Filters protein identification engine results by different criteria.
| potential predecessor tools |  IDFilter   | 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: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
  IDFilter <options>
Options (mandatory options marked with '*'):
  -in <file>*                       Input file  (valid formats: 'idXML')
  -out <file>*                      Output file  (valid formats: 'idXML')
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 score 
                                    is dependent on the most recent(!) preprocessing - it could be Mascot
                                    scores (if a MascotAdapter was applied before), or an FDR (if FalseDiscov
                                    eryRate was applied before), etc. (default: '0')
  -score:prot <score>               The score which should be reached by a protein hit to be kept. (default: 
                                    '0')
Filtering by significance threshold:
  -thresh:pep <fraction>            Keep a peptide hit only if its score is above this fraction of the peptid
                                    e significance threshold. (default: '0')
  -thresh:prot <fraction>           Keep a protein hit only if its score is above this fraction of the protei
                                    n significance threshold. (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 rem
                                    oved
                                    All proteins whose accession is not present in this file are removed. (v
                                    alid formats: 'fasta')
  -whitelist:by_seq_only            Match peptides with FASTA file by sequence instead of accession and disab
                                    le protein filtering.
Filtering by blacklisting (only instances not present in a blacklist file can pass):
  -blacklist:peptides <file>        Peptides having the same sequence as any peptide in this file will be 
                                    filtered out
                                    (valid formats: 'idXML')
Filtering by RT predicted by 'RTPredict':
  -rt:p_value <float>               Retention time filtering by the p-value predicted by RTPredict. (default:
                                    '0' min: '0' max: '1')
  -rt:p_value_1st_dim <float>       Retention time filtering by the p-value predicted by RTPredict for first 
                                    dimension. (default: '0' min: '0' max: '1')
Filtering by mz:
  -mz:error <float>                 Filtering by deviation to theoretical mass (disabled for negative values)
                                    . (default: '-1')
  -mz:unit <String>                 Absolute or relativ 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 scorin
                                    g 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' max:
                                    '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 isofor
                                    ms count as different proteins!
  -keep_unreferenced_protein_hits   Proteins not referenced by a peptide are retained in the idXML.
                                    
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 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |