OpenMS
2.5.0
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A tool for precursor ion selection based on identification results.
pot. predecessor tools | PrecursorIonSelector | pot. successor tools |
FeatureFinderCentroided | - |
This tool provides a precursor ion selection based on previous MS/MS identifications.
Different strategies can be chosen:
DEX | Dynamic exclusion of features with m/z matching predicted tryptic peptides masses of already identified proteins. |
SPS | Selection based on score reflecting the feature's suitability for fragmentation. |
Downshift | Similar to DEX, but features are not excluded, only ranked down in the feature list |
Upshift | Features with m/z matching predicted tryptic peptide masses of unidentified proteins are ranked up. |
IPS | Combination of Down- and Upshift. |
ILP_IPS | Iterative precursor ion selection using LP formulations. |
This method is described in: Zerck, A. and Nordhoff, E. and Resemann, A. and Mirgorodskaya, E. and Suckau, D. and Reinert, K. and Lehrach, H. and Gobom, J.: An iterative strategy for precursor ion selection for LC-MS/MS based shotgun proteomics, J Prot Res, 2009, 8 (7), 3239-3251.
Given the feature map of the LC-MS run and the identification results the tool determines the next precursors. The precursors are ranked depending on the chosen strategy.
It is also possible run a simulation of selection strategies on a complete LC-MS/MS run, e.g. to determine what would have been the most efficient strategy.
The command line parameters of this tool are:
PrecursorIonSelector -- PrecursorIonSelector Full documentation: http://www.openms.de/documentation/TOPP_PrecursorIonSelector.html Version: 2.5.0-nightly-2020-03-06 Mar 7 2020, 01:22:16, Revision: 84b1398 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: PrecursorIonSelector <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 <input file>* Input feature map file (featureXML) (valid formats: 'featureXML') -out <output file> Modified feature map (valid formats: 'featureXML') -next_feat <output file> Feature map (featureXML) file with the selected precursors (valid formats: 'featureXML') -ids <id file>* File containing results of identification (valid formats: 'idXML') -num_precursors <Int> Number of precursors to be selected (default: '1') -raw_data <file> Input profile data. (valid formats: 'mzML') -load_preprocessing The preprocessed db is loaded from file, not calculated. -store_preprocessing The preprocessed db is stored. -simulation Simulate the whole LC-MS/MS run. -sim_results <output file> File containing the results of the simulation run (valid formats: 'txt') -db_path <db-file> Db file (valid formats: 'fasta') -rt_model <rt-model-file> SVM Model for RTPredict (valid formats: 'txt') -dt_model <dt-model-file> SVM Model for PTPredict (valid formats: 'txt') -fixed_modifications <mods> The modifications i.e. Carboxymethyl (C) 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 Settings for the compound list creation and rescoring. 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_PrecursorIonSelector.html
INI file documentation of this tool:
For the parameters of the algorithm section see the algorithm's documentation:
OpenMS::PrecursorIonSelection