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OpenMS
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Applies a set of modifications to all PeptideIDs in an idXML file.
Given peptide sequences from an idXML file, this TOPP tool applies a set of static (i.e. unconditional) modifications to all AA's of a peptide sequences which have a matching origin (i.e. amino acid), and to the C/N-term. The modifications supported are the usual ones from UniMod.
The user can provide modification(s) explicitly, e.g. Carbamidomethyl (C), or use predefined sets.
Predefined sets:
Explicit modifications and predefined sets can be combined. Modifications already present on an AA/Terminus of the input will not be applied again. If more than one modification is to be applied to an AA/Terminus, annotation using single name is not sufficient anymore and the summed delta-mass has to be used. Modifications are not applied to AAs which already contain an unspecified delta-mass in the input.
The command line parameters of this tool are:
INI file documentation of this tool: