LuciPHOr is one of the gems that I ran into at KHUPO. I spoke to one of the developers and I can't wait to try this out. Upcoming weekend project: same dataset LuciPHOR and the TPP vs Proteome Discoverer 1.4 with PhosphoRS 3.0. Would LOVE to see this comparison. Considering I'm composing a phosphoproteomics paper right now, this might be a perfect place to use it.
Anyway, LuciPHOR is a phosphosite assignment program specifically designed to work in conjunction with the transproteomic pipeline. It is also primarily written for Linux. This shouldn't be a problem for us Windows slaves, cause we can probably just run it through the command line once we've compiled it. If I like it nearly as much as I expect to, I'll write up a GUI for it and post later. Again, this might fall onto my "to do list when I finally find that hyperbolic time chamber list" or "things for my clone to do the next time he's on a 16 hour flight and not intoxicated list."
Wow, I digress. The really cool thing about LuciPHOr, and why I am so totally sold on it is this: it has a FDR calculation for the localization of the phosphorylation. They call it the "False Localization Rate". It uses a lot of high level statistics, not my forte, but the data that I have seen looks really promising.
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