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/CAGJJY%3D90XX%2B7Hpe8VyxLsn8%3DKOLsrtfk3QsWkVBgr6ndfRUR4A%40mail.gmail.com.
