MyriMatchAdapter

Options

version

Version of the tool that generated this parameters file.

precursor_mass_tolerance

Precursor monoisotopic mass tolerance.

precursor_mass_tolerance_unit

Unit to be used for precursor mass tolerance.

precursor_mass_tolerance_avg

If this flag is set, the average mass is used in the precursor mass tolerance.

fragment_mass_tolerance

Fragment mass error in Dalton

fragment_mass_tolerance_unit

Unit to be used for fragment mass tolerance.

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)'

NumChargeStates

The number of charge states that MyriMatch will handle during all stages of the program.

TicCutoffPercentage

Noise peaks are filtered out by sorting the original peaks in descending order of intensity, and then picking peaks from that list until the cumulative ion current of the picked peaks divided by the total ion current (TIC) is greater than or equal to this parameter.

MaxDynamicMods

This parameter sets the maximum number of modified residues that may be in any candidate sequence.

MaxResultRank

This parameter sets the maximum rank of peptide-spectrum-matches to report for each spectrum.

CleavageRules

This parameter allows the user to control the way peptides are generated from the protein database. For more details, see http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MS&termId=MS:1001045&termName=cleavage%20agent%20name .

MinTerminiCleavages

By default, when generating peptides from the protein database, a peptide must start and end at a valid cleavage site. Setting this parameter to 0 or 1 will reduce that requirement, so that neither terminus or only one terminus of the peptide must match one of the cleavage rules specified in the CleavageRules parameter. This parameter is useful to turn a tryptic digest into a semi-tryptic digest.

MaxMissedCleavages

By default, when generating peptides from the protein database, a peptide may contain any number of missed cleavages. A missed cleavage is a site within the peptide that matches one of the cleavage rules (refer to CleavageRules). Settings this parameter to some other number will stop generating peptides from a sequence if it contains more than the specified number of missed cleavages.

MinPeptideMass

When preprocessing the experimental spectra, any spectrum with a precursor mass that is less than the specified mass will be disqualified.

MaxPeptideMass

When preprocessing the experimental spectra, any spectrum with a precursor mass that exceeds the specified mass will be disqualified.

MinPeptideLength

When digesting proteins, any peptide which does not meet or exceed the specified length will be disqualified.

MaxPeptideLength

When digesting proteins, any peptide which exceeds this specified length will be disqualified.

UseSmartPlusThreeModel

When this parameter is set, then for each peptide bond, an internal calculation is done to estimate the basicity of the b and y fragment sequence. The precursors protons are distributed to those ions based on that calculation, with the more basic sequence generally getting more of the protons..

NumIntensityClasses

Before scoring any candidates, experimental spectra have their peaks stratified into the number of intensity classes specified by this parameter.

ClassSizeMultiplier

When stratifying peaks into a specified, fixed number of intensity classes, this parameter controls the size of each class relative to the class above it (where the peaks are more intense).

MonoisotopeAdjustmentSet

This parameter defines a set of isotopes (0 being the instrument-called monoisotope) to try as the monoisotopic precursor m/z. To disable this technique, set the value to '0'.

SpectrumListFilters

Optional set of filters as described in the MyriMatch documentation.

ignoreConfigErrors

Ignore wrong parameter names or values. Use with maximum caution!

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)

Views

MyriMatchAdapter Std Output

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

MyriMatchAdapter Error Output

The text sent to standard error during the execution of MyriMatchAdapter. (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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