SimpleSearchEngine

Annotates MS/MS spectra using SimpleSearchEngine.

Web Documentation for 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.

Input Ports

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input file [mzML]
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input file [fasta]

Output Ports

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output file [idXML]

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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

Links

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