OpenMS
2.6.0
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Groups corresponding features from multiple maps.
potential predecessor tools | FeatureLinkerUnlabeled | potential successor tools |
FeatureFinderCentroided (or another feature detection algorithm) | ProteinQuantifier | |
MapAlignerPoseClustering (or another map alignment algorithm) | TextExporter | |
SeedListGenerator |
This tool provides an algorithm for grouping corresponding features in multiple runs of label-free experiments. For more details and algorithm-specific parameters (set in the INI file) see "Detailed Description" in the algorithm documentation or the INI file table below.
FeatureLinkerUnlabeled takes several feature maps (featureXML files) and stores the corresponding features in a consensus map (consensusXML file). Feature maps can be created from MS experiments (peak data) using one of the FeatureFinder TOPP tools.
Advanced users can convert the consensusXML generated by this tool to EDTA using FileConverter and plot the distribution of distances in RT (or m/z) between different input files (can be done in Excel). The distribution should be Gaussian-like with very few points beyond the tails. Points far away from the Gaussian indicate a too wide tolerance. A Gaussian with its left/right tail trimmed indicates a too narrow tolerance.
The command line parameters of this tool are:
FeatureLinkerUnlabeled -- Groups corresponding features from multiple maps. Full documentation: http://www.openms.de/documentation/TOPP_FeatureLinkerUnlabeled.html Version: 2.6.0 Sep 30 2020, 12:54:34, Revision: c26f752 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: FeatureLinkerUnlabeled <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 <files>* Input files separated by blanks (valid formats: 'featureXML', 'consensusXML') -out <file>* Output file (valid formats: 'consensusXML') -design <file> Input file containing the experimental design (valid formats: 'tsv') -keep_subelements For consensusXML input only: If set, the sub-features of the inputs are transferred to the output. 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 parameters 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/documentation/TOPP_FeatureLinkerUnlabeled.html
INI file documentation of this tool: