summarised experiment of the log2-transformed and normalized precursor ion
  • seNE: summarised experiment of the log2-transformed, normalized and aggregated protein level abundances.
  • fcol: annotation column with protein name for the precursor ions
  • fcolNE: annotation column with protein name for the protein level abundances
  • matchColsSeToseNE: a vector that matches the columns of seNE to these in se.

The function

  1. Initiates the matrix with log2 tranformed correction factors at NA.
  2. Matches the rows of se with these of seNE using the annotation columns
  3. Extracts the protein abundance values for the precursors from the matching rows and columns in the protein level assay.
calculate_usage_nfLog <- function(se, 
                               seNE, 
                               fcol = "Protein.Group", 
                               fcolNE = "Protein.Group", 
                               matchColsSeToseNE = 1:ncol(se)
                               )
{
    nf <- assay(se); nf[,] <- NA #1. 
    matchSeRowsToSeNERows <- match(
      rowData(se)[[fcol]], 
      rowData(seNE)[[fcolNE]]) #2.
    idsMatch <- which(!is.na(matchSeRowsToSeNERows))
    nf[idsMatch, ] <- assay(seNE)[matchSeRowsToSeNERows[idsMatch], matchColsSeToseNE] #3.
    return(nf)
}

Here we

  1. Match the samples of the phosho enriched samples to these of the non-enriched assay.
  2. Calculate the correction factors
  3. Make a new assay with usages by sweeping out the log2 protein abundances from from the log2 precursor abundances.
matchedSamps <- match(
  getWithColData(qf,"precursorsPTM_norm")$sampleId,
  getWithColData(qf,"proteins")$sampleId
  ) ## 1.

nfLog <- calculate_usage_nfLog(qf[["precursorsPTM_norm"]], 
                               qf[["proteins"]], 
                               fcol= "Protein.Group", 
                               fcolNE = "Protein.Group", 
                               matchColsSeToseNE = matchedSamps) ## 2.

qf <- sweep( #4. Subtract log2 norm factor elementwise (MARGIN = 1:2)
      qf,
      MARGIN = 1:2,
      STATS = nfLog,
      i = "precursorsPTM_norm",
      name = "precursorsPTM_usage"
      ) ## 3.

We only keep precursors for which the usage can be calculated in at least 6 samples.

n <- ncol(qf[["precursorsPTM_usage"]])
qf <- filterNA(qf, i = "precursorsPTM_usage", pNA = (n - nObs) / n)

We assess the distribution of the usages.

qf[, , "precursorsPTM_usage"] |> #1.
  longForm(colvars = colnames(colData(qf))) |>  #2. 
  data.frame() |> 
  filter(!is.na(value)) |>
  ggplot() + #3.
  aes(x = value,
      colour = strain,
      group = colname) +
  geom_density() +
  labs(subtitle = "Usage") +
  theme_minimal()
harmonizing input:
  removing 126 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'

#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 11796180 630.0   17413800 930.0         NA  17413800  930
Vcells 44063861 336.2  102851388 784.7      24576 312075668 2381
           used  (Mb) gc trigger  (Mb) limit (Mb)  max used (Mb)
Ncells 11796182 630.0   17413800 930.0         NA  17413800  930
Vcells 44063897 336.2  102851388 784.7      24576 312075668 2381

11.8.3 Model estimation

Again we can estimate the same model but now for the usages.

qf <- msqrob(
  qf,
  i = "precursorsPTM_usage",
  formula = model,
  robust = TRUE,
  overwrite = TRUE)

We enabled M-estimation (robust = TRUE) for improved robustness against outliers.

#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 12492451 667.2   22675350 1211.0         NA  17413800  930
Vcells 46024228 351.2  102851388  784.7      24576 312075668 2381
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 12492453 667.2   22675350 1211.0         NA  17413800  930
Vcells 46024264 351.2  102851388  784.7      24576 312075668 2381

11.8.4 Inference

Contrasts remain the same. We assess the contrast for each precursor.

qf <- hypothesisTest(qf, i = "precursorsPTM_usage", contrast = L, overwrite = TRUE)

We extract the results table from the proteins summarised experiment in the qf object.

inferencesUsage <- 
  msqrobCollect(qf[["precursorsPTM_usage"]], L)
#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 12492529 667.2   22675350 1211.0         NA  22675350 1211
Vcells 46830673 357.3  102851388  784.7      24576 312075668 2381
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 12492528 667.2   22675350 1211.0         NA  22675350 1211
Vcells 46830704 357.3  102851388  784.7      24576 312075668 2381

11.8.5 Report results

We report the results using a results table, volcano plots and heatmaps.

Results table

for (j in colnames(L)) {

  inference <- inferencesUsage |> 
    dplyr::filter(adjPval < alpha & contrast == j)

  cat("**Median - Contrast:**", j, "= 0 (", nrow(inference),
      "significant proteins)\n\n")

  cat('<div style="max-height:300px; overflow-y:auto;">')

  print(
    kable(
      inference |>
        dplyr::arrange(pval) |>
        dplyr::relocate(feature),
      row.names = FALSE
    )
  )

  cat('</div>')

  cat("\n\n\n---\n\n")
}

Median - Contrast: strainCtrl = 0 ( 36 significant proteins)

feature logFC se df t pval adjPval contrast
GQVVSEEQRPGT(UniMod:21)PLFTVK3 -1.8482677 0.1068439 15.836972 -17.298767 0.00e+00 0.0000003 strainCtrl
ETVES(UniMod:21)ESSQTALSK2 -0.9952475 0.0783042 16.197308 -12.710008 0.00e+00 0.0000119 strainCtrl
RAT(UniMod:21)YAGFLLADPK3 -2.7741769 0.2279059 11.950433 -12.172465 0.00e+00 0.0004465 strainCtrl
RGQVVSEEQRPGT(UniMod:21)PLFTVK3 -1.4603261 0.1402037 13.802960 -10.415744 1.00e-07 0.0004999 strainCtrl
ETVESESS(UniMod:21)QTALSK2 -1.9360818 0.1621744 10.909544 -11.938270 1.00e-07 0.0008275 strainCtrl
GSSS(UniMod:21)LYTLVINDAGK2 1.1442699 0.1346803 16.943653 8.496195 2.00e-07 0.0008472 strainCtrl
IS(UniMod:21)PPVVAYR2 -1.8883643 0.2283225 15.390528 -8.270603 5.00e-07 0.0017963 strainCtrl
GSS(UniMod:21)SLYTLVINDAGK3 1.0582663 0.1296797 15.395842 8.160619 6.00e-07 0.0017963 strainCtrl
LVQIT(UniMod:21)PDGK2 0.7593899 0.0947649 15.893705 8.013408 6.00e-07 0.0017963 strainCtrl
T(UniMod:21)GAAPQTTFNVAPNSTPIVSTAATGLQHK4 -1.0891227 0.1291096 14.475080 -8.435648 6.00e-07 0.0017963 strainCtrl
T(UniMod:21)GAAPQTTFNVAPNSTPIVSTAATGLQHK3 -0.6099364 0.0764334 15.165634 -7.979970 8.00e-07 0.0023318 strainCtrl
LYDLLGVS(UniMod:21)PSANEQELK2 -1.0772610 0.1437330 15.383013 -7.494876 1.60e-06 0.0042276 strainCtrl
VSSFNHS(UniMod:21)SSGMTSSDSLASEEVPSNK3 4.2615011 0.2899826 6.774257 14.695715 2.20e-06 0.0052068 strainCtrl
GSEIVIAT(UniMod:21)PGR2 -0.9925106 0.1377531 15.595807 -7.204996 2.40e-06 0.0054067 strainCtrl
DLARENS(UniMod:21)LETTFSSVNTR3 -0.7759475 0.1127871 16.683016 -6.879753 3.00e-06 0.0061279 strainCtrl
RGQVVSEEQRPGT(UniMod:21)PLFTVK4 -1.6691797 0.1777611 9.684021 -9.390016 3.60e-06 0.0069362 strainCtrl
DPIPSDPS(UniMod:21)ER2 -0.6518697 0.0984945 16.943653 -6.618339 4.40e-06 0.0076468 strainCtrl
RNT(UniMod:21)AIPTK2 1.0023303 0.1484774 15.995194 6.750728 4.70e-06 0.0076468 strainCtrl
NGLNELASS(UniMod:21)ATK2 0.8900045 0.1335761 16.492505 6.662903 4.70e-06 0.0076468 strainCtrl
NNEGSSNMNMNRNDLDDVS(UniMod:21)HYEMK3 3.6974238 0.4017140 8.943653 9.204121 7.40e-06 0.0115386 strainCtrl
EIVFAS(UniMod:21)PPRK2 -0.8539713 0.1367768 16.248668 -6.243540 1.09e-05 0.0161016 strainCtrl
M(UniMod:35)TEAGS(UniMod:21)LDLIDDAGENS(UniMod:21)DLEDRIDNSLPGSQR4 -2.8200375 0.2645438 7.206195 -10.660002 1.14e-05 0.0161016 strainCtrl
AES(UniMod:21)DAVAEANDIDD2 -0.5139705 0.0847688 16.815572 -6.063202 1.33e-05 0.0179509 strainCtrl
SDEEHTFENADAGAS(UniMod:21)ATYPM(UniMod:35)QC(UniMod:4)SALR3 3.0092552 0.2748446 6.811645 10.948935 1.43e-05 0.0185201 strainCtrl
NTTATPIQFADFNT(UniMod:21)SSNNLTPSQSVTNSGTQVAHGNNMEVDR4 3.1647276 0.2445506 5.787366 12.940991 1.72e-05 0.0198799 strainCtrl
RPTYSSS(UniMod:21)KSNNWTPGEASDTPPLPPHATPK4 -3.0060290 0.3923709 9.943653 -7.661193 1.77e-05 0.0198799 strainCtrl
MQNIAPS(UniMod:21)RSSESTPTSGPPLLPPR3 3.8203404 0.3076323 5.943653 12.418528 1.78e-05 0.0198799 strainCtrl
ETNNNLSNM(UniMod:35)NSS(UniMod:21)PAQNPK3 -3.5348867 0.2182677 4.943653 -16.195190 1.79e-05 0.0198799 strainCtrl
(UniMod:27)EYS(UniMod:21)NVDQYGHQR3 2.0973159 0.3162318 12.075387 6.632210 2.35e-05 0.0251931 strainCtrl
(UniMod:27)EKSPT(UniMod:21)PQT(UniMod:21)STASLSSVTK3 3.2079677 0.4670287 10.645516 6.868888 3.18e-05 0.0330043 strainCtrl
(UniMod:27)EAVVDDGS(UniMod:21)ENAFGIPEFTR2 1.2763621 0.2202474 15.015793 5.795128 3.52e-05 0.0352965 strainCtrl
NEHS(UniMod:21)NLAVEDNIPEEEPK3 -0.5980074 0.1085922 16.254505 -5.506911 4.52e-05 0.0434145 strainCtrl
SNNWTPGEAS(UniMod:21)DT(UniMod:21)PPLPPHATPK3 4.8956957 0.4653275 5.943653 10.520967 4.61e-05 0.0434145 strainCtrl
EQATDPILTATGPEDM(UniMod:35)QQSAS(UniMod:21)IVGPSSNANPVTATAATENQPK4 -3.4580659 0.5320764 10.825838 -6.499191 4.78e-05 0.0436994 strainCtrl
MSES(UniMod:21)PMFAANGMPK2 2.6889135 0.4182244 10.934164 6.429356 5.02e-05 0.0445779 strainCtrl
RAT(UniMod:21)YAGFLLADPK2 -2.3458417 0.3564194 10.268941 -6.581690 5.49e-05 0.0474368 strainCtrl

