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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Difference in protein number in sample when same raw file is searched again with other raw files DIANN 1.9.1 #1228

Open SMurphy368 opened 4 weeks ago

SMurphy368 commented 4 weeks ago

Hello, firstly thanks so much for this great software!

I have a query regarding data analysis with DIANN v 1.9.1. I analysed two samples together in DIANN and identified 7,260 proteins and 7,246 proteins respectively. I then reanalysed the same raw files again along with three additional samples. The settings used were exactly the same, however this time the software only reported 6,495 and 6,492 in those two files. The number of peptides identified was exactly the same when the two files were searched together and when searched with the additional three files.

I assume this is related to protein FDR? But I just wanted to get some clarification as to why this would happen please?

Many thanks for your help! Sandra

vdemichev commented 4 weeks ago

Hi Sandra,

Can you please share the logs?

Best, Vadim

SMurphy368 commented 4 weeks ago

Hi Vadim,

Sure please see attached.

Thank you! :) report.log_2files only.txt report.log_5 files.txt

vdemichev commented 4 weeks ago

In both cases the result is incorrect, please see the warning printed by DIA-NN. In 1.9.1 the in silico library needs to be generated in a separate pipeline step, otherwise if peptidoform scoring is enabled the results are incorrect (this was fixed in 1.9.2, but in 1.9.1 there's still a warning to indicate that something is wrong).

Best, Vadim

SMurphy368 commented 4 weeks ago

Hi Vadim,

Many thanks for your help with this, and for responding so quickly, much appreciated! I will try that.

Best wishes Sandra