PeptideIndexer

Refreshes the protein references for all peptide hits.

Web Documentation for PeptideIndexer

Options

version
Version of the tool that generated this parameters file.
decoy_string
String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins. If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix).
decoy_string_position
Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession? (ignored if decoy_string is empty)
missing_decoy_action
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), 'silent' (no action is taken, not even a warning)
write_protein_sequence
If set, the protein sequences are stored as well.
write_protein_description
If set, the protein description is stored as well.
keep_unreferenced_proteins
If set, protein hits which are not referenced by any peptide are kept.
unmatched_action
If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit.
aaa_max
Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs. AAAs are B, J, Z and X!
mismatches_max
Maximal number of mismatched (mm) amino acids allowed when matching to a protein database. The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's.
IL_equivalent
Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable). Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching.
log
Name of log file (created only when specified)
debug
Sets the debug level
threads
Sets the number of threads allowed to be used by the TOPP tool
no_progress
Disables progress logging to command line
force
Overrides tool-specific checks
test
Enables the test mode (needed for internal use only)
name
Enzyme which determines valid cleavage sites - e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input
specificity
Specificity of the enzyme. Default: deduce from input. '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 (enzyme is irrelevant).

Input Ports

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Input idXML file containing the identifications. [idXML]
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Input sequence database in FASTA format. Leave empty for using the same DB as used for the input idXML (this might fail). Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir' [fasta,opt.]

Output Ports

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Output idXML file. [idXML]

Views

PeptideIndexer Std Output
The text sent to standard out during the execution of PeptideIndexer.
PeptideIndexer Error Output
The text sent to standard error during the execution of PeptideIndexer. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

Further Links

Developers

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