Monday, March 31, 2014


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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