Tuesday, August 7, 2018

Protein ID with no MS/MS using complementary enzymes!!


Ummm....I don't hate this idea at all...I had to think about it on a long humid run and I decided that I might love the idea, or I'm out of brain electrolytes -- are those things? I don't even know.  I do know I strongly suggest you check out this brand new JPR paper. 


There are an awful lot of people out there identifying and quantifying peptides with triple quads. We know that a high enough resolution MS1 scan can match or outperform a QQQ SRM in complex mixtures -- and the magic number from independent studies is around 60,000 resolution.

However -- if you try to pull out a peptide from a complex mixture by just SIM at 60,000 resolution -- you're likely going to find a bunch of things that match -- maybe even some with nanoLC level retention time alignment values (+/-20 minutes or so -- which is possibly an exaggeration).

What if you were smarter about it and used complementary enzymes and extracted MS1s? Could you get away with lower resolution? Could you use MS1 scans and then get stupid high levels of confidence?  It would probably suck to compile that data -- unless -- some extremely productive software lab in Moscow was already churning out the scripts!  Ben, Put the link in before posting!!

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