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 |