I just happened across this one when 2 people asked me about a nice open source in silico fragmentation predictor in the same day. Sounds like search that will end up as a post!
I looked around, downloaded a few, and found my favorite, and it is mMass. You can check it out at mMass.org. This very nice piece of open sourceware has a ton of nice options, and is written by a guy who states that programming is his hobby. The world needs to find more hobby programmers like this!
The program is super easy to download, install and use. And the interface is very intuitive. Besides fragment prediction, it is also a file converter, sharer, and viewer. It can pick peaks, recalibrate your spectra and do some processing. And on and on.
Definitely definitely worth a free download!
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