Dear Thibault, Apologies for not being precise. Tandem2XML is a TPP tool but it is not a TPP analysis tool, it simply places the data in the (mostly) correct format that can then be given to InteractParser which corrects pepXML issues that could exist after the search engine. It is the first step of xinteract, which is the tool that "Analyze Peptides" tab uses in Petunia. I suggest you employ InteractParser or xinteract as the first step of the analysis after generation of the pepXML file by Tandem2XML in your tandem pipeline. On our cluster InteractParser is actually the last step of each search, and the first step of the peptide analysis by TPP.
Cheers, -David On Tue, Jan 9, 2018 at 2:40 AM, Thibault Robin <[email protected]> wrote: > Dear David, > > Thank you for your answer. > > Using InteractParser on the pepXML file did fix the issue and PTMProphet > is now properly working. However I can assure that the pepXML file was > generated by the TPP. > > Best, > > Thibault > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
