I represent the development team for ProteinCenter at Proxeon BioInformatics. Lately, we have had requests from our users about data import support for the iProphet XML format (PepXML?). We have found that the format resembles Scaffold protXML, except for some peptide modifications, which only seem to reside on n- and c-terminals. The modifications are not given as masses (as is usual), but rather integers (e.g. 145, 257, 272) that we have so far been unable to identify the reference for. Apparently, they represent neither UniMod, nor PSI modification identifiers.
We have also been unable to acquire any documentation on iProphet, so any help on this would be greatly appreciated. I thank you in advance, Martin Damsbo, Ph.D.
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