| OpenMS 2.5.0

PrecursorIonSelector

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/documentation/TOPP_PrecursorIonSelector.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    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:

Legend:
required parameter
advanced parameter
+PrecursorIonSelector PrecursorIonSelector
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'PrecursorIonSelector'
in Input feature map file (featureXML)input file*.featureXML
out modified feature map output file*.featureXML
next_feat feature map (featureXML) file with the selected precursors output file*.featureXML
ids file containing results of identification input file*.idXML
num_precursors 1 number of precursors to be selected
raw_data Input profile data.input file*.mzML
load_preprocessing false The preprocessed db is loaded from file, not calculated.true,false
store_preprocessing false The preprocessed db is stored.true,false
simulation false Simulate the whole LC-MS/MS run.true,false
sim_results File containing the results of the simulation run output file*.txt
db_path db file input file*.fasta
rt_model SVM Model for RTPredict input file*.txt
dt_model SVM Model for PTPredict input file*.txt
solver GLPK LP solver type GLPK,COINOR
fixed_modifications[] the modifications i.e. Carboxymethyl (C)
log Name of log file (created only when specified)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false
+++algorithm Settings for the compound list creation and rescoring.
type IPS Strategy for precursor ion selection.ILP_IPS,IPS,SPS,Upshift,Downshift,DEX
max_iteration 100 Maximal number of iterations.1:∞
rt_bin_capacity 10 Maximal number of precursors per rt bin.1:∞
step_size 1 Maximal number of precursors per iteration.1:∞
peptide_min_prob 0.2 Minimal peptide probability.
sequential_spectrum_order false If true, precursors are selected sequentially with respect to their RT.true,false
++++MIPFormulation
+++++thresholds
min_protein_probability 0.2 Minimal protein probability for a protein to be considered in the ILP 0.0:1.0
min_protein_id_probability 0.95 Minimal protein probability for a protein to be considered identified.0.0:1.0
min_pt_weight 0.5 Minimal pt weight of a precursor 0.0:1.0
min_mz 500.0 Minimal mz to be considered in protein based LP formulation.0.0:∞
max_mz 5000.0 Minimal mz to be considered in protein based LP formulation.0.0:∞
min_pred_pep_prob 0.5 Minimal predicted peptide probability of a precursor 0.0:1.0
min_rt_weight 0.5 Minimal rt weight of a precursor 0.0:1.0
use_peptide_rule false Use peptide rule instead of minimal protein id probability true,false
min_peptide_ids 2 If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id 1:∞
min_peptide_probability 0.95 If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified 0.0:1.0
+++++combined_ilp
k1 0.2 combined ilp: weight for z_i 0.0:∞
k2 0.2 combined ilp: weight for x_j,s*int_j,s 0.0:∞
k3 0.4 combined ilp: weight for -x_j,s*w_j,s 0.0:∞
scale_matching_probs true flag if detectability * rt_weight shall be scaled to cover all [0,1]true,false
+++++feature_based
no_intensity_normalization false 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_feature 1 The maximal number of precursors per feature.1:∞
++++Preprocessing
precursor_mass_tolerance 10.0 Precursor mass tolerance which is used to query the peptide database for peptides 0.0:∞
precursor_mass_tolerance_unit ppm 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_run 100000 Number of peptides for that the pt and rt are parallely predicted.1:∞
missed_cleavages 1 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_sequences false Flag if peptide sequences should be stored.
+++++rt_settings
min_rt 960.0 Minimal RT in the experiment (in seconds)1.0:∞
max_rt 3840.0 Maximal RT in the experiment (in seconds)
rt_step_size 30.0 Time between two consecutive spectra (in seconds)
gauss_mean-1.0 mean of the gauss curve
gauss_sigma 3.0 std of the gauss curve

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