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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Demultiplexing Overlapping Windows #190

Closed singjc closed 3 years ago

singjc commented 3 years ago

Hi Vadim,

Great easy to use software!!

I was wondering if DIA-NN does any demultiplexing of the data internally? For example for QExactive Plus DIA data that has overlapping windows.

  1. If using the raw thermo vendor files, does DIA-NN handle the demultiplexing?

  2. If using msconvert to centroid and convert the vendor data to mzML (using the suggested parameters in the manual), does DIA-NN handle the demultiplexing?

  3. If using msconvert to demultiplex, centroid and convert the data to mzML, would this still work as expected in DIA-NN?

Best,

Justin

vdemichev commented 3 years ago

Hi Justin,

DIA-NN fully supports overlapping windows, and it uses an algorithm which does not require demultiplexing. So it's recommended to analyse the data with DIA-NN directly, without any pre-processing.

Best, Vadim

singjc commented 3 years ago

Hi Vadim,

Thank you for the info, that's great to know!

Best,

Justin