Software for Proteomics Data Analysis (PDA)

1 Install R/Rstudio

You can install R from the CRAN repository. Yo will need R version 4.5 or higher.

You can install from the Posit website.

2 Install the GitHub and Bioconductor installers

Open Rstudio and paste the following command in the console:

install.packages("devtools")
install.packages("BiocManager")
BiocManager::install(version = "devel")

The first command will install a utility package that will enable to install packages from GitHub. The second line will install the Bioconductor package installer. Ensure the installation succeeded by running the following command:

BiocManager::version()

## [1] '3.22'

It should return 3.22 or higher.

3 Install QFeatures

The workshop will require a specific version of QFeatures, you can install it using the following command:

BiocManager::install("cvanderaa/QFeatures", ref = "uniquePrecId")

Test the package has been correctly installed using the following command:

library(QFeatures)
data(feat2)
joinAssays(feat2, 1:3, fcol = "Prot")

## An instance of class QFeatures (type: bulk) with 4 sets:
## 
##  [1] assay1: SummarizedExperiment with 10 rows and 4 columns 
##  [2] assay2: SummarizedExperiment with 4 rows and 4 columns 
##  [3] assay3: SummarizedExperiment with 7 rows and 4 columns 
##  [4] joinedAssay: SummarizedExperiment with 14 rows and 12 columns

4 Install msqrob2

The workshop will also require a specific version of msqrob2, you can install it using the following command:

BiocManager::install("statOmics/msqrob2") ## this installs msqrob2

Test whether the package has been correctly installed using the following command:

library(msqrob2)
data(pe)
pe <- aggregateFeatures(
    pe, i = "peptide", fcol = "Proteins", name = "protein"
)
msqrob(pe,i = "protein", formula = ~ condition)

## An instance of class QFeatures (type: bulk) with 2 sets:
## 
##  [1] peptide: SummarizedExperiment with 631 rows and 20 columns 
##  [2] protein: SummarizedExperiment with 100 rows and 20 columns

5 Install the graphical user interfaces

In this course, we will use 2 graphical user interfaces (GUIs): QFeaturesGUI for the data preprocessing and msqrob2gui for the data modelling. For installing the GUIs, you’ll again need to install specific versions as the software is still in a developmental stage.

Note, that QFeaturesGUI is actively developed and maintained by the Laurent Gatto lab. However, we forked QFeaturesGUI temporarily for this version of the course because we needed some additional functionalities.

BiocManager::install("statOmics/QFeaturesGUI") ## this installs QFeaturesGUI
BiocManager::install("statOmics/msqrob2gui", ref = "gui2modules") ## this installs msqrob2gui

Test whether the QFeaturesGUI package has been correctly installed using the following command:

QFeaturesGUI::importQFeatures()

This should open a new window. You can close it for now.

Test whether the msqrob2gui package has been correctly installed using the following command:

msqrob2gui::launchMsqrob2App()

Again, this should open a new window, but you can close it for now.

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This work is licensed under the CC BY-NC-SA 4.0 licence.