SimpleSearchEngine

Options

version

Version of the tool that generated this parameters file.

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)

enzyme

The enzyme used for peptide digestion.

decoys

Should decoys be generated?

mass_tolerance

+/- tolerance for precursor mass.

mass_tolerance_unit

Unit of precursor mass tolerance.

min_charge

Minimum precursor charge to be considered.

max_charge

Maximum precursor charge to be considered.

isotopes

Corrects for mono-isotopic peak misassignments. (E.g.: 1 = prec. may be misassigned to first isotopic peak)

mass_tolerance

Fragment mass tolerance

mass_tolerance_unit

Unit of fragment m

fixed

Fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)'

variable

Variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Oxidation (M)'

variable_max_per_peptide

Maximum number of residues carrying a variable modification per candidate peptide

PSM

Annotations added to each PSM.

min_size

Minimum size a peptide must have after digestion to be considered in the search.

max_size

Maximum size a peptide must have after digestion to be considered in the search (0 = disabled).

missed_cleavages

Number of missed cleavages.

motif

If set, only peptides that contain this motif (provided as RegEx) will be considered.

top_hits

Maximum number of top scoring hits per spectrum that are reported.

Views

SimpleSearchEngine Std Output

The text sent to standard out during the execution of SimpleSearchEngine.

SimpleSearchEngine Error Output

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

Workflows

• Peptide Identification from MSKNIME Hub
• Peptide-spectrum matchingKNIME Hub
• Protein label-free quantificationKNIME Hub
• Protein label-free quantificationKNIME Hub
• Search Engine CombinationKNIME Hub

Links

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Developers