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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Library Generation #384

Open MarST07 opened 2 years ago

MarST07 commented 2 years ago

Hello Vadim,

I ask myself how to process different sample runs in DIA to generate a huge sample specific library. I measured different sample types in gas-phase fractionation mode and I want to create one library from it. Is is useful to match between runs, or should I process all samples together as nonrelated runs? Is there a publication to read more about library generation via DIA-NN?

Thank you again for this great tool! Kind regards, Stella

vdemichev commented 2 years ago

Hi Stella,

If the purpose is to solely generate a spectral library from DIA data, MBR must be turned off. Please just see the documentation, there's nothing fancy about library generation (the most basic version was in DIA-NN 1.6.0 already and is featured in the original Nature Methods paper), so the current version of it is not described in a publication.

Best, Vadim

haianhle commented 2 years ago

Dear Vladim,

I have a question regarding project specific spectral library for DIA runs on DIA-NN. Usually we generate these libraries by running fractions with DDA and then processing the data with FragPipe. We use the same LC separation method and MS method for the library generation and samples. However, in principle, would a longer LC separation method that potentially resulted in more coverage (or in general the best method possible) for library generation more ideal (since we only have to run once and throughput is not as much of an constraint)? Thank you so much.

Best wishes, Anh