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required parameter

advanced parameter

+InclusionExclusionListCreatorCreates inclusion and/or exclusion lists.

version1.10.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'InclusionExclusionListCreator'

include Inclusion list input file in FASTA or featureXML format.input file*.featureXML,*.fasta

exclude Exclusion list input file in featureXML, idXML or FASTA format.input file*.featureXML,*.idXML,*.fasta

out Output file (tab delimited csv file).output file*.csv

rt_model RTModel file used for the rt prediction of peptides in FASTA files.input file*.txt

pt_model PTModel file used for the pt prediction of peptides in FASTA files (only needed for inclusion_strategy PreotinBased_LP).input file*.txt

inclusion_charges[] List containing the charge states to be considered for the inclusion list compounds, space separated.1:∞

inclusion_strategyALL strategy to be used for selectionFeatureBased_LP,ProteinBased_LP,ALL

exclusion_charges[] List containing the charge states to be considered for the exclusion list compounds (for idXML and FASTA input), space separated.1:∞

raw_data File containing the raw data (only needed for FeatureBased_LP).input file*.mzML

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

+++algorithmInclusion/Exclusion algorithm section

++++InclusionExclusionList

missed_cleavages0 Number of missed cleavages used for protein digestion.

+++++RT

unitminutes Create lists with units as seconds instead of minutesminutes,seconds

use_relativetrue Use relative RT window, which depends on RT of precursor.true,false

window_relative0.05 [for RT:use_relative == true] The relative factor X for the RT exclusion window, e.g. the window is calculated as [rt - rt*X, rt + rt*X].0:10

window_absolute90 [for RT:use_relative == false] The absolute value X for the RT exclusion window in [sec], e.g. the window is calculated as [rt - X, rt + X].0:∞

+++++merge

mz_tol10 Two inclusion/exclusion windows are merged when they (almost) overlap in RT (see 'rt_tol') and are close in m/z by this tolerance. Unit of this is defined in 'mz_tol_unit'.0:∞

mz_tol_unitppm Unit of 'mz_tol'ppm,Da

rt_tol1.1 Maximal RT delta (in seconds) which would allow two windows in RT to overlap (which causes merging the windows). Two inclusion/exclusion windows are merged when they (almost) overlap in RT and are close in m/z by this tolerance (see 'mz_tol'). Unit of this param is [seconds].0:∞

++++PrecursorSelection

ms2_spectra_per_rt_bin5 Number of allowed MS/MS spectra in a retention time bin.1:∞

min_peak_distance3 The minimal distance (in Da) of two peaks in one spectrum so that they can be selected.0:∞

selection_window2 All peaks within a mass window (in Da) of a selected peak are also selected for fragmentation.0:∞

exclude_overlapping_peaksfalse If true overlapping or nearby peaks (within min_peak_distance) are excluded for selection.true,false

+++++Exclusion

use_dynamic_exclusionfalse If true dynamic exclusion is applied.true,false

exclusion_time100 The time (in seconds) a feature is excluded.0:∞

+++++ProteinBasedInclusion

max_list_size1000 The maximal number of precursors in the inclusion list.1:∞

++++++rt

min_rt960 Minimal rt in seconds.0:∞

max_rt3840 Maximal rt in seconds.0:∞

rt_step_size30 rt step size in seconds.1:∞

rt_window_size100 rt window size in seconds.1:∞

++++++thresholds

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:∞

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