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MyriMatchAdapter (version 2.8+galaxy0)

Input file:

select mzml data sets(s)

Precursor monoisotopic mass tolerance:

Unit to be used for precursor mass tolerance:

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

Fragment mass error in Dalton:

Unit to be used for fragment mass tolerance:

FASTA protein database:

select fasta data sets(s)

Fixed modifications, specified using Unimod (www.unimod.org) terms:

e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'

Variable modifications, specified using Unimod (www.unimod.org) terms:

e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'

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

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 paramete:

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

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

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

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

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

Advanced Options

Advanced Options 0

Optional outputs: