Thursday, June 23, 2016

BatMass -- LC-MS/MS data visualization!

NA-NA-NA-NA-NA-NA-NA-NA-BATMASS!!!!  So glad this is out so I can finally talk about this!

Okay. SOOOOO...Orbitrap data is BIG DATA. For real. Unfortunately, we've been looking at it in such a limited way that we really haven't realized it yet. Don't worry, I'm going to ramble on and on about this as time permits. [Dedacted rambling about other cool things I can't talk about yet!!! Shut up Ben, shut up. You can see the ENTIRE PROTEOME ITS ALL THER..QUIT TYPING!!! Dedacted]

How do other fields deal with Big Data? P.S. this book is somewhat off topic, but awesome. You've got to step away from the small ways of dealing with things and look at the big picture. Its hard to do. Let go. And look for trends.

Enter BatMass. Batmass takes us away from looking at individual MS scans and away from searching against limited and often incorrect databases and sums your RAW files up into a picture. A zoomable, scalable, searchable, overlayable picture!

Check out this fuzzy example. Step away from these 9 RAW files and --- BOOM!  (One of these things is not like the others!)

Rapidly, visually locate what is different --- you can use it to find files where something went awry -- or to look for your differentially expressed molecules between files. Once you find them, you have an entire tool suite to 

Zoom in and extract the data of interest. Seriously! I love this concept (if you can't tell)... Better yet, its experiment-independent. BatMass doesn't care if this is a proteomics experiment or a metabolomics run or an untargeted food screening run - it just does its job and visualizes the differences it sees (this corn syrup has a pesticide we didn't even think to look for -- what?! Your drug changes the global lysine acetylome -- what?!?)

If you just want to get it and mess around with it -- its

You'll find a nice getting started guide for mass spec people and some overview videos. You'll also find resources (and the original source code) for developers who want to take this concept further or integrate it into their workflows!!  


  1. Them are some tasty visuals! (Less filling, tastes great)

  2. Very cool, do you know if there is a way to subtract the 2D views from each other? To remove the background of the blank or to subtract a control from a sample to see the peak differences?

  3. @Thomas Jefferies: Hi, i'm the author of the software. As of right now - no, there is not. It is not as easy as it sounds. Your masses won't match exactly between the runs (even if you do two technical replicates one right after another), neither will the intensities match! So you first need to do RT alignment (that's ok), but then you need some sort of intensity normalization between the runs. I mean this can all be done in a crude and approximate way, so that at least when you are zoomed out substantially things work as you imagine them to work. I'll try to add this feature soon. When it's implemented and pushed to GitHub, you'll get a notification on application restart, if you have BatMass already installed, that will allow you to automatically install the update.