Aaaaallllllrrrrriiiiiiggggghhhhtttt!!!!
I'm going to get excessively excited (surprise!) about this one before I actually even run any data through it. You know how sometimes we fragment more than one peptide at once, even when we don't want to? For a while people have been kicking around code that can figure out what the identity of the other peptides are. I heard a while back that MaxQuant had a feature like this built in.
Well, according to this sweet new paper from Vladimir Gorshov et al., this new node you see in my PD 2.1 screenshot above called "Complementary Finder" has the ability to do this as well. You can download this software (as well as easy installation instructions!!!) at Github here. At first glance the approach seems a good bit different than other ideas I've heard of, but I haven't delved in deep here yet.
I'll try to queue up some stuff through it tomorrow and share impressions, but they test the method in the paper by doing HeLa runs with isolation windows of 1,2, and 4 Da in width and show massive increases in peptide identifications. Super complex mixture? High numbers of MS/MS scans that include more than one peptide. Maybe you can use SuperQuant to figure out what all of them are!
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