Median - Contrast: strainProAla = 0 ( 58 significant proteins)

feature logFC se df t pval adjPval contrast
(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2 2.0007583 0.0807470 15.201633 24.778123 0.00e+00 0.0000000 strainProAla
S(UniMod:21)DSEVNQEAKPEVK2 2.0851157 0.1437238 16.193635 14.507793 0.00e+00 0.0000016 strainProAla
S(UniMod:21)DSEVNQEAKPEVK3 2.3155078 0.1874540 13.858093 12.352405 0.00e+00 0.0000656 strainProAla
LYDLLGVS(UniMod:21)PSANEQELK2 -1.5736386 0.1405310 15.383013 -11.197804 0.00e+00 0.0000656 strainProAla
AINS(UniMod:21)PIIR2 1.1395342 0.1173179 16.074020 9.713220 0.00e+00 0.0002442 strainProAla
RNT(UniMod:21)AIPTK2 1.4055365 0.1517256 15.995194 9.263673 1.00e-07 0.0004074 strainProAla
NNEES(UniMod:21)REEATAALK3 -0.8573307 0.0929604 15.486627 -9.222534 1.00e-07 0.0004864 strainProAla
INMGGGLFLSPEDIT(UniMod:21)KIASGLIS(UniMod:21)PVLGEVSER4 -5.0261755 0.3832550 8.914191 -13.114442 4.00e-07 0.0015288 strainProAla
APVAS(UniMod:21)PRPAAT(UniMod:21)PNLSK3 -0.7254025 0.0903886 16.348450 -8.025377 5.00e-07 0.0015776 strainProAla
HSRPLS(UniMod:21)IS(UniMod:21)ST(UniMod:21)TPLDLQR3 5.3704830 0.2719755 5.943653 19.746205 1.20e-06 0.0037231 strainProAla
GSSS(UniMod:21)LYTLVINDAGK2 0.9759734 0.1346803 16.943653 7.246595 1.40e-06 0.0039199 strainProAla
VSSFNHS(UniMod:21)SSGMTSSDSLASEEVPSNK3 4.3675411 0.2982378 6.774257 14.644494 2.20e-06 0.0057447 strainProAla
SDEEHTFENADAGAS(UniMod:21)ATYPM(UniMod:35)QC(UniMod:4)SALR3 3.3647961 0.2393724 6.811645 14.056741 2.80e-06 0.0066184 strainProAla
(UniMod:1)TT(UniMod:21)ASSSASQLQQR2 1.0472439 0.1505212 15.863188 6.957450 3.40e-06 0.0074838 strainProAla
GSS(UniMod:21)SLYTLVINDAGK3 0.8802596 0.1288067 15.395842 6.833958 4.90e-06 0.0092999 strainProAla
M(UniMod:35)TEAGS(UniMod:21)LDLIDDAGENS(UniMod:21)DLEDRIDNSLPGSQR4 -2.9411947 0.2453088 7.206195 -11.989765 5.10e-06 0.0092999 strainProAla
T(UniMod:21)GAAPQTTFNVAPNSTPIVSTAATGLQHK4 -0.9008766 0.1284796 14.475080 -7.011823 5.10e-06 0.0092999 strainProAla
APVAS(UniMod:21)PRPAAT(UniMod:21)PNLSK2 -0.7488539 0.1107006 15.377494 -6.764679 5.60e-06 0.0094000 strainProAla
T(UniMod:21)GAAPQTTFNVAPNSTPIVSTAATGLQHK3 -0.5462570 0.0804674 15.165634 -6.788552 5.80e-06 0.0094000 strainProAla
LVQIT(UniMod:21)PDGK2 0.6109495 0.0934934 15.893705 6.534683 7.10e-06 0.0106696 strainProAla
SST(UniMod:21)EHMLISPGR3 3.4504443 0.1934187 5.175661 17.839250 7.60e-06 0.0106696 strainProAla
NNEGSSNMNMNRNDLDDVS(UniMod:21)HYEMK3 3.6130811 0.3935977 8.943653 9.179630 7.60e-06 0.0106696 strainProAla
TPTPTPPVVAEPAIS(UniMod:21)PRPVSQR3 -0.4663034 0.0739539 16.775678 -6.305322 8.40e-06 0.0109398 strainProAla
MQNIAPS(UniMod:21)RSSESTPTSGPPLLPPR3 3.9673353 0.2808286 5.943653 14.127249 8.50e-06 0.0109398 strainProAla
QAGS(UniMod:21)PSSTVSSLAK2 0.9815689 0.1497656 15.013679 6.554036 9.10e-06 0.0112600 strainProAla
MSEES(UniMod:21)LFESSPQK2 -3.8347949 0.6096303 16.015957 -6.290361 1.07e-05 0.0127550 strainProAla
S(UniMod:21)DS(UniMod:21)EVNQEAKPEVK3 2.0185320 0.2384652 9.073396 8.464683 1.34e-05 0.0153179 strainProAla
AALDEPDLNAVMT(UniMod:21)NEDSIDLNASEVDHSSR3 2.6824678 0.3278499 9.097476 8.181999 1.73e-05 0.0191485 strainProAla
LRDLY(UniMod:21)LEQTESDSDFDEGSQANGSVPPLK3 -4.9926570 0.6690994 10.210581 -7.461756 1.92e-05 0.0204825 strainProAla
M(UniMod:35)TDPHLNTPQVSTS(UniMod:21)PTFER3 -3.1318378 0.4611515 11.721168 -6.791342 2.17e-05 0.0224006 strainProAla
S(UniMod:21)S(UniMod:21)IPAGTDPGSC(UniMod:4)GANFK3 -3.7429438 0.3652596 6.777048 -10.247352 2.27e-05 0.0226635 strainProAla
MS(UniMod:21)DSEVNQEAKPEVK3 2.6987332 0.4358959 13.988217 6.191234 2.36e-05 0.0227736 strainProAla
TGAAPQTTFNVAPNSTPIVSTAAT(UniMod:21)GLQHK3 -1.0815174 0.1731465 13.615245 -6.246256 2.43e-05 0.0227736 strainProAla
APVAS(UniMod:21)PRPAATPNLSK2 -0.5787964 0.0983087 14.876090 -5.887539 3.09e-05 0.0280994 strainProAla
GT(UniMod:21)QSQYESGLTSNK2 -0.5976299 0.1054515 15.850881 -5.667344 3.63e-05 0.0303160 strainProAla
SNNWTPGEAS(UniMod:21)DT(UniMod:21)PPLPPHATPK3 5.5877970 0.5097408 5.943653 10.962037 3.65e-05 0.0303160 strainProAla
MS(UniMod:21)DSEVNQEAKPEVK2 3.1037347 0.5412374 15.205809 5.734516 3.75e-05 0.0303160 strainProAla
LVPADS(UniMod:21)DEEEYETSHISDTPVSLSSANDR4 4.8949772 0.2853207 4.328816 17.156053 3.81e-05 0.0303160 strainProAla
MSES(UniMod:21)PMFAANGMPK2 2.7744928 0.4184729 10.934164 6.630041 3.82e-05 0.0303160 strainProAla
DIPGDEAYNS(UniMod:21)DDIM(UniMod:35)APLREK3 -3.9371653 0.3730761 5.943653 -10.553250 4.53e-05 0.0341862 strainProAla
S(UniMod:21)SSVYM(UniMod:35)DSEPAVNK2 -4.3428436 0.4110750 5.937846 -10.564601 4.53e-05 0.0341862 strainProAla
NTTATPIQFADFNT(UniMod:21)SSNNLTPSQSVTNSGTQVAHGNNMEVDR4 3.6741388 0.3411907 5.787366 10.768578 4.80e-05 0.0354081 strainProAla
SFGSGLKLKITDS(UniMod:21)NLENMEDVEAK3 3.1851425 0.2997127 5.762111 10.627317 5.32e-05 0.0363446 strainProAla
ETNNNLSNM(UniMod:35)NSS(UniMod:21)PAQNPK3 -2.8210861 0.2182677 4.943653 -12.924890 5.34e-05 0.0363446 strainProAla
TGLGTPNQQVSVPNIVS(UniMod:21)PK3 3.3709742 0.4316564 7.943653 7.809393 5.40e-05 0.0363446 strainProAla
IS(UniMod:21)M(UniMod:35)SPNRELLK3 -3.2032646 0.3147309 5.943653 -10.177790 5.56e-05 0.0363446 strainProAla
MKT(UniMod:21)TDTYPSLPK2 0.9145450 0.1545666 12.721892 5.916836 5.57e-05 0.0363446 strainProAla
(UniMod:27)ES(UniMod:21)VHNHSDGDDVDIPM(UniMod:35)DDSPVNEEAR4 2.8977437 0.2274719 4.943653 12.738910 5.72e-05 0.0363446 strainProAla
TVDPAS(UniMod:21)APNHSPEIDNLDDLVVLK4 2.2915891 0.3857961 12.506918 5.939896 5.75e-05 0.0363446 strainProAla
DASM(UniMod:35)QHDLIPLNSSDDYHNDASVTAATSNNFLSS(UniMod:21)PSSSDSLSK4 -2.9980051 0.4497650 9.838373 -6.665715 6.05e-05 0.0367797 strainProAla
LGLPHGS(UniMod:21)GPT(UniMod:21)SVYNNK2 -2.2257780 0.2534438 6.775273 -8.782137 6.06e-05 0.0367797 strainProAla
M(UniMod:35)KVEVDS(UniMod:21)FSGAK3 -0.9864823 0.1862873 16.781519 -5.295490 6.19e-05 0.0368632 strainProAla
(UniMod:28)QAGS(UniMod:21)PSSTVSSLAK2 1.3099345 0.2442919 15.672697 5.362169 6.82e-05 0.0398108 strainProAla
ALLELLDDS(UniMod:21)PVTPGETR3 1.5166606 0.2182537 8.891094 6.949071 7.10e-05 0.0407351 strainProAla
ITIDS(UniMod:21)PYLVC(UniMod:4)TEGEK2 0.5405267 0.1037362 16.500582 5.210591 7.77e-05 0.0437645 strainProAla
NVSTEHQNQSHPVNS(UniMod:21)ESHLIAEPNILTPYVPSESSQTPVMK4 3.1528234 0.2676530 4.943653 11.779517 8.34e-05 0.0461112 strainProAla
TT(UniMod:21)PSFVAFTDTER2 0.5073982 0.0989436 16.523363 5.128158 9.16e-05 0.0492623 strainProAla
RPLS(UniMod:21)QPTTSIGFPALEK3 -0.5812232 0.1112470 15.508035 -5.224620 9.23e-05 0.0492623 strainProAla

Median - Contrast: strainProAla - strainCtrl = 0 ( 115 significant proteins)

