search

vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
Other
272 stars 53 forks source link

DIA-NN reporting 0 on plasma DIA-PASEF data on library free search #472

Open iolanda-vendrell opened 2 years ago

iolanda-vendrell commented 2 years ago

Dear Vadim, We have been using DIA-NN for a while and it is great. Recently we have experienced some issues when trying to analyse TIMS-TOF DIA-PASEF data from plasma samples using either the library free approach or a spectral library build from high pH fractions. The issue we encountered is that randomely and for some samples it reports 0 identifications (ids and decoys very similar). For those that it reported 0 we check that the quality of raw data. Attached some logs of when the problem happend Test1_report.log.txt Test2_report.log.txt Test3_report.log.txt Test4_report.log.txt . We would appreaciate if you could point out where the problem is. best wishes, iolanda

vdemichev commented 2 years ago

Hi Iolanda,

What about MS and MS/MS calibration for those runs? IM calibration? Are these fine?

Best, Vadim

iolanda-vendrell commented 2 years ago

Hi Vadim,

Apologies for the late reply. I was on sick leave when you reply. I have asked my colleague to check the calibration for the MS, MS/MS and Ion mobility and they are fine. She managed to pull out the calibration history for the TIMS-TOF during that run. See document attached. Can be opened with notepad++ We had set up the DIA-NN LFQ quant few times and we noticed that not always the same file was reporting a 0. I think we deleted all the log files. We can try to reproduce it if that would help in the troubleshooting,

Many thanks in advance,

Best wishes,

Iolanda

From: Vadim Demichev @.> Sent: 29 August 2022 10:48 To: vdemichev/DiaNN @.> Cc: Iolanda Vendrell @.>; Author @.> Subject: Re: [vdemichev/DiaNN] DIA-NN reporting 0 on plasma DIA-PASEF data on library free search (Issue #472)

Hi Iolanda,

What about MS and MS/MS calibration for those runs? IM calibration? Are these fine?

Best, Vadim

— Reply to this email directly, view it on GitHubhttps://github.com/vdemichev/DiaNN/issues/472#issuecomment-1230036959, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AZKVD7X3RAUY7CL7LXWVAVTV3SBOBANCNFSM57A6HDPA. You are receiving this because you authored the thread.Message ID: @.**@.>>