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/CAGJJY%3D_Aa4V7cGEiTj1%3DPjJONVVMeeVivEh2WFBCfroC1QDZ_A%40mail.gmail.com.
