I seriously have a list of the next 10 things to investigate/write about, but this one just hopped the queue. If you haven't noticed, I'm doing a lot of crosslinking stuff right now. The MS/MS and data analysis is tricky stuff. Yesterday, my collaborator showed me Xcomb, a tool from my neighbors at the Goodlett lab (how is it that we don't know each other? Lets fix that soon!)
Xcomb gets around a whole lot of the difficulty of crosslinking studies by building you a custom crosslinked database. You give it the proteins you are looking for and it makes a FASTA file that contains a whole slew of new "proteins" that are your possible crosslinked species. Then you throw in your crosslinker mass as a dynamic mod and you can use any software you want to search for crosslinked species. Brilliant.
The original paper is here (yup, it is a few years old, but no less cool!)
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