Filters protein identification engine results by different criteria.
potential predecessor tools | ![]() ![]() | potential successor tools |
MascotAdapter (or other ID engines) | PeptideIndexer | |
IDFileConverter | ProteinInference | |
FalseDiscoveryRate | IDMapper | |
ConsensusID |
This tool is used to filter the identifications found by a peptide/protein identification tool like Mascot. Different filters can be applied:
To enable any of the filters, just change their default value. All active filters will be applied in order.
The command line parameters of this tool are:
IDFilter -- Filters results from protein or peptide identification engines based on different criteria. Version: 2.0.0 Mar 30 2016, 12:52:33, Revision: GIT-NOTFOUND Usage: IDFilter <options> Options (mandatory options marked with '*'): -in <file>* Input file (valid formats: 'idXML') -out <file>* Output file (valid formats: 'idXML') Filtering by precursor RT or m/z: -precursor:rt [min]:[max] Retention time range to extract. (default: ':') -precursor:mz [min]:[max] Mass-to-charge range to extract. (default: ':') -precursor:allow_missing When filtering by precursor RT or m/z, keep peptide IDs with missing precursor information ('RT'/'MZ' meta values)? Filtering by peptide/protein score. To enable any of the filters below, just change their default value. All active filters will be applied in order.: -score:pep <score> The score which should be reached by a peptide hit to be kept. The scor e is dependent on the most recent(!) preprocessing - it could be Mascot scores (if a MascotAdapter was applied before), or an FDR (if FalseDis coveryRate was applied before), etc. (default: '0') -score:prot <score> The score which should be reached by a protein hit to be kept. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides. (default: '0') Filtering by significance threshold: -thresh:pep <fraction> Keep a peptide hit only if its score is above this fraction of the pept ide significance threshold. (default: '0') -thresh:prot <fraction> Keep a protein hit only if its score is above this fraction of the prot ein significance threshold. Use in combination with 'delete_unreference d_peptide_hits' to remove affected peptides. (default: '0') Filtering by whitelisting (only instances also present in a whitelist file can pass): -whitelist:proteins <file> Filename of a FASTA file containing protein sequences. All peptides that are not a substring of a sequence in this file are r emoved All proteins whose accession is not present in this file are removed. (valid formats: 'fasta') -whitelist:by_seq_only Match peptides with FASTA file by sequence instead of accession and disable protein filtering. Filtering by blacklisting (only instances not present in a blacklist file can pass): -blacklist:peptides <file> Peptides having the same sequence and modification assignment as any peptide in this file will be filtered out. Use with blacklist:ignore_mo dification flag to only compare by sequence. (valid formats: 'idXML') -blacklist:ignore_modifications Compare blacklisted peptides by sequence only. Filtering by RT predicted by 'RTPredict': -rt:p_value <float> Retention time filtering by the p-value predicted by RTPredict. (defaul t: '0' min: '0' max: '1') -rt:p_value_1st_dim <float> Retention time filtering by the p-value predicted by RTPredict for firs t dimension. (default: '0' min: '0' max: '1') Filtering by mz: -mz:error <float> Filtering by deviation to theoretical mass (disabled for negative value s). (default: '-1') -mz:unit <String> Absolute or relative error. (default: 'ppm' valid: 'Da', 'ppm') Filtering best hits per spectrum (for peptides) or from proteins: -best:n_peptide_hits <integer> Keep only the 'n' highest scoring peptide hits per spectrum (for n>0). (default: '0' min: '0') -best:n_protein_hits <integer> Keep only the 'n' highest scoring protein hits (for n>0). (default: '0' min: '0') -best:strict Keep only the highest scoring peptide hit. Similar to n_peptide_hits=1, but if there are two or more highest scor ing hits, none are kept. -min_length <integer> Keep only peptide hits with a length greater or equal this value. Value 0 will have no filter effect. (default: '0' min: '0') -max_length <integer> 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. (default: '0' min: '0') -min_charge <integer> Keep only peptide hits for tandem spectra with charge greater or equal this value. (default: '1' min: '1') -var_mods Keep only peptide hits with variable modifications (fixed modifications from SearchParameters will be ignored). -unique If a peptide hit occurs more than once per PSM, only one instance is kept. -unique_per_protein Only peptides matching exactly one protein are kept. Remember that isof orms count as different proteins! -keep_unreferenced_protein_hits Proteins not referenced by a peptide are retained in the ids. -remove_decoys Remove proteins according to the information in the user parameters. Usually used in combination with 'delete_unreferenced_peptide_hits'. -delete_unreferenced_peptide_hits Peptides not referenced by any protein are deleted in the ids. Usually used in combination with 'score:prot' or 'thresh:prot'. 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)
INI file documentation of this tool:
OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 16:18:43 using doxygen 1.8.5 |