The decoys are generated by mascot on the fly. Yes - your solution sounds like the sensible one. Thanks for the suggestion.
Alastair Am Freitag, 23. November 2018 22:00:54 UTC+1 schrieb David Shteynberg: > > 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" < > spctools...@googlegroups.com <javascript:>> 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 > alastair.s...@googlemail.com: >> >> 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 < >>> spctools...@googlegroups.com 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 spctools-discu...@googlegroups.com. >>>> To post to this group, send email to spctools...@googlegroups.com. >>>> 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 spctools-discu...@googlegroups.com <javascript:>. > To post to this group, send email to spctools...@googlegroups.com > <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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
