Hi Eric, Thank you for your quick reply.
I am using Mayu with 1% FDR on PSM level (mFDR) for all three libraries. I also filter the list to get the protein level FDR of <1% with -protFDR=0.01:t. The values I mentioned are extracted from this list (lowest score). As far as I know, with these settings I am using a protein level FDR estimation of <1% (on all three). Is this the correct way I am using it? The search parameters for both engines are the same and other parameters are also kept the same for the libraries. I think a tool to remove shared peptides would be very useful! Since I did not find anything about this how to remove those, I am wondering how people 'normally' do this. Some papers mention a total of x proteotypic peptides and proteins, thus my guess is someone must know how to do this. Regards, Nikita On Monday, 23 September 2019 17:56:49 UTC+2, Eric Deutsch wrote: > > 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:* [email protected] <javascript:> < > [email protected] <javascript:>> *On Behalf Of *Nikita Boeren > *Sent:* Monday, September 23, 2019 4:16 AM > *To:* spctools-discuss <[email protected] <javascript:>> > *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 [email protected] <javascript:>. > 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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/c3e80d45-6847-4d30-ac5a-f799cf008583%40googlegroups.com.
