Hi David, This time I used *xinteract -NinteractDecoyCount.pep.xml -p0.05 -l7 -PPM -OANEdp -dDECOY0 Seq69478_QE2.pep.xml. * With TPP 5.2 the count of DECOY1 ids at 1% error rate is 84 and the total count of DECOY ids is 151 (out of 7102 PSMs). With TPP 6.0 the count of DECOY1 ids at 1% error rate is 7 and the total count of DECOY ids is 9 (out of 5308 PSMs). You can find the new interact files here:https://www.dropbox.com/t/s7ZqgkP1f0Yzl0Xn. Many thanks, Oded
On Wednesday, 14 April 2021 at 08:34:42 UTC+3 David Shteynberg wrote: > Hi Oded, > > I think the old 5.2.0 might be under estimating the error rate as compared > to the new release candidate. You cannot see the decoys here because of > the settings you used. However your database has two independent sets of > decoys available DECOY0 and DECOY1. Can you use one of the set for > PeptideProphet and use the other set to get a decoy count at a given > PeptideProphet probability cutoff. I suspect the 5.2.0 TPP will show more > unknown decoys than the new release candidate. Can you test if this is > the case here? I can run a more in depth analysis when I am back from > vacation next week. > > Cheers, > David > > On Tue, Apr 13, 2021, 2:07 PM Oded <[email protected]> wrote: > >> Dear David, >> This is PeptideProphet issue (we don't use iProphet for this analysis). >> With the search parameters that I sent you followed by running the >> PeptideProphet command of *xinteract -Ninteract.pep.xml -p0.05 -l7 -PPM >> -OANEp -dDECOY Seq69478_QE2.pep.xml,* >> and lastly using a cutoff of 1% error rate we obtain with TPP 5.2 2836 >> correct assignments and with TPP 6.0 only 2228 correct assignments. The >> probability for 1% error rate is 0.84 in TPP 5.2 and 0.9090 in TPP 6.0). >> In the following link, you will find the interact files (new and old): >> https://www.dropbox.com/t/mwtpCLeEJRLCwbi1 >> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fl%2FAACfc2b_KukHZAS1VuNo4sPM3gEXyXtDlPE&data=04%7C01%7Coklab%40technion.ac.il%7C342d2db781c2443416b108d8febfbc70%7Cf1502c4cee2e411c9715c855f6753b84%7C1%7C0%7C637539447557029368%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=LBdAB3QsH9rUxvNKMwKjOKYDbQXFxma9dREKgS5siWQ%3D&reserved=0> >> Thanks, >> Oded >> >> >> >> On Tuesday, 13 April 2021 at 03:38:33 UTC+3 David Shteynberg wrote: >> >>> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 [email protected]. >>>>>>>>> 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 [email protected]. >>>>>>> >>>>>> 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 [email protected]. >>>> >>> 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 [email protected]. >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/3030a2db-c902-4cb4-837d-20f385662a18n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/3030a2db-c902-4cb4-837d-20f385662a18n%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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