Dear Oded, Thanks for this. I ran a quick test and I actually observed a few more PSMs for PeptideProphet 6.0.0-rc14 for the same PeptideProphet probability cutoff for this dataset. Is the issue you see with PeptideProphet or iProphet results? Which spectra were getting excluded in the your testing of 5.2.0 vs 6.0.0, can you give me some specific examples? Are you certain you are using identical analysis parameters for PeptideProphet and what are those parameters?
Cheers, David On Mon, Apr 12, 2021, 2:15 PM Oded <oded.kleif...@gmail.com> wrote: > And also the search results with the new vs the old version (although I > think they are more or less the same): > https://www.dropbox.com/t/8VyBVdeuoWdk982q > > > On Tuesday, 13 April 2021 at 00:09:05 UTC+3 Oded wrote: > >> Hi David, >> You can find the mzML, Comet parameters and FASTA file here: >> https://www.dropbox.com/t/Yld0ZBWhsuFajeLj >> The link is valid for 7 days. >> Many thanks, >> Oded >> >> On Monday, 12 April 2021 at 23:46:08 UTC+3 David Shteynberg wrote: >> >>> I don't mind taking a crack at it over vacation. Please let me know >>> where I can pull the data from. I might not have quick solution for you but >>> I can get started looking for the problem. Which search engine did you use >>> here? I would need mzML data search results and the fasta database to get >>> started. >>> >>> Thanks! >>> >>> >>> >>> Thanks! >>> >>> On Mon, Apr 12, 2021, 1:38 PM Oded <oded.k...@gmail.com> wrote: >>> >>>> Hi David, >>>> Thank you for the quick reply. We are using TPP v6.0.0-rc14 >>>> Noctilucent, Build 202103031119-8400 (Windows_NT-x86_64). >>>> As for the data let me know when you are back and I will transfer you >>>> either the raw file or the search results. >>>> Enjoy your vacation. >>>> Thanks, >>>> Oded >>>> On Monday, 12 April 2021 at 22:17:53 UTC+3 David Shteynberg wrote: >>>> >>>>> Hi Oded, Which release candidate are you referring to? The earlier >>>>> candidates may have a bug that is corrected in a later version. If you can >>>>> share some data and specifics about the missing PSMs I can run it here and >>>>> troubleshoot the problem. >>>>> >>>>> Thanks! >>>>> >>>>> David >>>>> >>>>> P.S. I am on vacation this week so will troubleshoot next week. >>>>> >>>>> On Mon, Apr 12, 2021, 11:49 AM Oded <oded.k...@gmail.com> wrote: >>>>> >>>>>> Hi there, >>>>>> We recently download the TPP 6.0 RC and while using it we noticed >>>>>> that we obtain fewer peptides IDs than what we got for the same dataset >>>>>> and >>>>>> search output with version 5.2. >>>>>> Many of the missing peptides seem to have decent Expect value and >>>>>> MS/MS following a visual inspection. >>>>>> This seems that this is due to changes in PeptideProphet and are not >>>>>> related to the search itself that was done with Comet. >>>>>> Is there any additional parameter that should be included in the new >>>>>> version in order to restore the missing peptides? >>>>>> Many thanks, >>>>>> Oded >>>>>> >>>>>> -- >>>>>> 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-discu...@googlegroups.com. >>>>>> To view this discussion on the web visit >>>>>> https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%40googlegroups.com >>>>>> <https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%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-discu...@googlegroups.com. >>>> >>> To view this discussion on the web visit >>>> https://groups.google.com/d/msgid/spctools-discuss/7f5e47e5-56df-4552-88ca-b6d4396f3d8en%40googlegroups.com >>>> <https://groups.google.com/d/msgid/spctools-discuss/7f5e47e5-56df-4552-88ca-b6d4396f3d8en%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/3baf2dd3-f237-4c9d-82a2-54d563ccf5e6n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/3baf2dd3-f237-4c9d-82a2-54d563ccf5e6n%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/CAGJJY%3D-hted8DTkVMFGvTUamj%3D%2BJgr2Xc5LrfNtP1F7BjxT0SQ%40mail.gmail.com.
