-- over any of the fancy new 3D stuff!
I've also never been able to understand 3D mass spec data interpretation software and it mostly just makes me dizzy. However, I know super smart people that can and do use these, and JS-MS appears to be a nice new tool for everyone!
It has these advantages:
1) Vendor neutral (it looks like it takes any mZmL converted data)
2) It runs in Java (which you probably already have)
3) It is heavily optimized for speed and usability
4) It's free! (You can get it here).
The authors focus on comparing it to TOPPView, which is a really nice program that operates within the OpenMS framework. JS-MS doesn't require the installation of a full program like Open-MS, but it does appear to require a configured Maven environment. If you're already using OpenMS, you'll probably want to stick with your TOPPView. Heck, if you've got an LC-MS background, you might still be better off. Open-MS is built for you and you'll be able to figure it out.
However -- If you're a bioinformatics person or a programmer in general, you may already have Maven set up and you'd be better off going the JS-MS route. It's great to have more options as our field continues to expand!
The comparison I was really curious about was how this how JS-MS would compare to BatMass, which seems to have a lot of similar functionality, but I've only seen it utilize Thermo data and I'm too lazy to look up what files it is capable of accepting.
BatMass has the additional advantage of being the coolest looking icon and startup screen on your desktop -- maybe even your personal one, even if it's full of old 2D arcade games!
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