Okay - so this one has bugged me (and a lot of other people for a long time) - we can do a pretty great job now of predicting peptide fragmentation (unless the vast majority of PTMs are involved). Supposedly we can do a solid job of predicting peptide elution patterns (exclusively from C-18 reversed phase chromatography).
What has been missing is predicting what peptides from each protein will actually ionize (or fly).
This has been tried before, btw -
- however, is often the case in academic software development, many of these lead to 404 errors or software that only runs in Windows 95 - or....well....they aren't very good.
I'm a little sad to say this but when I did my normal round of sending a paper that I just found yesterday and was reading at lunch the responses were univerally ...skeptical at best.... but maybe this is finally it!
Introducing pFLY! (I read it at lunch yesterday and it's faded in my mind a little but I'm just about 99.0% that the p stands for Pug)
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