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required parameter

advanced parameter

+IDFilterFilters results from protein or peptide identification engines based on different criteria.

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

++1Instance '1' section for 'IDFilter'

in input file input file*.idXML

out output file output file*.idXML

min_length0 Keep only peptide hits with a length greater or equal this value. Value 0 will have no filter effect.0:∞

max_length0 Keep only peptide hits with a length less or equal this value. Value 0 will have no filter effect. Value is overridden by min_length, i.e. if max_length < min_length, max_length will be ignored.-∞:0

min_charge1 Keep only peptide hits for tandem spectra with charge greater or equal this value.1:∞

var_modsfalse Keep only peptide hits with variable modifications (fixed modifications from SearchParameters will be ignored).true,false

uniquefalse If a peptide hit occurs more than once, only one instance is kept. This will (for instance) remove redundant identifications from multiple charge states or concurrent CID+HCD spectra.If you are aiming towards quantitation, you probably do *not* want to use this flag!true,false

unique_per_proteinfalse Only peptides matching exactly one protein are kept. Remember that isoforms count as different proteins!true,false

keep_unreferenced_protein_hitsfalse Proteins not referenced by a peptide are retained in the idXML.true,false

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

+++scoreFiltering by peptide/protein score. To enable any of the filters below, just change their default value. All active filters will be applied in order.

pep0 The score which should be reached by a peptide hit to be kept. The score is dependent on the most recent(!) preprocessing - it could be Mascot scores (if a MascotAdapter was applied before), or an FDR (if FalseDiscoveryRate was applied before), etc.

prot0 The score which should be reached by a protein hit to be kept.

+++threshFiltering by significance threshold

pep0 Keep a peptide hit only if its score is above this fraction of the peptide significance threshold.

prot0 Keep a protein hit only if its score is above this fraction of the protein significance threshold.

+++whitelistFiltering by whitelisting (only instances also present in a whitelist file can pass)

proteins filename of a FASTA file containing protein sequences.
All peptides that are not a substring of a sequence in this file are removed
All proteins whose accession is not present in this file are removed.input file*.fasta

by_seq_onlyfalse Match peptides with FASTA file by sequence instead of accession and disable protein filtering.true,false

+++blacklistFiltering by blacklisting (only instances not present in a blacklist file can pass)

peptides Peptides having the same sequence as any peptide in this file will be filtered out
input file*.idXML

+++rtFiltering by RT predicted by 'RTPredict'

p_value0 Retention time filtering by the p-value predicted by RTPredict.0:1

p_value_1st_dim0 Retention time filtering by the p-value predicted by RTPredict for first dimension.0:1

+++mzFiltering by mz

error-1 Filtering by deviation to theoretical mass (disabled for negative values).

unitppm Absolute or relativ error.Da,ppm

+++bestFiltering best hits per spectrum (for peptides) or from proteins

n_peptide_hits0 Keep only the 'n' highest scoring peptide hits per spectrum (for n>0).0:∞

n_protein_hits0 Keep only the 'n' highest scoring protein hits (for n>0).0:∞

strictfalse Keep only the highest scoring peptide hit.
Similar to n_peptide_hits=1, but if there are two or more highest scoring hits, none are kept.true,false

n_to_m_peptide_hits: peptide hit rank range to extracts