AlphaDIA support?

[Loay Jabre]

Hi - 

I'm new to MSstats and already loving this ecosystem. Is there planned support/integration with outputs from alphaDIA ?

[Anthony Wu]

Hi,

There aren't any specific plans yet for support alphaDIA.  If you have any example datasets, we can add a backlog item to support a converter for alphaDIA.  

For a sample dataset, if you could provide a table containing quantifications at the fragment ion level (since MSstats performs differential abundance analysis at the MS2 level for DIA) along with the experimental design, that would be sufficient to get started.  

Tony

[Mateusz Staniak]

Hi,

in the meantime, if you're familiar with R, you can re-format alphaDIA files into the MSstats format by using generic functions from the MSstatsConvert package: MSstatsImport, MSstatsPreprocess, MSstatsBalancedDesign.

Kind regards,

Mateusz