OpenMS  3.0.0
MRMMapper

MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML).

potential predecessor tools $ \longrightarrow $ MRMMapper $ \longrightarrow $ potential successor tools
FileFilter OpenSwathAnalyzer
MRMTransitionGroupPicker

This tool reads an mzML containing chromatograms (presumably measured on an SRM instrument) and a TraML file that contains the data that was used to generate the instrument method to measure said data. It then maps the transitions in the TraML file to the chromatograms found in the mzML file and stores the chromatograms annotated with meta-data from the TraML file. Thus, the output chromatograms are an annotated copy of the input chromatograms with native id, precursor information and peptide sequence (if available) annotated in the chromatogram files.

The algorithm tries to match a given set of chromatograms and targeted assays. It iterates through all the chromatograms retrieves one or more matching targeted assay for the chromatogram. By default, the algorithm assumes that a 1:1 mapping exists. If a chromatogram cannot be mapped (does not have a corresponding assay) the algorithm issues a warning, the user can specify that the program should abort in such a case (see error_on_unmapped).

If multiple mapping is enabled (see map_multiple_assays parameter) then each mapped assay will get its own chromatogram that contains the same raw data but different meta-annotation. This *can* be useful if the same transition is used to monitor multiple analytes but may also indicate a problem with too wide mapping tolerances.

The thus mapped mzML file can then be used in a downstream analysis.

The command line parameters of this tool are:

MRMMapper -- MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_MRMMapper.html
Version: 3.0.0-pre-nightly-2022-07-20 Jul 21 2022, 00:07:28, Revision: ea0316e
To cite OpenMS:
  Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

Usage:
  MRMMapper <options>

This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript
ion or use the --helphelp option.

Options (mandatory options marked with '*'):
  -in <file>*        Input file containing chromatograms (converted mzXML file) (valid formats: 'mzML')
  -tr <file>*        Transition file (valid formats: 'traML')
  -out <file>*       Output file containing mapped chromatograms (valid formats: 'mzML')
                     
Common TOPP options:
  -ini <file>        Use the given TOPP INI file
  -threads <n>       Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini <file>  Writes the default configuration file
  --help             Shows options
  --helphelp         Shows all options (including advanced)

The following configuration subsections are valid:
 - algorithm   Algorithm parameters section

You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
For more information, please consult the online documentation for this tool:
  - http://www.openms.de/doxygen/nightly/html/TOPP_MRMMapper.html

The algorithm parameters for the Analyzer filter are:

Legend:
required parameter
advanced parameter
+MRMMapperMRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)
version3.0.0-pre-nightly-2022-07-20 Version of the tool that generated this parameters file.
++1Instance '1' section for 'MRMMapper'
in Input file containing chromatograms (converted mzXML file)input file*.mzML
tr transition fileinput file*.traML
out Output file containing mapped chromatogramsoutput file*.mzML
log Name of log file (created only when specified)
debug0 Sets the debug level
threads1 Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse Disables progress logging to command linetrue,false
forcefalse Overrides tool-specific checkstrue,false
testfalse Enables the test mode (needed for internal use only)true,false
+++algorithmAlgorithm parameters section
precursor_tolerance0.1 Precursor tolerance when mapping (in Th)
product_tolerance0.1 Product tolerance when mapping (in Th)
map_multiple_assaysfalse Allow to map multiple assays to chromatograms and duplicate these chromatograms in the output.true,false
error_on_unmappedfalse Treat remaining, unmapped chromatograms as an errortrue,false