Thursday, March 4, 2021

RawBeans -- Ultrafast, ultrasimple, ultrapowerful QC software for shotgun proteomics!


Once upon a time we had a cool program called RawMeat from VastScientific that was free and could rapidly look at any Thermo RAW file and provide all sorts of insight into your experiment. Vast got bought up by some corporation and all their software eventually disappeared (I'd still argue that peak finding software was competitive with anything out there right now -- it was designed for much smaller data files and can take months on today's massive data files). If you've got an older instrument RawMeat is still great and I can help you get it, but it doesn't work for anything beyond a certain Foundation version. 

I've mentioned RawBeans before, but wooo -- it's been updated and it's unbelievably easy and powerful now.  And it's got a paper now!

For real, it's super simple. You can get it here. And this is all you have to do (finding where Windows10 hides your MSConvert.exe is the hardest part). 

What can you do with a Lumos file in 101 seconds? (I have a weird mouse glitch but I ziptied all my PC wires together so they look really neat and I can't talk myself into replacing my infuriating mouse and redoing it all). 

(Click to expand, if you need to see the amazing output reports you can get). All of this populates into an HTML file. 

Did you get low IDs and you're wondering why? Run your file through RawBeans. If you maxed out your ion injection time then rerun the sample with a higher max ion injection time (also called fill time on other instruments). 

Best of all, it's vendor neutral! 


  1. Thanks for shout out! comments and suggestions regarding the tool are more than welcome...

  2. Great stuff! Very similar to the one developed earlier