Saturday, July 21, 2018

EuPA Practical Proteomics Day 5 (late) Recap! Kinase cascades and Crosslinking!!

EuPA Practical proteomics ended with a bang. 

Boris Macek talked about how to study PTMs -- and how to quantify and normalize them -- and then showed an awesome study that is in press right now. I'll be noisy when my Google Scholar alert dings me that it's out.

Then we went into crosslinking for the rest of the day with Juri Rappsilber (with Lutz Fischer for the hands-on section).

What's that above? That's just some crazy amazing crosslinking report I generated in the hands-on workshop on day 5 from some BiorXIV data we pulled down using ---



and the released at the workshop but not quite published yet(?) xiVIEW(!!) All of these tools were developed by the Rappsilber lab and --together -- they're ridiculously powerful.

P.S. This is also the team that developed the xiNET online interface -- which I've been using for downstream interpretation of every crosslinking experiment I've done this year. (If you buy the $500 Xlink nodes for PD 2.2 or 2.3 it will automatically output the data into the xiNET format.

This brings up a very important point about all of these amazing tools this great lab is giving the world for free -- they've also enabled an amazing degree of compatibility. It looks to me like I don't need to use xiSearch at all if I don't want to. It looks like I can take my crosslinked data from any tool that I use and then put it into xiFDR (once i get the format right) and clean up my data with their extremely well-thought-out FDR calculations. Then I can take that data to the next step.

I sat through this workshop in something akin to slack-jawed amazement. And when I did finally say something it was a loud profanity (sorry....). I'm doing a decent amount of crosslinking right now -- pretty much successfully -- but I'm handing off PPTs and Excel sheets to the people who gave me the samples -- these tools get you all the way to the biology and is something we'll be using for sure!

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