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 mapping by replacing the "id" parameter in the mzML with the "id" of the transition in the TraML file. It removes chromatograms for which it cannot find a mapping and throws an error if more than one transitions maps to a chromatogram. In strict mode (default) it also throws an error it not all chromatograms are found in the TraML file.

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)
Version: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

Usage:
  MRMMapper <options>

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')
  -precursor_tolerance <double>  Precursor tolerance when mapping (in Th) (default: '0.1')
  -product_tolerance <double>    Product tolerance when mapping (in Th) (default: '0.1')
  -no-strict                     Run in non-strict mode and allow some chromatograms to not be mapped.
  -allow_multiple_mappings       Allow multiple mappings (will take the last matching from the TraML)
                                 
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 algorithm parameters for the Analyzer filter are:

Legend:

required parameter

advanced parameter

+MRMMapperMRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)

version2.3.0 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

precursor_tolerance0.1 Precursor tolerance when mapping (in Th)

product_tolerance0.1 Product tolerance when mapping (in Th)

no-strictfalse run in non-strict mode and allow some chromatograms to not be mapped.true,false

allow_multiple_mappingsfalse Allow multiple mappings (will take the last matching from the TraML)true,false

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 Overwrite tool specific checks.true,false

testfalse Enables the test mode (needed for internal use only)true,false