The feature detection application for quantitation.

pot. predecessor tools	→ FeatureFinderMRM →	pot. successor tools
		FeatureLinkerUnlabeled (or another feature grouping tool)
		MapAlignerPoseClustering (or another alignment tool)

This module identifies "features" in a LC/MS map. By feature, we understand a peptide in a MS sample that reveals a characteristic isotope distribution. The algorithm computes positions in rt and m/z dimension and a charge estimate of each peptide.

How to find suitable parameters and details of the different algorithms implemented are described in the "TOPP tutorial" (on https://openms.readthedocs.io/).

Specialized tools are available for some experimental techniques: IsobaricAnalyzer.

The command line parameters of this tool are:

FeatureFinderMRM -- Detects two-dimensional features in LC-MS data.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_FeatureFinderMRM.html
Version: 3.1.0-pre-FVdeploy-2025-01-12 Jan 12 2025, 12:57:41, Revision: 26f583c
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  FeatureFinderMRM <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 (valid formats: 'mzML')
  -out <file>*       Output file (valid formats: 'featureXML')
                     
                     
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 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_FeatureFinderMRM.html

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+FeatureFinderMRMDetects two-dimensional features in LC-MS data.

version3.1.0-pre-FVdeploy-2025-01-12 Version of the tool that generated this parameters file.

++1Instance '1' section for 'FeatureFinderMRM'

in input fileinput file*.mzML

out output fileoutput file*.featureXML

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 section

min_rt_distance10.0 Minimal distance of MRM features in seconds.0.0:∞

min_num_peaks_per_feature5 Minimal number of peaks which are needed for a single feature1:∞

min_signal_to_noise_ratio2.0 Minimal S/N ratio a peak must have to be taken into account. Set to zero if the MRM-traces contains mostly signals, and no noise.0.0:∞

write_debug_filesfalse If set to true, for each feature a plot will be created, in the subdirectory 'debug'true, false

resample_tracesfalse If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimensiontrue, false

write_debuginfofalse If set to true, debug messages are written, the output can be somewhat lengthy.true, false

For the parameters of the algorithm section see the algorithms documentation:
OpenMS::FeatureFinderAlgorithmMRM FeatureFinderAlgorithmMRM