MaxQuant + SDRF enables great reproducibility with no downsides whatsoever!

 

As everyone in proteomics already knows there is absolutely no downside whatsoever to using MaxQuant for every proteomics experiment. It's super fast, visually stunning and modern, incredibly stable and gives you all sorts of insight into your experiments when they succeed and those exceptionally rare times when it just stops running 18 days into analyzing those 4 files.

How could you make our field's very favorite toolkit even better? No way, right? Oh. Do I have one for you. What if you could also get your metadata out in the soon-to-be-mandatory (those are single dashes, no generative AI here - every word on this blog is typed by this one weird dyslexic guy) SDRF format? 

BOOM. Direct SDRF! 

Nature Comms?!? Whoa. What a demonstration of how great it is to work with MaxQuant that you can score a high impact publication by getting it to export a .JSON table in the format you want!  Heads up editors - one of y'all is about to see our SDRF exporter for Proteome Discoverer as soon as I get an hour to figure out what computer I made it on! Heck, I'll throw in one for Metamorpheus too! Supplemental methods.

Disclaimers: Proteomics metadata is something we should be uploading properly. We arent. Hell, I'd say 75% of proteomics experiments aren't even having their data put on public repositories. My job is to draw attention to things by generally being a nuisance about it. Anything that makes getting data deposited with appropriate metadata is a very very good thing. Thank you to these authors for their work and effort.