Pwiz Free Parsing for Selective Reaction Monitoring (SRM) Mass Spectrometry (MS) .mzML Files
q3ML can de installed directly from GitHub using the remotes packages
remotes::install_github('wilsontom/q3ML')The package documentation can be browsed online at https://wilsontom/github.io/q3ML.
For mzML files that have been converted using msconvert pwiz Version 3.0.2000 or lower, then mzR should be used to open the files.
library(q3ML)
mzml_files <- list.files(system.file('extdata', package = 'q3ML'),
full.names = TRUE)
Pwiz_301 <- openFile(mzml_files[1])
! Use mzR for files converted with pwiz version <= 3.0.2000
Pwiz_301 <- mzR::openMSfile(mzml_files[1])
> Pwiz_V3_01
Mass Spectrometry file handle.
Filename: QC01_pwiz3_0_1.mzML
Number of scans: 0
For .mzML files which have been created using msconvert pwiz Version > 3.0.2 then q3ML can be used to parse the file, if mzR throws an error.
Pwiz_V3_02 <- mzR::openMSfile(mzml_files[2])
Error: Can not open file /home/R/x86_64-pc-linux-gnu-library/4.1/q3ML/extdata/QC01_pwiz3_0_2.mzML!
Original error was: Error in pwizModule$open(filename): [IO::HandlerBinaryDataArray] Unknown binary data type.
Pwiz_V3_02 <- openFile(mzml_files[2])
identical(Pwiz_V3_02$header,mzR::chromatogramHeader(Pwiz_V3_01))
[1] TRUE
identical(Pwiz_V3_02$peaks,mzR::chromatograms(Pwiz_V3_01))
[1] TRUE