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] > <javascript:>> 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] <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.
