Yes, the decoys are in a separate list in the .dat file. The database matches are in the section starting:
Content-Type: application/x-Mascot; name="peptides" while the decoys are in the section starting: Content-Type: application/x-Mascot; name="decoy_peptides" In the decoy PSM lists Mascot simply uses the name of the database entry from which the decoy sequence is derived - with no addition of 'REV' or 'decoy' or any other indication to the name - just to be extra confusing. So Mascot2XML will have to add some suitable prefix. Thanks, Alastair Am Donnerstag, 8. November 2018 17:07:30 UTC+1 schrieb David Shteynberg: > > As far as I am aware Mascot2XML reports all results including decoys > unless the decoys are encoded in a different way fron other IDs. Are you > sure that the dat file contains decoys? I will definitely look into this. > > -David > > On Thu, Nov 8, 2018, 2:25 AM alastair.skeffington via spctools-discuss < > [email protected] <javascript:> wrote: > >> Hello, >> >> Another query about Mascot2XML I'm afraid: >> >> As far as I can tell, no decoy results are carried over from the Mascot >> .dat file into the pep.xml file. Is there a reason for this? Is there >> anyway to include these results? >> >> Many thanks, >> Alastair >> >> -- >> 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> 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.
