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/fe1043c4-1182-46a2-8584-63dfe13b46e3n%40googlegroups.com.
