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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Question about MBR with specific spectral library #623

Open pchirania opened 1 year ago

pchirania commented 1 year ago

Hi Vadim,

I am searching diaPASEF data for quantification against a sample specific spectral library. The spectral library contains 11973 protein groups and I am identifying 10606 of these protein groups across my dataset without MBR. Would you recommend running MBR? Will that improve identification? Will that affect FDR calculation in anyway?

Looking forward to hearing from you.

Best, Payal

vdemichev commented 1 year ago

Hi Payal,

If the library is DDA-based, then MBR is likely to be beneficial. Please set library generation strategy to 'IDs, RT and IM profiling'. FDR will be fine anyway. When you run MBR, you can compare protein IDs with and without (without is the 'first-pass' report) - this to make sure MBR was really beneficial.

Best, Vadim