Example: MSGF+ search on Swiss-Prot

Ghent University

1 Load Libraries

library(TargetDecoy)

## Warning in fun(libname, pkgname): mzR has been built against a different Rcpp version (1.0.12)
## than is installed on your system (1.0.13.1). This might lead to errors
## when loading mzR. If you encounter such issues, please send a report,
## including the output of sessionInfo() to the Bioc support forum at 
## https://support.bioconductor.org/. For details see also
## https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.

library(RCurl)
library(mzID)

2 Download data in working directory

download.file( 
  url = "https://raw.githubusercontent.com/statOmics/PDA22GTPB/data/identification/pyrococcusMSGF%2B.mzid",
  destfile = "pyrococcusMSGF+.mzid"
  )

3 Load Data in R

path2File <- "pyrococcusMSGF+.mzid"
msgf <- mzID(path2File)

## reading pyrococcusMSGF+.mzid...

## Warning in type.convert.default(...): 'as.is' should be specified by the
## caller; using TRUE
## Warning in type.convert.default(...): 'as.is' should be specified by the
## caller; using TRUE
## Warning in type.convert.default(...): 'as.is' should be specified by the
## caller; using TRUE
## Warning in type.convert.default(...): 'as.is' should be specified by the
## caller; using TRUE
## Warning in type.convert.default(...): 'as.is' should be specified by the
## caller; using TRUE
## Warning in type.convert.default(...): 'as.is' should be specified by the
## caller; using TRUE
## Warning in type.convert.default(...): 'as.is' should be specified by the
## caller; using TRUE
## Warning in type.convert.default(...): 'as.is' should be specified by the
## caller; using TRUE
## Warning in type.convert.default(...): 'as.is' should be specified by the
## caller; using TRUE
## Warning in type.convert.default(...): 'as.is' should be specified by the
## caller; using TRUE
## Warning in type.convert.default(...): 'as.is' should be specified by the
## caller; using TRUE
## Warning in type.convert.default(...): 'as.is' should be specified by the
## caller; using TRUE
## Warning in type.convert.default(...): 'as.is' should be specified by the
## caller; using TRUE
## Warning in type.convert.default(...): 'as.is' should be specified by the
## caller; using TRUE

##  DONE!

4 Launch the Shiny Gadget

Explore the results for search eninge scores to find correct names of search engine scores in the mzID.

evalTargetDecoys(msgf)

5 Evaluate target decoy assumptions

evalTargetDecoys(msgf,"isdecoy","ms-gf:evalue")

• The plots show that the distribution of the MSGF+ PSM scores are nicely bimodal.

• The separation between good target PSM scores and bad target PSM scores is less pronounced than for peptide shaker. So it is beneficial to include the other engines with peptideshaker.

• We do not see deviations from the target decoy assumptions.