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]. 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.
comet_hiRes.params
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