OpenMS
2.4.0
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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. Version: 2.4.0 Oct 29 2018, 15:52:19, Revision: 9690d06 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. Have a look at the OpenMS documentation for more information.
INI file documentation of this tool:
For the parameters of the algorithm section see the algorithms documentation:
OpenMS::FeatureFinderAlgorithmMRM FeatureFinderAlgorithmMRM