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InclusionExclusionListCreator (version 2.3.0)

Inclusion list input file in FASTA or featureXML format:

(-include)

Exclusion list input file in featureXML, idXML or FASTA format:

(-exclude)

RTModel file used for the rt prediction of peptides in FASTA files:

(-rt_model)

PTModel file used for the pt prediction of peptides in FASTA files (only needed for inclusion_strategy PreotinBased_LP):

(-pt_model)

param_inclusion_charges

param_inclusion_charges 0

strategy to be used for selection:

(-inclusion_strategy)

param_exclusion_charges

param_exclusion_charges 0

File containing the raw data (only needed for FeatureBased_LP):

(-raw_data)

Number of missed cleavages used for protein digestion:

(-missed_cleavages)

Create lists with units as seconds instead of minutes:

(-unit)

Use relative RT window, which depends on RT of precurso:

(-use_relative)

[for RT:use_relative == true] The relative factor X for the RT exclusion window,:

(-window_relative) e.g. the window is calculated as [rt - rt*X, rt + rt*X]

[for RT:use_relative == false] The absolute value X for the RT exclusion window in [sec],:

(-window_absolute) e.g. the window is calculated as [rt - X, rt + X]

Two inclusion/exclusion windows are merged when they (almost) overlap in RT (see 'rt_tol') and are close in m/z by this tolerance:

(-mz_tol) Unit of this is defined in 'mz_tol_unit'

Unit of 'mz_tol':

(-mz_tol_unit)

Maximal RT delta (in seconds) which would allow two windows in RT to overlap (which causes merging the windows):

(-rt_tol) 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]

Number of allowed MS/MS spectra in a retention time bin:

(-ms2_spectra_per_rt_bin)

If true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection:

(-exclude_overlapping_peaks)

If true dynamic exclusion is applied:

(-use_dynamic_exclusion)

The time (in seconds) a feature is excluded:

(-exclusion_time)

The maximal number of precursors in the inclusion list:

(-max_list_size)

Minimal rt in seconds:

(-min_rt)

Maximal rt in seconds:

(-max_rt)

rt step size in seconds:

(-rt_step_size)

rt window size in seconds:

(-rt_window_size)

Minimal protein probability for a protein to be considered identified:

(-min_protein_id_probability)

Minimal pt weight of a precurso:

(-min_pt_weight)

Minimal mz to be considered in protein based LP formulation:

(-min_mz)

Minimal mz to be considered in protein based LP formulation:

(-max_mz)

Use peptide rule instead of minimal protein id probability:

(-use_peptide_rule)

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

(-min_peptide_ids)

If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified:

(-min_peptide_probability)

Flag indicating if intensities shall be scaled to be in [0,1]:

(-no_intensity_normalization) This is done for each feature separately, so that the feature's maximal intensity in a spectrum is set to 1

The maximal number of precursors per feature:

(-max_number_precursors_per_feature)

Advanced Options: