Dear Thibault,
I have looked at your example. It appears this is not a pepXML file
generated by the TPP, so the modification_tag is missing a bit of
information utilized by PTMProphet. For PTMProphet to work the encoding
has to appear with this attribute set in the pepXML file.
For your example:
<modification_info>
<mod_aminoacid_mass position="5" mass="166.9984" />
</modification_info>
<modification_info modified_peptide="KGDRS[167]PEPGQTWTR">
<mod_aminoacid_mass position="5" mass="166.9984" />
</modification_info>
I will consider adjusting PTMProphet to be able to process such pepXML in
the future.
However, you can try using InteractParser from the TPP to create the
modified_peptide tags and process the resulting pepXML using PTMProphet.
Let me know if that works for you.
-David
On Wed, Dec 20, 2017 at 2:27 AM, Thibault Robin <[email protected]> wrote:
> Dear David,
>
> Thank you for your answer.
>
> I have joined to this message an example pepXML snippet which produces the
> following warning:
>
>
>
>
> *WARNING: Illegal PTM-shuffled peptide detected with non-matching mass:
> KGDRSPEPGQTWTR Neutral Mass (from pepXML) = 1693.76 Neutral Computed
> Mass for Evaluation = 1613.79 PPM difference = 47212.4*
> Please let me know if it is sufficient and have great end-of-year
> holidays !
>
> Cheers,
>
> Thibault
>
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