0 ×

CompNovoCID

Generic Workflow Nodes for KNIME: OpenMS version 2.4.0.201810261314 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Performs a de novo peptide identification using the CompNovo engine.

Web Documentation for CompNovoCID

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
Overwrite tool specific checks.
test
Enables the test mode (needed for internal use only)
max_number_aa_per_decomp
maximal amino acid frequency per decomposition
tryptic_only
if set to true only tryptic peptides are reported
precursor_mass_tolerance
precursor mass tolerance
fragment_mass_tolerance
fragment mass tolerance
max_number_pivot
maximal number of pivot ions to be used
max_subscore_number
maximal number of solutions of a subsegment that are kept
decomp_weights_precision
precision used to calculate the decompositions, this only affects cache usage!
double_charged_iso_threshold
minimal isotope intensity correlation of doubly charged ions to be used to score the single scored ions
max_mz
maximal m/z value used to calculate isotope distributions
min_mz
minimal m/z value used to calculate the isotope distributions
max_isotope_to_score
max isotope peak to be considered in the scoring
max_decomp_weight
maximal m/z difference used to calculate the decompositions
max_isotope
max isotope used in the theoretical spectra to score
missed_cleavages
maximal number of missed cleavages allowed per peptide
number_of_hits
maximal number of hits which are reported per spectrum
estimate_precursor_mz
If set to true, the precursor charge will be estimated, e.g. from the precursor peaks of the ETD spectrum. The input is believed otherwise.
number_of_prescoring_hits
how many sequences are kept after first rough scoring for better scoring
fixed_modifications
fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'
variable_modifications
variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'
residue_set
The predefined amino acid set that should be used, see doc of ResidueDB for possible residue sets

Input Ports

input file in mzML format [mzML]

Output Ports

output file in idXML format [idXML]

Views

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

Best Friends (Incoming)

Best Friends (Outgoing)

Update Site

To use this node in KNIME, install Generic Workflow Nodes for KNIME: OpenMS from the following update site:

Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform.