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.
