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
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
PrecursorIonSelector <options>
This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti
on 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 <idxml file>* File containing results of identification (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
-db_path <db-file> Db file (valid formats: 'fasta')
-rt_model <rt-model-file> SVM Model for RTPredict
-dt_model <dt-model-file> SVM Model for PTPredict
-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.
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 algorithm's documentation:
OpenMS::PrecursorIonSelection
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |