q3ML

Pwiz Free Parsing for Selective Reaction Monitoring (SRM) Mass Spectrometry (MS) .mzML Files

Installation

q3ML can de installed directly from GitHub using the remotes packages

remotes::install_github('wilsontom/q3ML')

Learn More

The package documentation can be browsed online at https://wilsontom/github.io/q3ML.

Quick Start

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