Tuesday, October 15, 2019

Are your collaborators growing cells? You need the cRFP!

This new resource presented in JPR is a simple and great idea!

It also might explain a lot of things you might have seen using big databases for proteomics. When Amol's team at OptysTech started building their cloud based search engine, they kept coming up with tons and tons of cow proteins. Like -- way more cow proteins than what you'd expect from the fact that humans and cows are mammals. Every file we sent them was from cells grown in media. And people grow these cells in media supplemented with FBS. This does not stand for Flower and Balloon Supercharger. It is a super complex media derived from COWS.

This group goes through and characterizes the stuff that they find it in and show that subtracting it out (the same way you're probably using cRAP) and then all the sudden doing secretome (looking at the proteins released into the media) makes sense!

We should probably get into the scary thought of the reproducibility of FBS sources, vendors, lot to lot variability, time of FBS on the shelf, etc., somewhere else. I know one of the companies making the burgers that I can't personally distinguish from dead cow burgers has been posting openings for proteomics people, so maybe we can have an Impossible FBS soon? I mean, come on, vendors can't seem to make the same monoclonal antibody reliably, you can't tell me that every container of something this complex is the same....I mean...I hope it is, but it seems pretty unlikely.

At the very least make a new FASTA for proteins to ignore when you're running proteins from mammalian cell culture!

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