feature logFC se df t pval adjPval contrast
(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2 2.0718815 0.0818991 15.201633 25.297983 0.0000000 0.0000000 strainProAla - strainCtrl
GQVVSEEQRPGT(UniMod:21)PLFTVK3 2.3554048 0.1042088 15.836972 22.602750 0.0000000 0.0000000 strainProAla - strainCtrl
ETVES(UniMod:21)ESSQTALSK2 1.1121529 0.0762780 16.197308 14.580258 0.0000000 0.0000010 strainProAla - strainCtrl
S(UniMod:21)DSEVNQEAKPEVK2 1.8593632 0.1469425 16.193635 12.653676 0.0000000 0.0000063 strainProAla - strainCtrl
RGQVVSEEQRPGT(UniMod:21)PLFTVK3 1.8829844 0.1426789 13.802960 13.197357 0.0000000 0.0000200 strainProAla - strainCtrl
AINS(UniMod:21)PIIR2 1.2208742 0.1146020 16.074020 10.653168 0.0000000 0.0000481 strainProAla - strainCtrl
RAT(UniMod:21)YAGFLLADPK3 3.0804606 0.2239632 11.950433 13.754318 0.0000000 0.0000481 strainProAla - strainCtrl
IS(UniMod:21)PPVVAYR2 2.3977791 0.2279889 15.390528 10.517085 0.0000000 0.0000766 strainProAla - strainCtrl
EIVFAS(UniMod:21)PPRK2 1.3240693 0.1377710 16.248668 9.610654 0.0000000 0.0001395 strainProAla - strainCtrl
S(UniMod:21)DSEVNQEAKPEVK3 1.8834481 0.1763438 13.858093 10.680546 0.0000000 0.0001395 strainProAla - strainCtrl
ETVESESS(UniMod:21)QTALSK2 2.0626558 0.1644077 10.909544 12.545978 0.0000001 0.0002239 strainProAla - strainCtrl
(UniMod:1)TT(UniMod:21)ASSSASQLQQR2 1.4414307 0.1585706 15.863188 9.090148 0.0000001 0.0002802 strainProAla - strainCtrl
GSEIVIAT(UniMod:21)PGR2 1.2009457 0.1377531 15.595807 8.718102 0.0000002 0.0005012 strainProAla - strainCtrl
ASYPLT(UniMod:21)PR2 1.1063106 0.1280723 15.749328 8.638172 0.0000002 0.0005012 strainProAla - strainCtrl
RGQVVSEEQRPGT(UniMod:21)PLFTVK4 2.1765772 0.1773476 9.684021 12.272944 0.0000003 0.0006465 strainProAla - strainCtrl
NAVSTKPTPPPAPEASAES(UniMod:21)GLSS(UniMod:21)K3 1.1073904 0.1323121 15.768443 8.369535 0.0000003 0.0006465 strainProAla - strainCtrl
(UniMod:1)SS(UniMod:21)AITALTPNQVNDELNK2 0.7708770 0.0935191 16.110768 8.242990 0.0000004 0.0006465 strainProAla - strainCtrl
INMGGGLFLSPEDIT(UniMod:21)KIASGLIS(UniMod:21)PVLGEVSER4 -4.7276674 0.3791225 8.914191 -12.470026 0.0000006 0.0010360 strainProAla - strainCtrl
PTPPPAPEASAESGLSS(UniMod:21)K3 0.5702916 0.0759555 16.140373 7.508234 0.0000012 0.0019177 strainProAla - strainCtrl
EIVFAS(UniMod:21)PPR2 1.3149020 0.1707884 14.976598 7.699012 0.0000014 0.0021388 strainProAla - strainCtrl
HSRPLS(UniMod:21)IS(UniMod:21)ST(UniMod:21)TPLDLQR3 5.0425550 0.2719755 5.943653 18.540478 0.0000017 0.0025489 strainProAla - strainCtrl
NGLNELASS(UniMod:21)ATK2 -0.9456091 0.1340302 16.492505 -7.055195 0.0000023 0.0032074 strainProAla - strainCtrl
NILPQRT(UniMod:21)PRS(UniMod:21)AAK3 -0.8869830 0.1212636 14.811779 -7.314502 0.0000027 0.0036620 strainProAla - strainCtrl
DPIPSDPS(UniMod:21)ER2 0.6749551 0.0984945 16.943653 6.852721 0.0000029 0.0036620 strainProAla - strainCtrl
SAES(UniMod:21)EFTDK2 0.5656277 0.0828192 16.227194 6.829669 0.0000038 0.0046201 strainProAla - strainCtrl
ALLELLDDSPVT(UniMod:21)PGETR2 2.8678276 0.2883992 8.943653 9.943953 0.0000039 0.0046504 strainProAla - strainCtrl
QAGS(UniMod:21)PSSTVSSLAK2 1.0062638 0.1440249 15.013679 6.986737 0.0000044 0.0049618 strainProAla - strainCtrl
PTPPPAPEASAESGLSS(UniMod:21)K2 0.6803107 0.0951277 13.770331 7.151554 0.0000054 0.0059384 strainProAla - strainCtrl
PYTEES(UniMod:21)E1 2.1895001 0.3054818 13.618399 7.167367 0.0000056 0.0059571 strainProAla - strainCtrl
TGLGTPNQQVSVPNIVS(UniMod:21)PK3 3.4515710 0.3263016 7.943653 10.577856 0.0000059 0.0060265 strainProAla - strainCtrl
NAVSTKPTPPPAPEASAESGLSS(UniMod:21)K3 0.6317515 0.0973985 15.626658 6.486255 0.0000084 0.0081367 strainProAla - strainCtrl
RAT(UniMod:21)YAGFLLADPK2 2.8487272 0.3494948 10.268941 8.150986 0.0000085 0.0081367 strainProAla - strainCtrl
ENSTIQSSS(UniMod:21)SSNLR2 0.6529945 0.0955381 13.762171 6.834912 0.0000089 0.0082913 strainProAla - strainCtrl
(UniMod:1)SS(UniMod:21)AITALTPNQVNDELNK3 0.6416068 0.1043362 16.943653 6.149420 0.0000109 0.0098244 strainProAla - strainCtrl
NS(UniMod:21)PLAPIK1 -0.6134114 0.0990469 16.049002 -6.193139 0.0000127 0.0111775 strainProAla - strainCtrl
SST(UniMod:21)EHMLISPGR3 3.8233557 0.2460098 5.175661 15.541475 0.0000153 0.0129828 strainProAla - strainCtrl
DYGDAFEGIENTSLS(UniMod:21)PK2 0.5206040 0.0856060 16.048536 6.081396 0.0000157 0.0129828 strainProAla - strainCtrl
KIEENSNSPFNPLLS(UniMod:21)GEK3 -0.6993245 0.1143339 15.727959 -6.116512 0.0000160 0.0129828 strainProAla - strainCtrl
(UniMod:28)QAGS(UniMod:21)PSSTVSSLAK2 1.5409672 0.2540068 15.672697 6.066638 0.0000179 0.0140883 strainProAla - strainCtrl
RLSSVVTTS(UniMod:21)PDK2 -0.5540824 0.0905204 15.152310 -6.121078 0.0000187 0.0144000 strainProAla - strainCtrl
RPTYSSS(UniMod:21)KSNNWTPGEASDTPPLPPHATPK4 2.9668323 0.3923709 9.943653 7.561296 0.0000199 0.0149003 strainProAla - strainCtrl
AQHESSS(UniMod:21)PVLC(UniMod:4)TR3 0.8735449 0.1394756 14.042826 6.263065 0.0000205 0.0150314 strainProAla - strainCtrl
SGLPEPNSQIVS(UniMod:21)PELAK2 -0.6052133 0.1036982 16.421202 -5.836293 0.0000228 0.0159776 strainProAla - strainCtrl
DSTNEFVGS(UniMod:21)PSLTSPQYIPS(UniMod:21)PLSSTK3 1.7549233 0.2910847 14.943653 6.028909 0.0000235 0.0159776 strainProAla - strainCtrl
(UniMod:27)ES(UniMod:21)VHNHSDGDDVDIPM(UniMod:35)DDSPVNEEAR4 3.4755760 0.2274719 4.943653 15.279146 0.0000237 0.0159776 strainProAla - strainCtrl
S(UniMod:21)FELC(UniMod:4)EDR2 0.9103099 0.1567568 16.445756 5.807150 0.0000240 0.0159776 strainProAla - strainCtrl
SQSNGDEEDS(UniMod:21)ILK2 0.5599062 0.0975505 16.937017 5.739653 0.0000244 0.0159776 strainProAla - strainCtrl
SDGKVS(UniMod:21)PEVVYVAEK3 0.5275550 0.0923148 15.874303 5.714737 0.0000329 0.0208825 strainProAla - strainCtrl
QASAAVS(UniMod:21)EK2 -0.7324025 0.1295463 16.332162 -5.653595 0.0000333 0.0208825 strainProAla - strainCtrl
NFHAEVSTPQVLS(UniMod:21)AKK3 -0.5537069 0.1000574 16.470690 -5.533891 0.0000408 0.0251310 strainProAla - strainCtrl
DKT(UniMod:21)SSDDLLNWLQSR3 0.6639109 0.1188601 15.901911 5.585651 0.0000419 0.0253017 strainProAla - strainCtrl
IRS(UniMod:21)EPTLNASSSDHK3 0.6092121 0.1109014 16.476516 5.493279 0.0000442 0.0261674 strainProAla - strainCtrl
RGT(UniMod:21)IATLDDSSYSIDGGK3 0.9540220 0.1661297 14.086101 5.742635 0.0000497 0.0279565 strainProAla - strainCtrl
TLSLIQSYS(UniMod:21)LLDKPDEAIEK3 1.2434008 0.2059821 12.434757 6.036452 0.0000506 0.0279565 strainProAla - strainCtrl
S(UniMod:21)SVATTASTESSEQGPK2 1.4592232 0.2423153 12.452816 6.022003 0.0000514 0.0279565 strainProAla - strainCtrl
VVVNT(UniMod:21)PREPVR3 -0.8347893 0.1509717 15.444442 -5.529441 0.0000520 0.0279565 strainProAla - strainCtrl
SDT(UniMod:21)PLLYR2 1.1425875 0.2035850 14.704306 5.612335 0.0000533 0.0279565 strainProAla - strainCtrl
ALLELLDDS(UniMod:21)PVTPGETR3 1.4626482 0.2035628 8.891094 7.185245 0.0000550 0.0279565 strainProAla - strainCtrl
KPPVTT(UniMod:21)PR2 -0.6430105 0.1203641 16.891322 -5.342209 0.0000551 0.0279565 strainProAla - strainCtrl
QSAVT(UniMod:21)PNQS(UniMod:21)GTPTPSASTTSLTSLNEK4 0.9245268 0.1311385 9.131197 7.050004 0.0000557 0.0279565 strainProAla - strainCtrl
QELNKLS(UniMod:21)PEK2 -0.5693319 0.1060106 16.550376 -5.370518 0.0000557 0.0279565 strainProAla - strainCtrl
(UniMod:27)EKSPT(UniMod:21)PQT(UniMod:21)STASLSSVTK3 -3.0321531 0.4712402 10.645516 -6.434411 0.0000563 0.0279565 strainProAla - strainCtrl
KDS(UniMod:21)PSFLPGQQR3 0.5833984 0.1081128 16.132497 5.396200 0.0000577 0.0281767 strainProAla - strainCtrl
DNNLDNT(UniMod:21)YLNGK2 -0.4940556 0.0915549 16.062031 -5.396276 0.0000586 0.0281767 strainProAla - strainCtrl
NILPQRT(UniMod:21)PRS(UniMod:21)AAK2 -1.1804792 0.2104377 14.136054 -5.609638 0.0000621 0.0293828 strainProAla - strainCtrl
QET(UniMod:21)LTESLK2 0.5411621 0.1016681 16.094071 5.322831 0.0000673 0.0313869 strainProAla - strainCtrl
DFS(UniMod:21)PVHK2 -1.1468873 0.2103519 14.864181 -5.452233 0.0000690 0.0316679 strainProAla - strainCtrl
AC(UniMod:4)VVYGGS(UniMod:21)PIGNQLR2 0.6400190 0.1210600 15.907293 5.286790 0.0000752 0.0335204 strainProAla - strainCtrl
VNS(UniMod:21)SSTIR2 0.4916219 0.0945035 16.766385 5.202157 0.0000752 0.0335204 strainProAla - strainCtrl
SQS(UniMod:21)NGDEEDSILK2 1.1255279 0.2108794 15.352211 5.337306 0.0000767 0.0335962 strainProAla - strainCtrl
EGPSS(UniMod:21)PASILPAK2 -0.5337460 0.1032171 16.943653 -5.171101 0.0000775 0.0335962 strainProAla - strainCtrl
TLTPQNKQS(UniMod:21)PANTK3 -0.5488952 0.1044576 15.907295 -5.254715 0.0000801 0.0339015 strainProAla - strainCtrl
MS(UniMod:21)DSEVNQEAKPEVK3 2.2718231 0.4141013 13.988217 5.486153 0.0000804 0.0339015 strainProAla - strainCtrl
WQS(UniMod:21)EAEDQTEAEIIADR3 1.0562360 0.1792142 11.603818 5.893706 0.0000839 0.0348826 strainProAla - strainCtrl
NS(UniMod:21)PLAPIK2 -0.5575666 0.1053512 15.012401 -5.292457 0.0000901 0.0365914 strainProAla - strainCtrl
TSS(UniMod:21)DLGIFGHR2 0.5781662 0.1089579 14.848939 5.306328 0.0000910 0.0365914 strainProAla - strainCtrl
SNDSFINDDRNS(UniMod:21)FTNATTNAR3 0.5902190 0.1149105 16.433957 5.136338 0.0000916 0.0365914 strainProAla - strainCtrl
S(UniMod:21)LDEIIGSNK1 -0.6570783 0.1230775 14.389574 -5.338737 0.0000953 0.0375739 strainProAla - strainCtrl
LINTISDDDAPQS(UniMod:21)PR2 0.3884449 0.0757567 16.237530 5.127532 0.0000968 0.0376856 strainProAla - strainCtrl
EIQEALS(UniMod:21)EKPTREPTPSVK3 -0.4585421 0.0908605 16.943653 -5.046663 0.0001004 0.0384534 strainProAla - strainCtrl
NAVSTKPTPPPAPEASAES(UniMod:21)GLSSK4 0.5932089 0.1096447 13.616983 5.410283 0.0001012 0.0384534 strainProAla - strainCtrl
VGAENDGDS(UniMod:21)SLFLR2 -0.4697870 0.0908777 15.373926 -5.169445 0.0001057 0.0396444 strainProAla - strainCtrl
ITAQESIKS(UniMod:21)PEAAR3 -0.4672433 0.0930015 16.840097 -5.024040 0.0001071 0.0396444 strainProAla - strainCtrl
LAS(UniMod:21)LDNLR2 0.8466997 0.1626645 14.805479 5.205191 0.0001113 0.0396444 strainProAla - strainCtrl
VSIS(UniMod:21)HDDLQAVAVAVSTK2 1.4419688 0.2668696 13.299234 5.403271 0.0001113 0.0396444 strainProAla - strainCtrl
NYPNHIGLGLFDIHS(UniMod:21)PR3 0.8532128 0.1689875 16.332859 5.048971 0.0001115 0.0396444 strainProAla - strainCtrl
SFYPNS(UniMod:21)NKK2 -1.5513768 0.2641792 10.880858 -5.872442 0.0001121 0.0396444 strainProAla - strainCtrl
S(UniMod:21)PVVDGIVR2 0.7902940 0.1484180 13.679829 5.324786 0.0001160 0.0405488 strainProAla - strainCtrl
RGS(UniMod:21)WC(UniMod:4)C(UniMod:4)LVSSQK3 0.5951334 0.1176455 15.858939 5.058702 0.0001194 0.0410720 strainProAla - strainCtrl
S(UniMod:21)FELC(UniMod:4)EDRWWER3 0.9652345 0.1892849 15.415643 5.099374 0.0001201 0.0410720 strainProAla - strainCtrl
KTS(UniMod:21)SDLGIFGHR3 0.8025664 0.1592852 15.621130 5.038549 0.0001301 0.0435605 strainProAla - strainCtrl
ITAQESIKS(UniMod:21)PEAAR2 -0.4866011 0.0955194 15.065122 -5.094263 0.0001303 0.0435605 strainProAla - strainCtrl
IEAPS(UniMod:21)PSVNKK2 -0.4495955 0.0892201 15.516404 -5.039171 0.0001326 0.0438656 strainProAla - strainCtrl
VVVNT(UniMod:21)PREPVR2 -0.7853791 0.1528306 14.430485 -5.138886 0.0001368 0.0447846 strainProAla - strainCtrl
EERS(UniMod:21)NNLLTPQPTNFTTK3 -0.6160504 0.1255770 16.764643 -4.905758 0.0001388 0.0449670 strainProAla - strainCtrl
LGLPHGS(UniMod:21)GPT(UniMod:21)SVYNNK2 -1.8671502 0.2435920 6.775273 -7.665073 0.0001413 0.0452833 strainProAla - strainCtrl
TTS(UniMod:21)NPSSILHDLPR2 -0.5970773 0.1176373 14.754198 -5.075579 0.0001439 0.0456591 strainProAla - strainCtrl
DIPGDEAYNS(UniMod:21)DDIM(UniMod:35)APLREK3 -4.5038176 0.5276093 5.943653 -8.536274 0.0001491 0.0459552 strainProAla - strainCtrl
ETERS(UniMod:21)PSSSPIHNATK3 0.4804431 0.0955866 15.023895 5.026261 0.0001498 0.0459552 strainProAla - strainCtrl
ILGTS(UniMod:21)PDMIDSAENR2 0.7514516 0.1407486 12.579640 5.338961 0.0001505 0.0459552 strainProAla - strainCtrl
T(UniMod:21)RNPLTHSTPK3 -2.3177156 0.2722097 5.943653 -8.514449 0.0001512 0.0459552 strainProAla - strainCtrl
(UniMod:1)SIC(UniMod:4)EQY(UniMod:21)YPEEPTKPTVK2 1.7987033 0.3578900 14.943653 5.025855 0.0001523 0.0459552 strainProAla - strainCtrl
LEAEEIPS(UniMod:21)EDQNEFLLER3 1.0489698 0.2119744 15.379908 4.948569 0.0001627 0.0479565 strainProAla - strainCtrl
IHFPLVSYS(UniMod:21)PVLSK3 1.1620088 0.2234585 13.194257 5.200110 0.0001630 0.0479565 strainProAla - strainCtrl
SSAVPQTS(UniMod:21)PGQPR2 -0.3794305 0.0772219 15.634112 -4.913510 0.0001665 0.0479565 strainProAla - strainCtrl
SENPDVT(UniMod:21)FGQVGR2 -0.4775492 0.0971039 15.565394 -4.917918 0.0001671 0.0479565 strainProAla - strainCtrl
LSTEDEEIHS(UniMod:21)AR3 -0.5579761 0.1147679 16.187061 -4.861779 0.0001676 0.0479565 strainProAla - strainCtrl
YAS(UniMod:21)SSSTDIENDDEK2 0.5810017 0.1210413 16.943653 4.800030 0.0001683 0.0479565 strainProAla - strainCtrl
VDIIANDQGNRT(UniMod:21)TPSFVAFTDTER3 0.5789923 0.1112553 12.957906 5.204179 0.0001717 0.0484528 strainProAla - strainCtrl
(UniMod:27)ENSSELPDS(UniMod:21)YDYSDSEFEDNLERR3 -3.6464498 0.3627175 4.943653 -10.053139 0.0001777 0.0496543 strainProAla - strainCtrl
ITAQESIKS(UniMod:21)PEAARK3 -0.6566213 0.1365118 16.427414 -4.809996 0.0001791 0.0496543 strainProAla - strainCtrl
EVSNSTVDADNGAS(UniMod:21)DFEAGQQFATELDQGEK3 1.6876535 0.2884649 9.654792 5.850464 0.0001854 0.0497877 strainProAla - strainCtrl
VTPT(UniMod:21)KTEVIIR2 1.0805705 0.2117751 13.378263 5.102444 0.0001855 0.0497877 strainProAla - strainCtrl
DTVDSGNVT(UniMod:21)TTESTER2 -0.4489829 0.0940048 16.638379 -4.776172 0.0001857 0.0497877 strainProAla - strainCtrl
GNLGNRFS(UniMod:21)PTK2 -0.4485452 0.0940041 16.687504 -4.771549 0.0001861 0.0497877 strainProAla - strainCtrl

