Thank you so much for the quick reply! I did not realize Comet did this. I will change my params file and run the search again.
Thanks again On Thursday, March 1, 2018 at 3:55:35 PM UTC-5, Jimmy Eng wrote: > > Francesca, > > Quick answer: set "decoy_search = 0" because your FASTA already has > decoy entries in it. > > The "decoy_search" parameter controls whether or not you have Comet > generate decoys "on-the-fly". Since your database already has decoy > entries, you need to set "decoy_search = 0". Otherwise, you're telling > Comet to take all of your sequences in your FASTA, including your decoy > entries, and create a new internally-generated decoy peptide for each > peptide it reads from the database. > > So if you have a decoy protein "DECOY9389", you're having Comet take those > decoy peptides and score them. But by setting "decoy_entry = 1", you're > also directing Comet to generate new decoys of those decoy peptides. When > Comet generates new decoys, it appends "DECOY_", based on the > "decoy_prefix" parameter, to the beginning of the existing protein name. > In this example, it would be "DECOY_DECOY9389". > > > Jimmy > > On Thu, Mar 1, 2018 at 12:41 PM, Francesca Barry <[email protected] > <javascript:>> wrote: > >> Hello, >> >> I just realized a possible issue I've been having when using Comet to >> perform a concatenated decoy search on my .mzml file. I just noticed that >> the decoy matches are being displayed/outputted in different ways. >> >> In both the .pep.xml and .pin output files (I need to run Percolator >> after), the decoy hits are being displayed as one of the 3 forms (i.e. all >> 3 forms are present in the same file): >> >> DECOYsp|Q8IZQ1|WDFY3_HUMAN >> DECOY6157 >> DECOYDECOY9389 >> >> When I check back in the .fasta file, the DECOYDECOY results are >> reversing the decoys (so they become the original forward peptides), which >> is wrong. I'm not sure why I'm getting all 3 forms, especially the >> DECOYDECOY matches in the output files. My .fasta is a concatenated version >> of the forward and reverse (decoy) peptides. >> >> What's more interesting is that when I convert the .pep.xml file to .mzID >> so I can further process the results, the .mzID does not contain any >> DECOYDECOY entries. >> >> Very confused as to what is happening and any help would be much >> appreciated. I would especially like to sort out this issue I'm having with >> Comet. >> >> Thanks, >> >> Francesca >> >> PS. I have also uploaded the .params file for Comet in case there is an >> error in there. >> >> -- >> 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.
