Are the decoys available in the database or generated by Mascot on the fly? Although it is easy to modify Mascot2XML to process decoy peptide unless these can be mapped back to database decoy proteins it wouldn't make sense to utilize these decoys at the validation step. I couldn't find the decoys in the database you sent me. I would suggest you create decoys in the fasta file and let Mascot treat them as any other protein sequence to ge the most use of these for validation purposes.
David On Nov 23, 2018 7:49 AM, "alastair.skeffington via spctools-discuss" < [email protected]> wrote: Hi David, Have you had a chance to look into this? Thanks! Alastair Am Samstag, 10. November 2018 10:42:05 UTC+1 schrieb [email protected]: > > 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] 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]. >>> 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. -- 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.