Volcanoplots

plotVolcano(inferencesUsage) + 
  facet_wrap(~contrast) + 
  labs(title = "Usage")

inferencesUsage |> 
  filter(adjPval < alpha) |> 
  mutate(DA = sign(logFC) |> as.factor() |> recode("-1"= "down","1" = "up")) |>
  group_by(contrast, DA) |> 
  ggplot(aes(x = contrast)) +
  geom_bar(aes(fill = factor(DA)),
           colour = "black") +
  theme_minimal() + 
  theme(axis.text.x = element_text(angle = 90))

We observe that the number of significant precursors reduced drastically.

Heatmaps

lapply(colnames(L),
                   function(contrast, se, alpha)
                   {
                     sig <- rowData(se)[[contrast]] |> 
                       filter(adjPval < alpha) |> 
                       rownames()
                     if (length(sig) > 2)
                     {
                     quants <- t(scale(t(assay(se[sig,]))))
                     colnames(quants) <- se$sampleId #specific to this dataset to get short colnames
                     rowclushlp <- quants
                     rowclushlp[is.na(rowclushlp)] <- min(quants,na.rm=TRUE) - 2
                     rowclus <- hclust(dist(rowclushlp))
                     annotations <- columnAnnotation(
                       group = se$strain
                       ) #3.
                     set.seed(1234) ## annotation colours are randomly generated by default
                     return(
                       Heatmap(show_row_names = FALSE,
                       quants, 
                       name = "log2 intensity",
                       top_annotation = annotations, 
                       column_title = paste0(contrast, " = 0"),
                       cluster_rows = rowclus
                       )
                     )
                     } else return(ggplot() + theme_minimal() + ggtitle(paste0(contrast, " = 0")))
                   },
                   se = getWithColData(qf, "precursorsPTM_usage"),
                   alpha = alpha)

Detail plots

We can explore the data for a protein to validate the statistical inference results. For example, let’s explore the normalised precursor abundance, usages as well as the summarised protein intensities for the precursor with the most significant log2 usage.

(target_feature <- inferencesUsage |> 
   dplyr::slice(which.min(pval)) |> 
   pull(feature)
)
[1] "(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2"
inferencesUsage |> 
  filter(feature == target_feature)
                                                                     logFC
strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2                -0.07112323
strainProAla.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2               2.00075827
strainProAla - strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2  2.07188151
                                                                       se
strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2                0.08446100
strainProAla.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2              0.08074697
strainProAla - strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2 0.08189908
                                                                     df
strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2                15.20163
strainProAla.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2              15.20163
strainProAla - strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2 15.20163
                                                                        t
strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2                -0.8420837
strainProAla.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2              24.7781228
strainProAla - strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2 25.2979833
                                                                       pval
strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2                4.127935e-01
strainProAla.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2              1.044776e-13
strainProAla - strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2 7.673615e-14
                                                                    adjPval
strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2                8.319430e-01
strainProAla.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2              3.234626e-09
strainProAla - strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2 2.361018e-09
                                                                                contrast
strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2                               strainCtrl
strainProAla.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2                           strainProAla
strainProAla - strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2 strainProAla - strainCtrl
                                                                                            feature
strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2                (UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2
strainProAla.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2              (UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2
strainProAla - strainCtrl.(UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2 (UniMod:1)SDS(UniMod:21)EVNQEAKPEVK2

We again make a similar plot as before.

ptm <-  qf[target_feature, , c("precursorsPTM_norm", "precursorsPTM_usage")] |> #1
  longForm(colvars = colnames(colData(qf)), rowvars = "Protein.Group") |> #2
  data.frame()
Warning: 'experiments' dropped; see 'drops()'
harmonizing input:
  removing 108 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'
protein <- qf[unique(ptm$Protein.Group), , c("proteins")] |> #1
  longForm(colvars = colnames(colData(qf)), rowvars = "Protein.Group") |> #2
  data.frame()
Warning: 'experiments' dropped; see 'drops()'
harmonizing input:
  removing 126 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'
ptm_protein <- rbind(ptm, protein)
ylims <- ptm_protein |> 
  group_by(assay) |> 
  summarise(cent = mean(range(value,na.rm=TRUE)), ampl = diff(range(value,na.rm=TRUE))) |> 
  mutate(lower = cent - max(ampl)/2, 
         upper = cent + max(ampl)/2) |> 
  select(-c(cent, ampl))

outplot <- ptm_protein |>
  ggplot() +
  aes(x = sampleId,
      y = value) +
  geom_line(aes(group = rowname), linewidth = 0.1) +
  geom_point(aes(colour = strain)) +
  facet_wrap(~ assay, scales = "free") +
  ggh4x::facetted_pos_scales(
    y = list(
      assay == ylims$assay[1] ~ scale_y_continuous(limits = unlist(ylims[1,c("lower","upper")])),
      assay == ylims$assay[2] ~ scale_y_continuous(limits = unlist(ylims[2,c("lower","upper")])),
      assay == ylims$assay[3] ~ scale_y_continuous(limits = unlist(ylims[3,c("lower","upper")]))
    )
    ) +
  labs(subtitle = target_feature) +
  theme_minimal() +
  theme(axis.text.x = element_blank())
print(outplot)

rbind(ptm, protein) %>%
  {
  ggplot(.) +
  aes(x = strain,
      y = value) +
  geom_boxplot(aes(colour = strain)) +
  facet_wrap(~ assay, scales = "free") +
  geom_jitter(aes(shape = rowname)) +
  scale_shape_manual(values = seq_len(dplyr::n_distinct(.$rowname))) +
  ggtitle(target_feature) +
  theme_minimal() +
  theme(axis.text.x = element_blank()) +
  guides(shape = "none")
  }

