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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Match between runs (MBR) #619

Open jessegmeyerlab opened 1 year ago

jessegmeyerlab commented 1 year ago

In the popup help for MBR it says that it just uses the spectral library from the first search for the second analysis. That makes it sound like it just tries again to get ids without forcing integrations. I just want to check that its not doing something like the MBR definition from maxquant or ionquant in trying to integrate where there isn't necessarily an ID in other runs?

vdemichev commented 1 year ago

Yes, it does exactly that.

st-pf commented 1 year ago

hello, I have an additional question to this: is there a way to discriminate between prot IDs found in the first search and those found via MBR, e.g. is there an indicator added to those in one of the output files of DIA-NN? thank you in advance s

vdemichev commented 1 year ago

No, the second search (MBR) affects all q-values of all precursors and proteins.

kwebber3 commented 7 months ago

@vdemichev What are the first_pass matrices? Could I consider these pre-MBR identifications?