What a great idea! There are so many factors in crosslinking studies:
1) Did the reagent get in?
2) Were the ratios of crosslinker to protein appropriate?
3) Did we incubate it long enough?
4) Did we digest the proteins properly given the new factor of this weird crosslinker thing?
5) WHICH OF THESE 10 NEW CROSSLINKING PROGRAMS DO WE USE?
6) WHY DOES EACH CROSSLINKING PROGRAM HAVE 4,000 PROCESSING OPTIONS?!?!?
7) SHOULD I GO BACK TO WORKING AT TOYS-R-US?
8) TOYS-R-US IS CLOSED??? WHEN DID THAT HAPPEN?
The resources and the approach provided in this new study allow us to rule out factors 5-10 (it got increasingly strange for a Monday so I deleted a few):
If you are going to benchmark your crosslinking tool of choice against others out there (they provide some great guidance in the paper by comparing several) you're going to want to go straight to ProteomeXchange/PRIDE 014337 here.
(Minor note, related to a separate paper open on my desktop, please don't forget to cite the repositories and ProteomeXchange in your papers. They need proof we're using them to keep them going!)
You know what may actually be a better use of these Xlinked libraries that contain multiple crosslinkers (DSS, DSSO, DSBU) fragmented in multiple ways (HF-X, ETHCD, Lumos MS3 workflow)?
You can use these to learn how to use the crosslinking programs! There are, for real, lots of options in most of them and now you have expertly created files where you know what is in them!
If you can't find the crosslinked peptides, you're doing something wrong!
If you find too many, including ones that can't possibly exist? You're doing something wrong!
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