It sounds like a problem with the way your decoys might be getting generated. How do you generate the decoy?
On Tue, Apr 4, 2017 at 8:59 AM, Chih-Chiang Tsou <[email protected]> wrote: > Hi David, > > Thanks for the prompt response. > So what I am trying to do is to avoid decoy hit Blocking the possible true > hit. > > The way I perform the analysis is to search data against a FASTA file > which has reversed sequences appended. Then during PeptideProphet analysis > I specify the decoy prefix and in the end use the probabilities for > target/decoy hits to estimate FDR. One potential problem for me is that if > a spectrum happens to match a decoy as best hit, with a very high score > let's say XCorr 2.0, and the second hit with Xcorr 1.9, which si actually > the true hit, would be discarded after PeptideProphet analysis. > > If PeptideProphet takes only top hit, could I do two separate searches > using target-FASTA and Decoy-FASTA and specify two input files in > PeptideProphet? Any suggestions? > > > Thanks, > Chih-Chiang > > On Tuesday, April 4, 2017 at 9:45:11 AM UTC-5, David Shteynberg wrote: >> >> No. It uses the top hit only. >> >> On Tue, Apr 4, 2017 at 7:34 AM, Chih-Chiang Tsou <[email protected]> >> wrote: >> >>> Hi >>> >>> Is there any option in xinteract to tell PeptideProphet take topN hits >>> for each spectrum for probability calculation? >>> >>> Thanks, >>> Chih-Chiang >>> >>> -- >>> 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.
