Hi Nikita, perhaps someone has some better answers than I do, but here is what I can say based on your description.
Regarding the cutoff, I wonder if in your combined analysis you are using a peptide-level FDR of 1%, whereas in the single analyses you are using an PSM-level FDR of 1%? A peptide-level FDR of 1% is more stringent than a PSM-level FDR of 1% and this might account for the difference? I am not aware of a mode to remove shared peptides from a library, although this does sound like a useful feature. Maybe someone else knows? Regards, Eric *From:* spctools-discuss@googlegroups.com <spctools-discuss@googlegroups.com> *On Behalf Of *Nikita Boeren *Sent:* Monday, September 23, 2019 4:16 AM *To:* spctools-discuss <spctools-discuss@googlegroups.com> *Subject:* [spctools-discuss] Questions about spectral library generation different search engines and shared peptides Dear TPP team and users, I am a graduate student and I am trying to figure out a few things regarding spectral library generation using TPP for SWATH analysis. My questions do not involve direct issues with the use of TPP, but more about the results. My workflow is: Comet or X!Tandem search, PeptideProphet, iProphet, Mayu (1% protein FDR), SpectraST and SpectraST2TSV. I have used both Comet and X!Tandem search engines to create two libraries. Also, I combined those two search outputs (via iProphet) to create another library. In contrast of what I expected, my final list of proteins in my combined library is less than using only Comet results (see Venn diagram). How can this happen? The cut off probabilities corresponding to protein FDR <1% for Comet (0.897393) and X!Tandem (0.872656) were as expected lower than combined (0.966806). Can anyone explain me why the combined library contains less proteins? Also, I would like to ask you how to remove shared peptides from the library without getting format issues in further workflows? Thank you in advance. Regards, Nikita -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/2da1064d-e4bb-41ea-9fa1-553c3d27c580%40googlegroups.com <https://groups.google.com/d/msgid/spctools-discuss/2da1064d-e4bb-41ea-9fa1-553c3d27c580%40googlegroups.com?utm_medium=email&utm_source=footer> . -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/4c669586f1b2c19c33f6a010b4a0ea78%40mail.gmail.com.
