OpenMS
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The feature detection application for quantitation.
pot. predecessor tools | → FeatureFinderMRM → | pot. successor tools |
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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-nightly-2024-04-19 Apr 20 2024, 01:59:17, Revision: 88f4931 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:
For the parameters of the algorithm section see the algorithms documentation:
OpenMS::FeatureFinderAlgorithmMRM FeatureFinderAlgorithmMRM