AlphaDIA - I don't understand why it is different but it IS open source!

 

I really did read the full body of the text for the published manuscript on AlphaDIA. I kept looking for the "why is this different than the DIA tools that I currently use" and I never had that "OH! That's why this is different!" moment. For real, WTF is a learning transfer? I'm either a poor reader or it is never fully explained in the text anywhere. 

However it 

1) Processes Orbitrap data

2) Processes TIMSTOF data

3) Processes SCIEX ZenoTOF data

4) Processes Astral TOF data

And it is fully open source! YEAH!  Which doesn't matter a lot to academics cause 2 of the main tools you probably use are free to you and it doesn't make a difference. But it matters to a lot of people! 

Looking at just the baseline numbers for what we get in DIA-NN and SpectroNaut on our cancer cell line digests on the TIMSTOF Ultra and the numbers I get when I reanalyze other people's Astral data, the AlphaDIA numbers seem on the lower end, but within reasonable expectations. Also, it's worth noting the Github went live 4 years ago and the preprint is at least 18 months old, so these might be older files. Proteomics hardware/methods and informatics improvements have been nuts the last couple of years, so it's tough to tell how much all that factors in here. 

If you haven't looked at it in a while, I'm happy to report the Github has some neat little animated walkthroughs and things. 

OH YEAH! And it runs on MacIntoshes. So if you're just done with Windows 11 enough that you're going to buy hardware from the US POTUS's very close friend Mr. Apple himself.

You can read about it here.