MRMConverteR

convert MRM-MS (.mzML) files to LC-MS style .mzML

devtools::install_github('wilsontom/MRMConverteR')

Usage

MRM-MS .mzML files should have been created using the ProteoWizard msconvert tool.

NOTE this package has only been tested with MRM-MS data acquired on a TSQ Vantage (ThermoScientific) which were then converted to .mzML using ProteoWizard 3.0.10246 64-bit.

There is only one function exported from MRMConverteR: convert

The function input is (1) the .mzML to convert and (2) the destination path for the converted file. Filenames of converted files are the same as the input; with convert- prepended. The return option is if instead you want to retain the new LC-MS style peak-list in the console and not write to a new .mzML file. The default for this option is FALSE.

library(MRMConverteR)

convert('inst/extdata/example_qqq.mzML', 'inst/extdata', return = FALSE)

list.files('inst/extdata')
[1] "convert-example_qqq.mzML" "example_qqq.mzML"

library(mzR)

MRMfile <- openMSfile('inst/extdata/example_qqq.mzML')

# Original MRM file has no scans; only chromatograms
MRMfile
Mass Spectrometry file handle.
Filename:  example_qqq.mzML
Number of scans:  0

nChrom(MRMfile)
[1] 82


LCfile <- openMSfile('inst/extdata/convert-example_qqq.mzML')

# The new LC-MS style converted file now has readable scans
LCfile
Mass Spectrometry file handle.
Filename:  convert_example_qqq.mzML
Number of scans:  2872

# and no chromatograms
nChrom(LCfile)
[1] 0