Friday, May 19, 2017

Global proteome-scale crosslinking! Thousands of protein-protein interactions in one go!

Ever tried to crosslink some proteins, digest them and figure out what proteins were interacting with what (whom..?)

If you have, you should probably understand why I've been so excited about these new reagents, instrument methods and data processing software that make this way easier!! And the first paper I know about that uses this is now out!

I've talked about the MS-cleavable reagent they use on the blog previously as well as the data processing workflows. We saw some applications at ASMS, but this paper does true global scale work!

They crosslink the an entire E.coli proteome as well as a human cell line and pull out information on thousands of protein interactions! The do reduce the complexity by SCX fractionation -- but thousands of protein-protein interactions in one experiment?!?!  Come on -- if you've pulled this off before, you are way better at this than me!

Have you been down this road before and are skeptical? Don't worry, I don't blame you.

Maybe the awesome people at the Heck lab made XlinkX 2.0 a publicly available web Application that you can just go and use here.

Maybe they also put the example files from the E.coli (converted to MGF) available at this awesome site as well so you can check it out!

This team has been actively collaborating to bring the XlinkX 2.0 code into Proteome Discoverer as additional nodes if you want to search data like this within a framework you already know!

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