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 |