Wednesday, April 27, 2016

Want a SAFER way to determine protein-protein interactions?

I always get really excited when somebody outside the field asks if we can do protein-protein interactions with mass spectrometry!  "Hell yeah we....wait, actually yeah we can but its still pretty hard to do..." Better to say..."Yes, but there are 15 different ways you can do it and ten ways to do the downstream analysis..."?   So far the enthusiastic shouting voice in my head still always wins, fortunately!

I like this new method in this month's JPR. Its called SAFER, which stands for something.  Its a much less complicated way of thinking about your protein-protein interactions, and from the data they present here -- both stuff they generate themselves on their Orbitrap Velos as well as stuff they get from PRIDE -- it may work better than stuff you might be using like t-tests or even the great SAINT methodology.

Unlike SAINT, there is no nice program to download. SAFER takes your data from MaxQuant and Perseus and then you do some manual filtering and do PCA analysis. So if your normal pipeline revolves around MaxQuant you don't have to learn much else. If you aren't using MaxQuant as your pipeline it looks simple enough that you could make it work with your label free quan software, but you'll have to put in a little more legwork to put the method together.

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