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PeptideIndexer

Refreshes the protein references for all peptide hits from a idXML file.

pot. predecessor tools $ \longrightarrow $ PeptideIndexer $ \longrightarrow $ pot. successor tools
IDFilter or
any protein/peptide processing tool
FalseDiscoveryRate

Each peptide hit is annotated by a target_decoy string, indicating if the peptide sequence is found in a 'target', a 'decoy' or in both 'target+decoy' protein. This information is crucial for the FalseDiscoveryRate IDPosteriorErrorProbability tools.

Note
Make sure that your protein names in the database contain a correctly formatted decoy string. This can be ensured by using DecoyDatabase. If the decoy identifier is not recognized successfully all proteins will be assumed to stem from the target-part of the query.
E.g., "sw|P33354_REV|YEHR_ECOLI Uncharacterized lipop..." is invalid, since the tool has no knowledge of how SwissProt entries are build up. A correct identifier could be "rev_sw|P33354|YEHR_ECOLI Uncharacterized li ..." or "sw|P33354|YEHR_ECOLI_rev Uncharacterized li", depending on if you are using prefix annotation or not.
This tool will also give you some target/decoy statistics when its done. Look carefully!

This tool supports relative database filenames, which (when not found in the current working directory) is looked up in the directories specified by 'OpenMS.ini:id_db_dir' (see TOPP for Advanced Users).

By default the tool will fail, if an unmatched peptide occurs, i.e. the database does not contain the corresponding protein. You can force the tool to return successfully in this case by using the flag 'allow_unmatched'.

Some search engines (such as Mascot) will replace ambiguous AA's ('B', 'Z', and 'X') in the protein database with unambiguous AA' in the reported peptides, e.g., exchange 'X' with 'H'. This will cause this peptide not to be found by exactly matching its sequence to the database. However, we can recover these cases by using tolerant search (done automatically).

Two search modes are available:

No matter if exact or tolerant search is used, we require ambiguous AA's in peptide sequence to match exactly in the protein DB (i.e., 'X' in peptide only matches 'X' in database). The exact mode is much faster (about x10) and consumes less memory (about x2.5), but might fail to report a few protein hits with ambiguous AAs for some peptides. Usually these proteins are putative, however. The exact mode also supports usage of multiple threads (use @ -threads option) to speed up computation even further, at the cost of some memory. This is only for the exact search though (Aho Corasick). If tolerant searching needs to be done for unassigned peptides, the latter will consume the major time portion.

Once a peptide sequence is found in a protein sequence, this does not imply that the hit is valid! This is where enzyme specificity comes into play. By default, we demand that the peptide is fully tryptic (since the enzyme parameter is set to "trypsin" and specificity is "full"). So unless the peptide coincides with C- and/or N-terminus of the protein, the peptide's cleavage pattern should fulfill the trypsin cleavage rule [KR][^P]. We make one exception for peptides which start at the second AA of the protein where the first AA of the protein is methionin (M), which is usually cleaved off in vivo, e.g., the two peptides AAAR and MAAAR would both match a protein starting with MAAAR.

You can relax the requirements further by chosing semi-tryptic (only one of two "internal" termini must match requirements) or none (essentially allowing all hits, no matter their context).

The command line parameters of this tool are:

PeptideIndexer -- Refreshes the protein references for all peptide hits.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976

Usage:
  PeptideIndexer <options>

Options (mandatory options marked with '*'):
  -in <file>*                     Input idXML file containing the identifications. (valid formats: 'idXML')
  -fasta <file>*                  Input sequence database in FASTA format. Non-existing relative file-names 
                                  are looked up via'OpenMS.ini:id_db_dir' (valid formats: 'fasta')
  -out <file>*                    Output idXML file. (valid formats: 'idXML')
  -decoy_string <string>          String that was appended (or prepended - see 'prefix' flag below) to the 
                                  accession of the protein database to indicate a decoy protein. (default:
                                  '_rev')
  -missing_decoy_action <action>  Action to take if NO peptide was assigned to a decoy protein (which indicat
                                  es wrong database or decoy string): 'error' (exit with error, no output),
                                  'warn' (exit with success, warning message) (default: 'error' valid: 'error
                                  ', 'warn')

The enzyme determines valid cleavage-sites and the cleavage specificity set by the user determines how these 
are enforced.:
  -enzyme:name                    Enzyme which determines valid cleavage sites, e.g., for trypsin it should 
                                  (unless at protein terminus) end on K or R and the AA-before should also
                                  be K or R, and not followed by proline. (default: 'Trypsin' valid: 'Trypsin
                                  ')
  -enzyme:specificity             Specificity of the enzyme.
                                  'full': both internal cleavage-sites must match.
                                  'semi': one of two internal cleavage-sites must match.
                                  'none': allow all peptide hits no matter their context. Therefore, the e
                                  nzyme chosen does not play a role here (default: 'full' valid: 'full', 'sem
                                  i', 'none')

  -write_protein_sequence         If set, the protein sequences are stored as well.
  -prefix                         If set, the database has protein accessions with 'decoy_string' as prefix.
  -keep_unreferenced_proteins     If set, protein hits which are not referenced by any peptide are kept.
  -allow_unmatched                If set, unmatched peptide sequences are allowed. By default (i.e. this flag
                                  is not set) the program terminates with error status on unmatched peptides
                                  .
  -full_tolerant_search           If set, all peptide sequences are matched using tolerant search. Thus poten
                                  tially more proteins (containing ambiguous AA's) are associated. This is
                                  much slower!
  -aaa_max <AA count>             Maximal number of ambiguous amino acids (AAA) allowed when matching to a 
                                  protein DB with AAA's. AAA's are 'B', 'Z', and 'X' (default: '4' min: '0')
                                  
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:

Legend:
required parameter
advanced parameter
+PeptideIndexerRefreshes the protein references for all peptide hits.
version1.11.1 Version of the tool that generated this parameters file.
++1Instance '1' section for 'PeptideIndexer'
in Input idXML file containing the identifications.input file*.idXML
fasta Input sequence database in FASTA format. Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir'input file*.fasta
out Output idXML file.output file*.idXML
decoy_string_rev String that was appended (or prepended - see 'prefix' flag below) to the accession of the protein database to indicate a decoy protein.
missing_decoy_actionerror Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message)error,warn
write_protein_sequencefalse If set, the protein sequences are stored as well.true,false
prefixfalse If set, the database has protein accessions with 'decoy_string' as prefix.true,false
keep_unreferenced_proteinsfalse If set, protein hits which are not referenced by any peptide are kept.true,false
allow_unmatchedfalse If set, unmatched peptide sequences are allowed. By default (i.e. this flag is not set) the program terminates with error status on unmatched peptides.true,false
full_tolerant_searchfalse If set, all peptide sequences are matched using tolerant search. Thus potentially more proteins (containing ambiguous AA's) are associated. This is much slower!true,false
aaa_max4 Maximal number of ambiguous amino acids (AAA) allowed when matching to a protein DB with AAA's. AAA's are 'B', 'Z', and 'X'0:∞
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
+++enzymeThe enzyme determines valid cleavage-sites and the cleavage specificity set by the user determines how these are enforced.
nameTrypsin Enzyme which determines valid cleavage sites, e.g., for trypsin it should (unless at protein terminus) end on K or R and the AA-before should also be K or R, and not followed by proline.Trypsin
specificityfull Specificity of the enzyme.
'full': both internal cleavage-sites must match.
'semi': one of two internal cleavage-sites must match.
'none': allow all peptide hits no matter their context. Therefore, the enzyme chosen does not play a role here
full,semi,none

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5