We compare the intensities for the top 5 DA phospo-precursors for the first contrast to these of their corresponding protein in the non-enriched assay and to the usages.

contr = colnames(L)[1]
top5 <- inferencesPTM |> 
  filter(contrast == contr) |> 
  arrange(pval) |> 
  head(n = 5) |> 
  pull(feature)

for (feat in top5)
{
  ptm_data <- qf[,,c("precursorsPTM_norm","precursorsPTM_usage")] |> 
    longForm(colvars = colnames(colData(qf)), rowvars = "Protein.Group") |>
    data.frame() |> 
    filter(rowname==feat)
  feature_protein <- ptm_data |> 
    pull("Protein.Group") |> 
    unique()
  prot_data <- qf[,,"proteins"]|>
    longForm(colvars = colnames(colData(qf)), rowvars = "Protein.Group") |>
    data.frame() |> 
    filter(Protein.Group==feature_protein) 
  ptm_protein <- rbind(ptm_data, prot_data)
  ylims <- ptm_protein |> 
  group_by(assay) |> 
  summarise(cent = mean(range(value,na.rm=TRUE)), ampl = diff(range(value,na.rm=TRUE))) |> 
  mutate(lower = cent - max(ampl)/2, 
         upper = cent + max(ampl)/2) |> 
  select(-c(cent, ampl))
  
  comparison_plot <- ptm_protein |>
    ggplot() +
    aes(x = sampleId,
        y = value) +
    geom_line(aes(group = rowname), linewidth = 0.1) +
    geom_point(aes(colour = strain)) +
    facet_wrap(~ assay, scales = "free") +
    labs(
      title = paste0(feat," / ", feature_protein),
      subtitle = paste("padj PTM =", 
                       inferencesPTM |> 
                         filter(feature == feat & contrast == contr) |> 
                         pull(adjPval) |> 
                         round(digits = 3),
                       "padj usage =", 
                       inferencesUsage |> 
                         filter(feature == feat & contrast == contr) |> 
                         pull(adjPval) |>
                         round(digits = 3))
    ) +
    theme_minimal() +
    theme(axis.text.x = element_blank()) +
    ggh4x::facetted_pos_scales(
    y = list(
      assay == ylims$assay[1] ~ scale_y_continuous(limits = unlist(ylims[1,c("lower","upper")])),
      assay == ylims$assay[2] ~ scale_y_continuous(limits = unlist(ylims[2,c("lower","upper")])),
      assay == ylims$assay[3] ~ scale_y_continuous(limits = unlist(ylims[3,c("lower","upper")]))
    )
    ) 
 print(comparison_plot)
}

We compare the intensities for the top 5 DU phospo-precursors for the first contrast to these of their corresponding protein in the non-enriched assay and to their unadjusted abundances.

contr = colnames(L)[1]
top5 <- inferencesUsage |> 
  filter(contrast == contr) |> 
  arrange(pval) |> 
  head(n = 5) |> 
  pull(feature)

for (feat in top5)
{
  ptm_data <- qf[,,c("precursorsPTM_norm","precursorsPTM_usage")] |> 
    longForm(colvars = colnames(colData(qf)), rowvars = "Protein.Group") |>
    data.frame() |> 
    filter(rowname==feat)
  feature_protein <- ptm_data |> 
    pull("Protein.Group") |> 
    unique()
  prot_data <- qf[,,"proteins"]|>
    longForm(colvars = colnames(colData(qf)), rowvars = "Protein.Group") |>
    data.frame() |> 
    filter(Protein.Group==feature_protein) 
  ptm_protein <- rbind(ptm_data, prot_data)
  ylims <- ptm_protein |> 
  group_by(assay) |> 
  summarise(cent = mean(range(value,na.rm=TRUE)), ampl = diff(range(value,na.rm=TRUE))) |> 
  mutate(lower = cent - max(ampl)/2, 
         upper = cent + max(ampl)/2) |> 
  select(-c(cent, ampl))
  
  comparison_plot <- ptm_protein |>
    ggplot() +
    aes(x = sampleId,
        y = value) +
    geom_line(aes(group = rowname), linewidth = 0.1) +
    geom_point(aes(colour = strain)) +
    facet_wrap(~ assay, scales = "free") +
    labs(
      title = paste0(feat," / ", feature_protein),
      subtitle = paste("padj PTM =", 
                       inferencesPTM |> 
                         filter(feature == feat & contrast == contr) |> 
                         pull(adjPval) |> 
                         round(digits = 3),
                       "padj usage =", 
                       inferencesUsage |> 
                         filter(feature == feat & contrast == contr) |> 
                         pull(adjPval) |>
                         round(digits = 3))
    ) +
    theme_minimal() +
    theme(axis.text.x = element_blank()) +
    ggh4x::facetted_pos_scales(
    y = list(
      assay == ylims$assay[1] ~ scale_y_continuous(limits = unlist(ylims[1,c("lower","upper")])),
      assay == ylims$assay[2] ~ scale_y_continuous(limits = unlist(ylims[2,c("lower","upper")])),
      assay == ylims$assay[3] ~ scale_y_continuous(limits = unlist(ylims[3,c("lower","upper")]))
    )
    ) 
 print(comparison_plot)
}

#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 12493745 667.3   22675350 1211.0         NA  22675350 1211
Vcells 40828341 311.5  102851388  784.7      24576 312075668 2381
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 12493753 667.3   22675350 1211.0         NA  22675350 1211
Vcells 40828387 311.5  102851388  784.7      24576 312075668 2381

11.9 Differential usage analysis at the PTM level

Multiple precursors are carrying the same PTM (cover the PTM at a certain position in the protein). We can aggregate them together.

11.9.1 Data processing

The variable Protein.Sites in the DIA-NN parquet file contains information on the exact modified residue position in the full protein sequence.

We first will make a new assay with duplicates for the precursors that contain multiple phospho sites.

  1. We extract the usage assay
  2. We extract the row data with the original variables (drop msqrob2 colums)
  3. Add a new variable with the modification type, which can derived from the variable Modified.Sequence. Indeed, all modifications start with string “UniMod:” followed by a number, i.e. 21 is a phoshorylation. So we extract all patterns “UniMod:[0-9]+” (UniMod: to match the literal text “UniMod:”, [0-9] to match any digit (0–9) and + to match one or more digits. We then replace pattern Uniprot: with an empty string.
  4. Add a new variable with the location of the modification on the original protein, which can be extracted from the variable Protein.Sites. Indeed, this variables contains the residu and its position in the protein sequence. If the sequence contains multiple modifications, the sites are separated with a ,. Regex (?<=:)[^\]]+ extracts all characters immediately after the colon without returning the colon and ignores ], e.g. for “[P52871:A2,S4]” it will return “A2,S4”. The resulting string is then splitted and subsequently the residue (first character) is removed.
  5. Replace the rowData of se
  6. Make vector of the row numbers with duplicates for the sequences containing multiple PTMs
  7. Make a corresponding vector with the positions of the individual PTM sites
  8. Make a corresponding vector with the modification type
  9. Extract the ids of rows that correspond to phospho sites
  10. Make a new summarised experiment with duplicate entries for precursors with multiple phospho sites.
  11. Add the position of the phospho site
  12. Add a variable with the Protein.Group name and the phospho site position attached to it.
  13. Make the rownames unique by appending the phospho site position to it.
  14. Add the assay to the QFeatures object.
se <- qf[["precursorsPTM_usage"]] #1. 

rd <- rowData(se)[,names(rowData(qf[["precursorsPTM"]]))] |> ##2.
  as.data.frame() |> 
  mutate(
    mods  = str_extract_all(Modified.Sequence, 
                           "UniMod:[0-9]+") |> 
      lapply(FUN = gsub, pattern="UniMod:",replacement=""), ##3.
    pos = str_extract(Protein.Sites, 
                      "(?<=:)[^\\]]+") |> 
      strsplit(split = ",") |> 
      lapply(FUN=substr,start=2,stop=10000) |> 
      lapply(FUN=as.integer) ##4.
  )

rowData(se) <- rd ##5.

ids <- rep(rd |> 
             nrow() |>
             seq_len(), 
           rd |>
             pull(pos) |>
             sapply(FUN = length))##6.
pos <- unlist(rd$pos) ##7.
mod <- unlist(rd$mods) ##8. 

phosIds <- ids[mod == "21"] ##9.


seDup <- se[phosIds,] ##10.
rowData(seDup)$pos <- pos[mod == "21"] ##11.

rowData(seDup)$Protein.Group.Mod <- paste(
  rowData(seDup)$Protein.Group,
  rowData(seDup)$pos, sep = "_") ##12.

rownames(seDup) <- paste(rownames(seDup), rowData(seDup)$pos, sep = "_") ##13.
qf <- addAssay(qf, seDup, "precursorsPTM_usage_unnested") ##14.

We now aggregate the data of precursors that map to the same PTM position on a protein in one protein expression value.

qf <- aggregateFeatures(qf, 
                   i = "precursorsPTM_usage_unnested",
                   fcol = "Protein.Group.Mod", 
                   name = "ptm_usage",
                   fun = function(X, ...) iq::maxLFQ(X)$estimate
                   )
Your quantitative data contain missing values. Please read the relevant
section(s) in the aggregateFeatures manual page regarding the effects
of missing values on data aggregation.

Aggregated: 1/1

We assess the distribution of the PTM usages.

qf[, , "ptm_usage"] |> #1.
  longForm(colvars = colnames(colData(qf))) |>  #2. 
  data.frame() |> 
  filter(!is.na(value)) |>
  ggplot() + #3.
  aes(x = value,
      colour = strain,
      group = colname) +
  geom_density() +
  labs(subtitle = "Usage") +
  theme_minimal()
harmonizing input:
  removing 162 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'

We remove temporarily objects

rm(se, seDup, mod, pos, ids, phosIds)
#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 12677605 677.1   22675350 1211.0         NA  22675350 1211
Vcells 48104261 367.1  102851388  784.7      24576 312075668 2381
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 12677595 677.1   22675350 1211.0         NA  22675350 1211
Vcells 48104277 367.1  102851388  784.7      24576 312075668 2381

11.9.2 Model estimation

Again we can estimate the same model but now for the usages.

qf <- msqrob(
  qf,
  i = "ptm_usage",
  formula = model,
  robust = TRUE)

We enabled M-estimation (robust = TRUE) for improved robustness against outliers.

#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 13131877 701.4   22675350 1211.0         NA  22675350 1211
Vcells 49438642 377.2  102851388  784.7      24576 312075668 2381
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 13131879 701.4   22675350 1211.0         NA  22675350 1211
Vcells 49438678 377.2  102851388  784.7      24576 312075668 2381

11.9.3 Inference

Contrasts remain the same. We assess the contrast for each precursor.

qf <- hypothesisTest(qf, i = "ptm_usage", contrast = L)

We extract the results table from the proteins summarised experiment in the qf object.

inferencesPtmUsage <- 
  msqrobCollect(qf[["ptm_usage"]], L)
#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 13194430 704.7   22675350 1211.0         NA  22675350 1211
Vcells 50733407 387.1  102851388  784.7      24576 312075668 2381
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 13194426 704.7   22675350 1211.0         NA  22675350 1211
Vcells 50733433 387.1  102851388  784.7      24576 312075668 2381

11.9.4 Report results

We report the results using a results table, volcano plots and heatmaps.

