wilsontom/q3ml

Selective Reaction Monitoring (SRM) Mass Spectrometry (MS) mzML Parser

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