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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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MS spectrum predictor in library free mode DIANN1.9 #1049

Open giovanni-cro opened 2 months ago

giovanni-cro commented 2 months ago

Dear Vadim,

thank you for your work on DIANN and its new release. I was wondering if the MS spectra in silico prediction is unchanged with respect to the previous version (if I understood correctly, the latter was based on the MS simulator). Moreover, is there a target CE for the spectral library prediction? When I run DIANN I don't have to specify any particular CE, so I was wondering if different experiments with different CEs might have a different outcome on the generated spectral libraries.

Thank you in advance, Giovanni

vdemichev commented 2 months ago

Hi Giovanni,

It's imporved in some aspects, also it's a lot faster for large (tens of millions) libraries. There will be further improvements to the predictor in next versions.

No, it's deep learning, the MS Simulator-like module has been removed in 1.9.

No CE option in DIA-NN, as the differences between CE values are so minor they become negligible with MBR.

Best, Vadim

giovanni-cro commented 2 months ago

Thank you very much! Best, Giovanni