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. 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