Legend:

required parameter

advanced parameter

+PrecursorIonSelectorPrecursorIonSelector

version1.10.0 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 identification (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 run

db_path db fileinput file*.fasta

rt_model SVM Model for RTPredict

dt_model SVM Model for PTPredict

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

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 ILP0:1

min_protein_id_probability0.95 Minimal protein probability for a protein to be considered identified.0:1

min_pt_weight0.5 Minimal pt weight of a precursor0:1

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

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

min_pred_pep_prob0.5 Minimal predicted peptide probability of a precursor0:1

min_rt_weight0.5 Minimal rt weight of a precursor0:1

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 identified0:1

+++++combined_ilp

k10.2 combined ilp: weight for z_i0:∞

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

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

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

++++Preprocessing

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

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 parallely 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.

+++++rt_settings

min_rt960 Minimal RT in the experiment (in seconds)1:∞

max_rt3840 Maximal RT in the experiment (in seconds)

rt_step_size30 Time between two consecutive spectra (in seconds)

gauss_mean-1 mean of the gauss curve

gauss_sigma3 std of the gauss curve