OpenMS: 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	$\longrightarrow$ PeptideIndexer $\longrightarrow$	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 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. However, we can recover these cases by using tolerant search in these cases (done automatically). In all cases we require ambiguous AA's in peptide sequence to match exactly in the protein DB (i.e., 'X' in peptide only matches 'X').

Two search modes are available:

exact: Peptide sequences require exact match in protein database. If no protein for this peptide can be found, tolerant matching is automatically used for this peptide. Thus, the results for these peptides are identical for both search modes.
tolerant: Allow ambiguous AA's in protein sequence, e.g., 'M' in peptide will match 'X' in protein. This mode might yield more protein hits for some peptides (even though they have exact matches as well).

The exact mode is much faster (about x10) and consumes less memory (about x2.5), but might fail to report a few proteins 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.

The command line parameters of this tool are:

PeptideIndexer -- Refreshes the protein references for all peptide hits.
Version: 1.10.0 Mar  7 2013, 08:30:22, Revision: unknown

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')
  -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.

version1.10.0 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