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

Overrides 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

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.)

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