modifications.xml

modifications.xml is a configuration file used by QuiXoT and pRatio. It includes information about the modifications considered in the experiment. QuiXoT tags sequence post-translational modifications using the former SEQUEST notation, with a non-alphanumerical ASCII character (such as @#*^) following the single-character code of the modified amino acid; for example, IM@ADDYGWDVTDAR is the peptide IMADDYGWDVTDAR with a modification in methionine (which could be, for example, a methionine oxidation).

When pRatio finds a modification while generating the QuiXML file, it will first look into the modifications.xml file to check if it has been already assigned a character there. If no character is found for the corresponding modification, pRatio will assign a new character by order of appearance, including it in this file. To avoid confusion, it is convenient to use always the same modifications.xml file with the common modifications along a project.

Currently, up to 30 modifications are usable; each of them is used by pRatio in the following default order:

*#@^-${_!=|(){}][:;+0123456789

You can find here a sample file: File:Modifications.zip.