Results table

for (j in colnames(L)) {

  inference <- inferencesPtmUsage |> 
    dplyr::filter(adjPval < alpha & contrast == j)

  cat("**Median - Contrast:**", j, "= 0 (", nrow(inference),
      "significant proteins)\n\n")

  cat('<div style="max-height:300px; overflow-y:auto;">')

  print(
    kable(
      inference |>
        dplyr::arrange(pval) |>
        dplyr::relocate(feature),
      row.names = FALSE
    )
  )

  cat('</div>')

  cat("\n\n\n---\n\n")
}

Median - Contrast: strainCtrl = 0 ( 33 significant proteins)

feature logFC se df t pval adjPval contrast
P32324_763 -1.6927585 0.0917931 16.250700 -18.441012 0.00e+00 0.0000001 strainCtrl
P32324_569 -0.9952475 0.0789379 16.400086 -12.607977 0.00e+00 0.0000075 strainCtrl
P32324_713 -2.6258869 0.2112654 13.381730 -12.429329 0.00e+00 0.0000674 strainCtrl
P32324_572 -1.9360818 0.1633248 11.112322 -11.854185 1.00e-07 0.0005111 strainCtrl
P49167_50 1.1442699 0.1344706 17.146431 8.509444 1.00e-07 0.0005111 strainCtrl
P32599_88 -0.8161790 0.0865461 14.414079 -9.430565 2.00e-07 0.0005111 strainCtrl
P32324_557 -1.8883643 0.2272816 15.593306 -8.308479 4.00e-07 0.0011862 strainCtrl
P49167_49 1.0582663 0.1295957 15.598620 8.165904 5.00e-07 0.0012399 strainCtrl
P38968_396 0.7593899 0.0951348 16.096483 7.982251 5.00e-07 0.0012399 strainCtrl
P25294_14 -1.0772610 0.1434632 15.585791 -7.508973 1.50e-06 0.0029640 strainCtrl
P38713_440 4.2615011 0.2882973 6.977035 14.781619 1.60e-06 0.0029640 strainCtrl
P24783_243 -0.9925106 0.1375819 15.798585 -7.213964 2.20e-06 0.0037743 strainCtrl
P16474_461 1.0023303 0.1481254 16.197972 6.766769 4.20e-06 0.0062721 strainCtrl
P38181_43 0.8900045 0.1333837 16.695283 6.672514 4.30e-06 0.0062721 strainCtrl
P15274_94 -3.4608404 0.4352252 11.558673 -7.951838 5.10e-06 0.0068885 strainCtrl
P35180_87 -0.5825995 0.0960762 17.036076 -6.063931 1.25e-05 0.0143803 strainCtrl
Q12191_286 3.1647276 0.2426027 5.990144 13.044896 1.27e-05 0.0143803 strainCtrl
P47129_206 3.8203404 0.3046938 6.146431 12.538293 1.31e-05 0.0143803 strainCtrl
P35180_172 -0.5139705 0.0852123 17.018350 -6.031648 1.34e-05 0.0143803 strainCtrl
P47135_123 1.4996611 0.2339126 13.930864 6.411201 1.66e-05 0.0169330 strainCtrl
Q01560_224 -0.6061690 0.1031075 16.917066 -5.878999 1.86e-05 0.0180276 strainCtrl
P00815_514 -0.7889347 0.1319660 15.185227 -5.978316 2.40e-05 0.0222512 strainCtrl
Q12271_991 3.2079677 0.4632099 10.848294 6.925516 2.69e-05 0.0238021 strainCtrl
Q04779_68 -0.5980074 0.1087306 16.457283 -5.499901 4.38e-05 0.0372015 strainCtrl
P32607_2 -3.6867193 0.4140249 6.979826 -8.904583 4.65e-05 0.0379041 strainCtrl
P05749_55 6.4094068 0.4779809 4.738617 13.409337 5.98e-05 0.0423395 strainCtrl
P05749_57 6.4094068 0.4779809 4.738617 13.409337 5.98e-05 0.0423395 strainCtrl
P05749_61 6.4094068 0.4779809 4.738617 13.409337 5.98e-05 0.0423395 strainCtrl
Q12363_436 -1.7348244 0.3057279 13.821177 -5.674407 6.03e-05 0.0423395 strainCtrl
P42945_841 -1.4844036 0.2765285 15.513844 -5.367995 6.98e-05 0.0459683 strainCtrl
P53303_269 0.9962285 0.1840269 15.115075 5.413495 6.99e-05 0.0459683 strainCtrl
P35732_273 -0.7536289 0.1453613 17.112317 -5.184522 7.31e-05 0.0465306 strainCtrl
P38013_171 1.4663620 0.2854371 17.146431 5.137252 8.02e-05 0.0494850 strainCtrl

Median - Contrast: strainProAla = 0 ( 37 significant proteins)

feature logFC se df t pval adjPval contrast
P25294_14 -1.5736386 0.1402672 15.585791 -11.218866 0.00e+00 0.0001463 strainProAla
P16474_461 1.4055365 0.1513660 16.197972 9.285685 1.00e-07 0.0006994 strainProAla
Q05050_393 -5.0261755 0.3804217 9.116969 -13.212116 3.00e-07 0.0020222 strainProAla
P32599_88 -0.6906942 0.0837567 14.414079 -8.246440 8.00e-07 0.0033014 strainProAla
Q07950_77 5.3704830 0.2695045 6.146431 19.927246 8.00e-07 0.0033014 strainProAla
P49167_50 0.9759734 0.1344706 17.146431 7.257896 1.30e-06 0.0043174 strainProAla
P38713_440 4.3675411 0.2965045 6.977035 14.730099 1.60e-06 0.0047686 strainProAla
Q12117_289 -0.6514795 0.0915145 15.682227 -7.118864 2.70e-06 0.0069192 strainProAla
Q03533_3 1.0472439 0.1501312 16.065966 6.975525 3.10e-06 0.0069192 strainProAla
Q06010_439 1.1230659 0.1615640 15.126717 6.951214 4.40e-06 0.0084473 strainProAla
P49167_49 0.8802596 0.1287233 15.598620 6.838384 4.60e-06 0.0084473 strainProAla
P47129_206 3.9673353 0.2781461 6.146431 14.263493 6.10e-06 0.0103325 strainProAla
P38968_396 0.6109495 0.0938583 16.096483 6.509276 7.00e-06 0.0109543 strainProAla
P15274_94 -2.7936460 0.3728751 11.558673 -7.492177 9.10e-06 0.0132387 strainProAla
P27466_343 -4.9926570 0.6628412 10.413359 -7.532207 1.58e-05 0.0214527 strainProAla
P32607_2 -3.7429438 0.3611440 6.979826 -10.364132 1.72e-05 0.0219390 strainProAla
P32599_111 -1.0815174 0.1725991 13.818023 -6.266065 2.20e-05 0.0262916 strainProAla
P24000_7 -0.8164666 0.1373779 15.547322 -5.943217 2.32e-05 0.0262916 strainProAla
P38928_651 -4.3428436 0.4052367 6.140624 -10.716808 3.34e-05 0.0355112 strainProAla
P17106_67 -0.5976299 0.1056597 16.053659 -5.656175 3.53e-05 0.0355112 strainProAla
Q12191_286 3.6741388 0.3384731 5.990144 10.855040 3.66e-05 0.0355112 strainProAla
Q12373_353 -0.5652907 0.1015264 16.330996 -5.567920 3.94e-05 0.0364570 strainProAla
Q12306_2 0.4616846 0.0849830 17.031675 5.432670 4.45e-05 0.0394037 strainProAla
P16862_163 0.5191360 0.0959890 16.884814 5.408285 4.82e-05 0.0394110 strainProAla
Q06836_388 -2.2257780 0.2528713 6.978052 -8.802018 5.02e-05 0.0394110 strainProAla
Q12149_640 2.2915891 0.3830766 12.709696 5.982065 5.03e-05 0.0394110 strainProAla
P15992_208 -1.0687461 0.1913388 14.744397 -5.585622 5.54e-05 0.0418253 strainProAla
Q06108_969 -2.6455100 0.4690092 13.912381 -5.640636 6.24e-05 0.0440817 strainProAla
P38853_537 3.1528234 0.2663120 5.146431 11.838833 6.28e-05 0.0440817 strainProAla
Q12019_4443 -0.6147425 0.1163580 15.850955 -5.283199 7.66e-05 0.0487954 strainProAla
P32324_763 0.4770509 0.0913882 16.250700 5.220048 8.01e-05 0.0487954 strainProAla
P05749_55 5.7636221 0.4594214 4.738617 12.545392 8.14e-05 0.0487954 strainProAla
P05749_57 5.7636221 0.4594214 4.738617 12.545392 8.14e-05 0.0487954 strainProAla
P05749_61 5.7636221 0.4594214 4.738617 12.545392 8.14e-05 0.0487954 strainProAla
P25491_58 -1.9684991 0.2375495 6.791442 -8.286690 8.60e-05 0.0489042 strainProAla
P32774_102 -0.6146229 0.1203290 17.068305 -5.107855 8.64e-05 0.0489042 strainProAla
P10591_36 0.5073982 0.0991781 16.726141 5.116031 9.04e-05 0.0497717 strainProAla

Median - Contrast: strainProAla - strainCtrl = 0 ( 108 significant proteins)

feature logFC se df t pval adjPval contrast
P32324_763 2.1698095 0.0933511 16.250700 23.243535 0.0000000 0.0000000 strainProAla - strainCtrl
P32324_569 1.1121529 0.0768953 16.400086 14.463213 0.0000000 0.0000009 strainProAla - strainCtrl
P32324_713 3.0035670 0.2097059 13.381730 14.322762 0.0000000 0.0000114 strainProAla - strainCtrl
P16862_163 0.9615896 0.0949133 16.884814 10.131240 0.0000000 0.0000666 strainProAla - strainCtrl
P32324_557 2.3977791 0.2269496 15.593306 10.565250 0.0000000 0.0000666 strainProAla - strainCtrl
P00815_514 1.3059254 0.1351987 15.185227 9.659304 0.0000001 0.0002063 strainProAla - strainCtrl
P32324_572 2.0626558 0.1655739 11.112322 12.457613 0.0000001 0.0002063 strainProAla - strainCtrl
Q03533_3 1.4414307 0.1581598 16.065966 9.113763 0.0000001 0.0002406 strainProAla - strainCtrl
P24783_243 1.2009457 0.1375819 15.798585 8.728953 0.0000002 0.0004151 strainProAla - strainCtrl
Q01662_95 1.1063106 0.1279841 15.952106 8.644125 0.0000002 0.0004151 strainProAla - strainCtrl
Q05050_393 -4.7276674 0.3763197 9.116969 -12.562901 0.0000005 0.0008496 strainProAla - strainCtrl
Q08979_610 0.9214698 0.1138236 15.372814 8.095593 0.0000006 0.0010596 strainProAla - strainCtrl
P16862_167 0.6303716 0.0800056 15.484083 7.879090 0.0000008 0.0013101 strainProAla - strainCtrl
Q07950_77 5.0425550 0.2695045 6.146431 18.710465 0.0000012 0.0017178 strainProAla - strainCtrl
P22203_3 0.7412991 0.1008642 16.439922 7.349476 0.0000014 0.0018776 strainProAla - strainCtrl
P47035_679 -1.0045670 0.1325666 14.591666 -7.577830 0.0000020 0.0023655 strainProAla - strainCtrl
Q06010_439 1.1862477 0.1601743 15.126717 7.405979 0.0000021 0.0023655 strainProAla - strainCtrl
P38181_43 -0.9456091 0.1338371 16.695283 -7.065372 0.0000021 0.0023655 strainProAla - strainCtrl
P22203_2 0.8174736 0.1193296 16.373426 6.850551 0.0000034 0.0036713 strainProAla - strainCtrl
P31385_82 0.6460889 0.0935269 15.915680 6.908056 0.0000036 0.0036713 strainProAla - strainCtrl
P36123_867 0.5656277 0.0833656 16.429972 6.784908 0.0000038 0.0036764 strainProAla - strainCtrl
Q12363_436 2.1895001 0.3037274 13.821177 7.208767 0.0000048 0.0043791 strainProAla - strainCtrl
P40066_81 0.9380922 0.1391068 15.736327 6.743685 0.0000051 0.0043791 strainProAla - strainCtrl
P35180_87 0.6234918 0.0956293 17.036076 6.519883 0.0000052 0.0043791 strainProAla - strainCtrl
P32644_212 0.6529945 0.0959738 13.964949 6.803884 0.0000087 0.0070145 strainProAla - strainCtrl
P47035_676 -0.7641278 0.1193511 15.405181 -6.402351 0.0000105 0.0081663 strainProAla - strainCtrl
P47035_385 -0.8821967 0.1456136 15.688410 -6.058476 0.0000181 0.0132100 strainProAla - strainCtrl
Q12363_98 0.5759240 0.0950597 15.646656 6.058548 0.0000183 0.0132100 strainProAla - strainCtrl
P23201_1087 -0.5687071 0.0947155 15.727783 -6.004373 0.0000198 0.0137989 strainProAla - strainCtrl
Q12363_200 0.5599062 0.0977837 17.139795 5.725965 0.0000240 0.0161803 strainProAla - strainCtrl
Q08972_110 0.6650956 0.1157119 16.371625 5.747861 0.0000274 0.0179040 strainProAla - strainCtrl
P19097_1872 1.3107861 0.2152537 13.848551 6.089495 0.0000293 0.0185284 strainProAla - strainCtrl
Q02455_1710 -0.6915129 0.1178104 14.643173 -5.869708 0.0000340 0.0208601 strainProAla - strainCtrl
P17123_118 0.5783995 0.1030330 16.167609 5.613730 0.0000373 0.0222532 strainProAla - strainCtrl
Q12495_294 0.6639109 0.1188671 16.104689 5.585322 0.0000401 0.0223597 strainProAla - strainCtrl
P32389_528 0.6092121 0.1109659 16.679294 5.490084 0.0000426 0.0223597 strainProAla - strainCtrl
P47035_1017 -0.7604924 0.1318212 14.408249 -5.769122 0.0000434 0.0223597 strainProAla - strainCtrl
P07149_971 1.2434008 0.2050281 12.637535 6.064540 0.0000452 0.0223597 strainProAla - strainCtrl
Q12680_2070 0.9540220 0.1656330 14.288879 5.759855 0.0000456 0.0223597 strainProAla - strainCtrl
Q04336_956 1.4592232 0.2410134 12.655594 6.054531 0.0000456 0.0223597 strainProAla - strainCtrl
P53946_9 -0.7002631 0.1296835 17.146431 -5.399786 0.0000465 0.0223597 strainProAla - strainCtrl
P49687_431 -0.4743980 0.0871979 16.590899 -5.440475 0.0000480 0.0223597 strainProAla - strainCtrl
Q12271_991 -3.0321531 0.4673870 10.848294 -6.487457 0.0000481 0.0223597 strainProAla - strainCtrl
P09436_406 1.1425875 0.2027569 14.907084 5.635259 0.0000486 0.0223597 strainProAla - strainCtrl
P53114_268 1.2906180 0.2301329 14.930319 5.608142 0.0000508 0.0228545 strainProAla - strainCtrl
P47035_357 -0.6430105 0.1203089 17.094100 -5.344663 0.0000526 0.0231850 strainProAla - strainCtrl
Q12280_1347 -1.1468873 0.2094536 15.066959 -5.475615 0.0000629 0.0271154 strainProAla - strainCtrl
Q12363_193 1.1255279 0.2099661 15.554989 5.360523 0.0000701 0.0280723 strainProAla - strainCtrl
P32468_326 -0.4473303 0.0860681 17.146431 -5.197401 0.0000707 0.0280723 strainProAla - strainCtrl
Q12306_2 0.4446711 0.0853963 17.031675 5.207150 0.0000708 0.0280723 strainProAla - strainCtrl
P38631_1178 0.7910246 0.1501937 16.345442 5.266696 0.0000716 0.0280723 strainProAla - strainCtrl
P06634_263 0.6400190 0.1210541 16.110071 5.287050 0.0000721 0.0280723 strainProAla - strainCtrl
P53236_607 0.4916219 0.0947963 16.969163 5.186087 0.0000748 0.0283651 strainProAla - strainCtrl
P03871_264 1.0562360 0.1785411 11.806596 5.915926 0.0000756 0.0283651 strainProAla - strainCtrl
P25366_291 0.5781662 0.1091327 15.051717 5.297824 0.0000884 0.0320105 strainProAla - strainCtrl
P10961_458 0.5902190 0.1149506 16.636735 5.134546 0.0000885 0.0320105 strainProAla - strainCtrl
P47035_803 -1.5513768 0.2625980 11.083636 -5.907801 0.0000989 0.0339954 strainProAla - strainCtrl
P38213_323 0.5894801 0.1157870 16.445349 5.091073 0.0001002 0.0339954 strainProAla - strainCtrl
Q08977_470 0.8466997 0.1621370 15.008257 5.222125 0.0001031 0.0339954 strainProAla - strainCtrl
P36166_330 -0.8792587 0.1696024 15.322922 -5.184236 0.0001038 0.0339954 strainProAla - strainCtrl
P05694_706 0.8532128 0.1684630 16.535637 5.064691 0.0001040 0.0339954 strainProAla - strainCtrl
P53303_23 -0.5612435 0.1119357 17.110816 -5.013981 0.0001044 0.0339954 strainProAla - strainCtrl
P35177_1293 -0.4697870 0.0913546 15.576704 -5.142455 0.0001069 0.0339954 strainProAla - strainCtrl
P17123_125 0.5839602 0.1143861 15.896178 5.105167 0.0001081 0.0339954 strainProAla - strainCtrl
Q06685_430 0.7902940 0.1482397 13.882608 5.331192 0.0001091 0.0339954 strainProAla - strainCtrl
P17106_19 -0.5663603 0.1133371 16.723109 -4.997131 0.0001156 0.0344404 strainProAla - strainCtrl
P19097_1479 1.2304170 0.2472816 16.886378 4.975773 0.0001175 0.0344404 strainProAla - strainCtrl
P38630_61 -1.1790944 0.1870369 9.373277 -6.304074 0.0001176 0.0344404 strainProAla - strainCtrl
Q06836_388 -1.8671502 0.2430418 6.978052 -7.682425 0.0001199 0.0344404 strainProAla - strainCtrl
P24276_578 0.6006073 0.1209989 16.858120 4.963740 0.0001211 0.0344404 strainProAla - strainCtrl
P25366_290 0.8025664 0.1588462 15.823908 5.052474 0.0001217 0.0344404 strainProAla - strainCtrl
P17076_22 -2.3177156 0.2707529 6.146431 -8.560260 0.0001224 0.0344404 strainProAla - strainCtrl
P47035_1066 -0.5307200 0.1073855 16.859620 -4.942196 0.0001266 0.0351450 strainProAla - strainCtrl
Q12158_349 -0.6160504 0.1254723 16.967421 -4.909852 0.0001331 0.0364373 strainProAla - strainCtrl
P07259_1085 0.7514516 0.1404961 12.782418 5.348559 0.0001402 0.0378672 strainProAla - strainCtrl
P38631_1185 0.5208195 0.1060385 16.503785 4.911609 0.0001433 0.0382120 strainProAla - strainCtrl
P09733_274 1.1620088 0.2222959 13.397035 5.227305 0.0001479 0.0389008 strainProAla - strainCtrl
P47035_1032 -0.4107450 0.0847307 17.043259 -4.847655 0.0001499 0.0389220 strainProAla - strainCtrl
P50276_42 1.6876535 0.2861599 9.857570 5.897588 0.0001604 0.0406028 strainProAla - strainCtrl
P39009_139 0.5810017 0.1209785 17.146431 4.802521 0.0001622 0.0406028 strainProAla - strainCtrl
P23201_961 -0.4649970 0.0926319 14.687024 -5.019837 0.0001623 0.0406028 strainProAla - strainCtrl
P11633_53 -0.4775492 0.0974667 15.768172 -4.899614 0.0001671 0.0407769 strainProAla - strainCtrl
P10591_35 0.5789923 0.1116077 13.160684 5.187747 0.0001680 0.0407769 strainProAla - strainCtrl
P05750_44 1.0805705 0.2107311 13.581041 5.127723 0.0001691 0.0407769 strainProAla - strainCtrl
Q00684_429 -0.3794305 0.0778497 15.836891 -4.873887 0.0001738 0.0414284 strainProAla - strainCtrl
P17649_7 1.7103359 0.3460379 14.942645 4.942626 0.0001790 0.0418946 strainProAla - strainCtrl
P12754_131 0.4595307 0.0957374 16.529099 4.799909 0.0001799 0.0418946 strainProAla - strainCtrl
P25357_416 0.9037854 0.1858181 15.618381 4.863817 0.0001844 0.0419063 strainProAla - strainCtrl
Q12159_8 -0.4493205 0.0913213 14.976268 -4.920215 0.0001858 0.0419063 strainProAla - strainCtrl
P33314_1066 -0.4485452 0.0943069 16.890282 -4.756229 0.0001862 0.0419063 strainProAla - strainCtrl
P00815_524 0.4530860 0.0953425 16.459300 4.752194 0.0002009 0.0437364 strainProAla - strainCtrl
P25297_15 2.5289533 0.3954244 8.076172 6.395542 0.0002018 0.0437364 strainProAla - strainCtrl
P41318_106 0.9158580 0.1874916 14.884616 4.884794 0.0002025 0.0437364 strainProAla - strainCtrl
P25558_1350 -0.3670884 0.0777594 16.814965 -4.720824 0.0002029 0.0437364 strainProAla - strainCtrl
Q02455_774 -0.5506372 0.1129022 14.741759 -4.877117 0.0002112 0.0444822 strainProAla - strainCtrl
P35201_134 -0.7098323 0.1506181 16.648611 -4.712797 0.0002117 0.0444822 strainProAla - strainCtrl
Q12176_818 -0.5971696 0.1271016 16.752419 -4.698366 0.0002148 0.0444822 strainProAla - strainCtrl
Q01217_529 0.5343197 0.1092066 14.456267 4.892740 0.0002167 0.0444822 strainProAla - strainCtrl
Q03780_390 -0.5776465 0.1222648 16.324823 -4.724551 0.0002174 0.0444822 strainProAla - strainCtrl
P08153_278 0.6951872 0.1379839 12.794210 5.038178 0.0002385 0.0481018 strainProAla - strainCtrl
Q03361_726 -0.7526987 0.1618762 16.646419 -4.649840 0.0002417 0.0481018 strainProAla - strainCtrl
P27466_343 -4.0168004 0.7366109 10.413359 -5.453083 0.0002425 0.0481018 strainProAla - strainCtrl
P32500_412 -0.4932956 0.1066440 16.913539 -4.625630 0.0002446 0.0481018 strainProAla - strainCtrl
P47116_587 0.3771683 0.0817350 16.863750 4.614524 0.0002522 0.0491092 strainProAla - strainCtrl
P02994_240 0.4713281 0.1011285 16.161567 4.660685 0.0002545 0.0491092 strainProAla - strainCtrl
P38850_699 -0.7764632 0.1673903 16.231325 -4.638638 0.0002635 0.0495121 strainProAla - strainCtrl
P38720_163 0.9859957 0.2075622 14.871771 4.750362 0.0002638 0.0495121 strainProAla - strainCtrl
P33750_161 0.5304439 0.1090147 13.729791 4.865800 0.0002639 0.0495121 strainProAla - strainCtrl

Volcanoplots

plotVolcano(inferencesPtmUsage) + 
  facet_wrap(~contrast) + 
  labs(title = "PTM Usage")

inferencesPtmUsage |> 
  filter(adjPval < alpha) |> 
  mutate(DA = sign(logFC) |> as.factor() |> recode("-1"= "down","1" = "up")) |>
  group_by(contrast, DA) |> 
  ggplot(aes(x = contrast)) +
  geom_bar(aes(fill = factor(DA)),
           colour = "black") +
  theme_minimal() + 
  theme(axis.text.x = element_text(angle = 90))

Heatmaps

lapply(colnames(L),
                   function(contrast, se, alpha)
{
                     sig <- rowData(se)[[contrast]] |> 
                       filter(adjPval < alpha) |> 
                       rownames()
                     if (length(sig) > 2)
                     {
                     quants <- t(scale(t(assay(se[sig,]))))
                     colnames(quants) <- se$sampleId #specific to this dataset to get short colnames
                     rowclushlp <- quants
                     rowclushlp[is.na(rowclushlp)] <- min(quants,na.rm=TRUE) - 2
                     rowclus <- hclust(dist(rowclushlp))
                     annotations <- columnAnnotation(
                       group = se$strain
                       ) #3.
                     set.seed(1234) ## annotation colours are randomly generated by default
                     return(
                       Heatmap(show_row_names = FALSE,
                       quants, 
                       name = "log2 intensity",
                       top_annotation = annotations, 
                       column_title = paste0(contrast, " = 0"),
                       cluster_rows = rowclus
                       )
                     )
                     } else return(ggplot() + theme_minimal() + ggtitle(paste0(contrast, " = 0")))
                   },
                   se = getWithColData(qf, "ptm_usage"),
                   alpha = alpha)

Detail plots

We can explore the data for a protein to validate the statistical inference results. For example, let’s explore the precursor, summarized PTM and summarised protein intensities for the PTM with the most significant log2 fold change.

(target_feature <- inferencesPtmUsage |> 
   dplyr::slice(which.min(pval)) |> 
   pull(feature)
)
[1] "P32324_763"
inferencesPtmUsage |> 
  filter(feature == target_feature)
                                          logFC         se      df          t
strainCtrl.P32324_763                -1.6927585 0.09179315 16.2507 -18.441012
strainProAla.P32324_763               0.4770509 0.09138822 16.2507   5.220049
strainProAla - strainCtrl.P32324_763  2.1698095 0.09335110 16.2507  23.243535
                                             pval      adjPval
strainCtrl.P32324_763                2.529190e-12 5.152465e-08
strainProAla.P32324_763              8.009496e-05 4.879538e-02
strainProAla - strainCtrl.P32324_763 6.704455e-14 1.358255e-09
                                                      contrast    feature
strainCtrl.P32324_763                               strainCtrl P32324_763
strainProAla.P32324_763                           strainProAla P32324_763
strainProAla - strainCtrl.P32324_763 strainProAla - strainCtrl P32324_763
ptm <-  qf[target_feature, , c("precursorsPTM_usage_unnested", "ptm_usage")] |> #1
  longForm(colvars = colnames(colData(qf)), rowvars = "Protein.Group") |> #2
  data.frame()
Warning: 'experiments' dropped; see 'drops()'
harmonizing input:
  removing 144 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'
precursor <- qf[ptm |> 
                   filter(assay =="precursorsPTM_usage_unnested") |>
                   pull(rowname) |>
                   sub(pattern = "_.*", replacement = "") |> 
                   unique(), , "precursorsPTM_norm"] |>
  longForm(colvars = colnames(colData(qf)), rowvars = "Protein.Group") |> #2
  data.frame()
Warning: 'experiments' dropped; see 'drops()'
harmonizing input:
  removing 162 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'
protein <- qf[unique(ptm$Protein.Group), , c("proteins")] |> #1
  longForm(colvars = colnames(colData(qf)), rowvars = "Protein.Group") |> #2
  data.frame()
Warning: 'experiments' dropped; see 'drops()'
harmonizing input:
  removing 162 sampleMap rows not in names(experiments)
  removing 18 colData rownames not in sampleMap 'primary'
ptm_protein <- rbind(ptm, precursor, protein)
ylims <- ptm_protein |> 
  group_by(assay) |> 
  summarise(cent = mean(range(value,na.rm=TRUE)), ampl = diff(range(value,na.rm=TRUE))) |> 
  mutate(lower = cent - max(ampl)/2, 
         upper = cent + max(ampl)/2) |> 
  select(-c(cent, ampl))

ptm_protein |>
  filter(!is.na(value)) |>
  ggplot() +
  aes(x = sampleId,
      y = value) +
  geom_line(aes(group = rowname), linewidth = 0.1) +
  geom_point(aes(colour = strain)) +
  facet_wrap(~ assay, scales = "free") +
  ggh4x::facetted_pos_scales(
    y = list(
      assay == ylims$assay[1] ~ scale_y_continuous(limits = unlist(ylims[1,c("lower","upper")])),
      assay == ylims$assay[2] ~ scale_y_continuous(limits = unlist(ylims[2,c("lower","upper")])),
      assay == ylims$assay[3] ~ scale_y_continuous(limits = unlist(ylims[3,c("lower","upper")])),
      assay == ylims$assay[4] ~ scale_y_continuous(limits = unlist(ylims[4,c("lower","upper")]))
    )
    ) +
  labs(subtitle = paste0("Protein:", sub("_"," / phosho-position: ", target_feature))) +
  theme_minimal() +
  theme(axis.text.x = element_blank())

rbind(ptm, precursor, protein) %>%
  {
  ggplot(.) +
  aes(x = strain,
      y = value) +
  geom_boxplot(aes(colour = strain)) +
  facet_wrap(~ assay, scales = "free") +
  geom_jitter(aes(shape = rowname)) +
  scale_shape_manual(values = seq_len(dplyr::n_distinct(.$rowname))) +
  labs(subtitle = paste0("Protein:", sub("_"," / phosho-position: ", target_feature))) +
  theme_minimal() +
  theme(axis.text.x = element_blank()) +
  guides(shape = "none")
  }
Warning: Removed 24 rows containing non-finite outside the scale range
(`stat_boxplot()`).
Warning: Removed 24 rows containing missing values or values outside the scale range
(`geom_point()`).

#Garbage collection to free space 
gc(); gc()
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 13195263 704.8   22675350 1211.0         NA  22675350 1211
Vcells 46556212 355.2  102851388  784.7      24576 312075668 2381
           used  (Mb) gc trigger   (Mb) limit (Mb)  max used (Mb)
Ncells 13195262 704.8   22675350 1211.0         NA  22675350 1211
Vcells 46556243 355.2  102851388  784.7      24576 312075668 2381

11.9.5 Along Protein Mapping

In this section we will make Along Protein graphs. Therefore we need sequence information on the protein sequence, which we can find in the fasta file from uniprot that was used for mapping.

Note, that it is recommended to use the fasta that was used for the mapping. However, this file was not uploaded by the authors so we use the version of the current release for illustration purposes.

  1. Read fasta file
fastaFile <- bfcrpath(bfc,"https://rest.uniprot.org/uniprotkb/stream?compressed=true&download=true&format=fasta&query=%28%28proteome%3AUP000002311%29+AND+reviewed%3Dtrue%29")
fasta <- seqinr::read.fasta(fastaFile, seqtype = "AA", as.string = T) #2.
  1. Extract the proteins from the fasta file.
# read in fasta file for protein sequence & length -> to calculate the coverage
mapping <- data.frame(fullName = fasta |> names(), 
                      accession = fasta |> names() |> stringr::str_split_i("\\|", 2),
                      sequence = unlist(fasta)) |> 
  mutate(length = nchar(sequence))
rownames(mapping) <- mapping$accession

PTM barcode plot

We make a barplot for all phosphorylated residues on protein P32324

We first gather the data:

  1. We extract the protein name
  2. we filter all PTMs for that protein
  3. we add the phospho-position in the rowData to it
  4. we make a new variable type to indicate if the PTM usage is up, down, non-significant or missing
prot <- sub("_.*","", target_feature) ## 1.
ptmListProt <- inferencesPtmUsage |> 
  filter(grepl(prot, feature)) |> ## 2. 
  left_join(rowData(qf[["ptm_usage"]]) |> 
              as.data.frame() |> 
              select(Protein.Group.Mod, pos),
            by = c("feature" = "Protein.Group.Mod")) |> ## 3. 
  mutate(type = ifelse(is.na(adjPval),  
                       "missing", 
                       ifelse(adjPval < 0.05, 
                              ifelse(logFC < 0, 
                                     "down",
                                     "up"),
                              "non-sig")) ## 4.
  )

We make the barplot by adding a geom_point layer and a vertical line (geom_vline) to indicate the residue position.

ptmListProt |> 
  ggplot(aes(x=pos,y=0,col=type)) +
  geom_point() +
  geom_vline(aes(xintercept=pos,col=type)) + 
  xlab("residue") + 
  ylab("") +
  scale_color_manual(values = c("black","grey","blue","red"), 
                     breaks = c("missing","non-sig","down", "up")) +
  theme(
    axis.ticks.y = element_blank(),
    axis.text.y = element_blank(), 
    panel.grid = element_blank(),
    panel.background = element_blank(),
    panel.border = element_rect(color = "black", fill = NA),
    strip.background = element_rect(color = "black")
    ) +
  xlim(0, mapping[prot,"length"]) +
  ggtitle(paste0(prot, ": Phospho residues")) +
  facet_grid(contrast~.)

Along protein plot for all precursors

We first gather the data from all precursors that map to protein P32324

prot <- sub("_.*","", target_feature) ## 1.

precursorListProt <- inferencesUsage |> 
  left_join(rowData(qf[["precursorsPTM_usage"]]) |> 
              as.data.frame() |> 
              select(Precursor.Id, Protein.Group, Stripped.Sequence, Protein.Sites, Modified.Sequence),
            by = c("feature" = "Precursor.Id")) |> ## 2. 
  filter(Protein.Group == prot) |> ## 3. 
  mutate(seqOrder = as.factor(feature) |> as.numeric(),
         type = ifelse(is.na(adjPval),  
                       "missing", 
                       ifelse(adjPval < 0.05, 
                              ifelse(logFC < 0, 
                                     "down",
                                     "up"),
                              "non-sig")), ## 4.
         tmp = str_locate_all(mapping[prot,"sequence"], Stripped.Sequence),
         start = purrr::map(tmp, ~ .x[, "start"]),
         end = purrr::map(tmp, ~ .x[, "end"])) |>
  unnest(c(start, end))

Add location of Phospo residues.

  1. Add a new variable with the modification type (21 is phosho)
  2. Add a new variable with the location of the modification on the original protein
  3. Make vector of the row numbers with duplicates for the sequences containing multiple PTMs
  4. Make a corresponding vector with the positions of the individual PTM sites
  5. Make a corresponding vector with the modification type
  6. Extract the ids of rows that correspond to phospho sites
  7. Make a data.frame with duplicate entries for precursors with multiple phospho sites with variables seqOrder, type and contrast
  8. Add the position of the phospho site
precursorListProt <-  precursorListProt |> mutate(
    mods  = str_extract_all(Modified.Sequence, 
                           "UniMod:[0-9]+") |> 
      lapply(FUN = gsub, pattern="UniMod:",replacement=""), ##1.
    pos = str_extract(Protein.Sites, 
                      "(?<=:)[^\\]]+") |> 
      strsplit(split = ",") |> 
      lapply(FUN=substr,start=2,stop=10000) |> 
      lapply(FUN=as.integer)) ## 2.

ids <- rep(precursorListProt |> 
             nrow() |>
             seq_len(), 
           precursorListProt |>
             pull(pos) |>
             sapply(FUN = length))## 3.
pos <- unlist(precursorListProt$pos) ## 4.
mod <- unlist(precursorListProt$mods) ## 5. 

phosIds <- ids[mod == "21"] ## 6.


precursorPosListProt <- precursorListProt[phosIds,] |> ## 7.
  select(seqOrder,type, contrast) |>
  mutate(pos = pos[mod == "21"]) ## 8.

Make along protein plot.

precursorListProt |> 
  ggplot(aes(y=seqOrder)) +
    geom_segment(aes(x = start, xend = end, yend = seqOrder, color = type),
                  linewidth = 1) + 
    xlim(0, mapping[prot,"length"]) +
  ylab("Precursors") + xlab("Residue") +  #6. 
  scale_y_continuous(breaks = precursorListProt$seqOrder, labels = precursorListProt$Stripped.Sequence) +
  scale_color_manual(values = c("black","grey","blue","red", "black"), 
                     breaks = c("missing","non-sig","down", "up", "black")) +
  geom_segment(data = precursorPosListProt,
               aes(x = pos, xend = pos, y = seqOrder - 0.5, yend = seqOrder + 0.5, 
                   color = "black"), linewidth = 1) +
  facet_grid(contrast~.) +
  theme(
    axis.ticks.y = element_blank(),
    axis.text.y = element_blank(), #We suppress the feature sequence here because there are too many sequences
    panel.grid = element_blank(),
    panel.background = element_blank(),
    panel.border = element_rect(color = "black", fill = NA),
    strip.background = element_rect(color = "black")
    ) +
    labs(title = paste0(prot, " along with precursors"),
           subtitle = "(phospho residue in black vertical line)")