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.

Note: Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

PrecursorIonSelector -- PrecursorIonSelector
Full documentation: http://www.openms.de/doxygen/release/3.0.0/html/TOPP_PrecursorIonSelector.html
Version: 3.0.0 Jul 14 2023, 11:57:33, Revision: be787e9
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/doxygen/release/3.0.0/html/TOPP_PrecursorIonSelector.html

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+PrecursorIonSelectorPrecursorIonSelector

version3.0.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'PrecursorIonSelector'

in Input feature map file (featureXML)input file*.featureXML

out modified feature mapoutput file*.featureXML

next_feat feature map (featureXML) file with the selected precursorsoutput file*.featureXML

ids file containing results of identificationinput file*.idXML

num_precursors1 number of precursors to be selected

raw_data Input profile data.input file*.mzML

load_preprocessingfalse The preprocessed db is loaded from file, not calculated.true, false

store_preprocessingfalse The preprocessed db is stored.true, false

simulationfalse Simulate the whole LC-MS/MS run.true, false

sim_results File containing the results of the simulation runoutput file*.txt

db_path db fileinput file*.fasta

rt_model SVM Model for RTPredictinput file*.txt

dt_model SVM Model for PTPredictinput file*.txt

solverGLPK LP solver typeGLPK, COINOR

fixed_modifications[] the modifications i.e. Carboxymethyl (C)

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue, false

forcefalse Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false

+++algorithmSettings for the compound list creation and rescoring.

typeIPS Strategy for precursor ion selection.ILP_IPS, IPS, SPS, Upshift, Downshift, DEX

max_iteration100 Maximal number of iterations.1:∞

rt_bin_capacity10 Maximal number of precursors per rt bin.1:∞

step_size1 Maximal number of precursors per iteration.1:∞

peptide_min_prob0.2 Minimal peptide probability.

sequential_spectrum_orderfalse If true, precursors are selected sequentially with respect to their RT.true, false

++++MIPFormulation

+++++thresholds

min_protein_probability0.2 Minimal protein probability for a protein to be considered in the ILP0.0:1.0

min_protein_id_probability0.95 Minimal protein probability for a protein to be considered identified.0.0:1.0

min_pt_weight0.5 Minimal pt weight of a precursor0.0:1.0

min_mz500.0 Minimal mz to be considered in protein based LP formulation.0.0:∞

max_mz5000.0 Minimal mz to be considered in protein based LP formulation.0.0:∞

min_pred_pep_prob0.5 Minimal predicted peptide probability of a precursor0.0:1.0

min_rt_weight0.5 Minimal rt weight of a precursor0.0:1.0

use_peptide_rulefalse Use peptide rule instead of minimal protein id probabilitytrue, false

min_peptide_ids2 If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id1:∞

min_peptide_probability0.95 If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified0.0:1.0

+++++combined_ilp

k10.2 combined ilp: weight for z_i0.0:∞

k20.2 combined ilp: weight for x_j,s*int_j,s0.0:∞

k30.4 combined ilp: weight for -x_j,s*w_j,s0.0:∞

scale_matching_probstrue flag if detectability * rt_weight shall be scaled to cover all [0,1]true, false

+++++feature_based

no_intensity_normalizationfalse Flag indicating if intensities shall be scaled to be in [0,1]. This is done for each feature separately, so that the feature's maximal intensity in a spectrum is set to 1.true, false

max_number_precursors_per_feature1 The maximal number of precursors per feature.1:∞

++++Preprocessing

precursor_mass_tolerance10.0 Precursor mass tolerance which is used to query the peptide database for peptides0.0:∞

precursor_mass_tolerance_unitppm Precursor mass tolerance unit.ppm, Da

preprocessed_db_path Path where the preprocessed database should be stored

preprocessed_db_pred_rt_path Path where the predicted rts of the preprocessed database should be stored

preprocessed_db_pred_dt_path Path where the predicted rts of the preprocessed database should be stored

max_peptides_per_run100000 Number of peptides for that the pt and rt are parallelly predicted.1:∞

missed_cleavages1 Number of allowed missed cleavages.0:∞

taxonomy Taxonomy

tmp_dir Absolute path to tmp data directory used to store files needed for rt and dt prediction.

store_peptide_sequencesfalse Flag if peptide sequences should be stored.true, false

+++++rt_settings

min_rt960.0 Minimal RT in the experiment (in seconds)1.0:∞

max_rt3840.0 Maximal RT in the experiment (in seconds)

rt_step_size30.0 Time between two consecutive spectra (in seconds)

gauss_mean-1.0 mean of the gauss curve

gauss_sigma3.0 std of the gauss curve

For the parameters of the algorithm section see the algorithm's documentation:
OpenMS::PrecursorIonSelection