Friday, May 17, 2019

Focus on the spectra that matter, duh!!

How did I miss this!??!  Looks like I retweeted it months ago, but didn't read it?!? 

How much time are you spending processing PSMs from proteins like this?

12 minuted CE-MS/MS run -- 145 PSMs from Tubulin B4. Who cares about Tubulin B4? Literally no one who has ever lived on the planet earth. Okay -- maybe 6 people who ever lived on this planet.  I don't care about tubulin. Especially not enough to waste 145 MS/MS events in a 12 min CE-MS/MS run.

Why don't I care?
Because it isn't changing. I only care about quantitatively changing proteins. Or PTMs that are quantitatively changing. If the ratio is 1:1, no one cares about your dumb protein.

How do we do proteomics, though?

We identify everything -- then we quantify it. If we're really lucky our software does both at the same time.

What we should do is use something like Quandenser/Triqler (a DINOSAUR IS INVOLVED, which is another program, but that's okay) to find out what is changing first -- THEN ID IT! 

You can get this program from THE Matthew here.  This program works for label free stuff.

Unrelated project, but related idea --

If you want to do something similar for TMT/iTRAQ, you can get RIDAR from Conor Jenkins GitHub here. 

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