MSstats has shown up in my ramblings more than once here, but always in the context of MSstatsQC. I just sat through an awesome talk that demonstrated that it is capable of much more than this.
You can check out MSstats directly here.
Highlights? An R package that can take data from MaxQuant, Proteome Discoverer, Skyline, OpenMS, OpenSwath, and other stuff (its at least 7 of them) and make sense of it all with advanced statistics all over the place.
The inference algorithm appears to be called the "Accelerated time failure model". I don't know yet how it compares to the ones we more typically use (like the k nearest neighbor) but it sure sounds way cooler.
There is so much power here. Choose wisely.
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