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.

allow_nterm_protein_cleavage

Allow the protein N-terminus amino acid to clip.

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).

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

• 01-MaCProQCKNIME Hub
• 01-PIA_first_analysisKNIME Hub
• 01t-PIA_with_multiple_search_enginesKNIME Hub
• 02-download_and_analyze_raw_fileKNIME Hub
• basic_peptide_identificationKNIME Hub
• Show all 24 workflows

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Developers