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.
