FeatureFinderMRM

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.

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/release/3.0.0/html/TOPP_FeatureFinderMRM.html
Version: 3.0.0 Jul 14 2023, 11:57:33, Revision: be787e9
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:
  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/release/3.0.0/html/TOPP_FeatureFinderMRM.html

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

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

version3.0.0 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