Saturday, September 13, 2014

JUMP -- A new way of looking at high resolution MS/MS spectra?

I have to admit, on my first glance through this paper early this morning it made me drop a bunch of profanities in my living room.  Then I moved down to the figures and stared at the ceiling for a while and realized that this has some merit and may just be a way of looking at MS/MS spectra that I've never considered and that I maybe I was just being sleepy, under caffeinated, and a little old fashioned.  BTW, if you know me you know I pretty much drop profanities all the time.  (Recent uncited studies circulating Facebook have suggested that people who swear a lot may be more honest...just saying...aaaannnnnddddd....Snopes says this is another viral silly thing...fucking skeptics...nevermind.....)

So what is the idea behind JUMP?  It is that we may be able to make a positive ID of a peptide from an MS/MS spectra by looking for specific mass tags without requiring the comprehensive b/y ion distribution we need for a traditional match.  JUMP is even capable of helping to make confirmations based on tags of individual amino acids present.  Yes, I know, this is what made me start cursing, but let's take this apart.

Let's say I selected a doubly charged peptide for fragmentation in my Q Exactive and it had a mass per charge of:  413.232

And I had a peptide in my database that matched that:  AHVETLR

How much information would I really need to say that this m/z is this peptide?  I've got high res accurate mass, that has to narrow it down some.  Could I confirm it was it if I only had b ions?  My hunch is that most engines wouldn't score it super well, but they would probably make a match under most conditions if we had all of the b's.

What if I just had the TLR as a dominant ion (389.25)?  Is that enough for a confirmation?  What are the odds of that occurring at random?  Roughly 25*25*25 (leucine=isoleucine), so 1 in 16k.  It would happen a bunch of times in a complex proteome, but how often would it perfectly coincide in fragmentation with an ion of this mass range?  Probably pretty rarely.

Okay, so I'm less mad about this.  Single peptide tags?  That I'm still more than a little uneasy about.  1 in 25?   But I see what they are getting at.

The authors run through all the requisite statistics in the paper, FDR plots with various metrics and demonstrate how many more peptides they get than the existing, accepted engines.  They ought to, I often tell Proteome Discoverer "if that MS/MS spectra has <10 peaks with a S/N of 5, through that spectra in the garbage".  And JUMP would make identifications off of lots of those that I throw away.

Interested in a new way of thinking about MS/MS spectra and matching them to your proteome?  You should check out this paper in press at MCP.

P.S.  Did the math that helped lower my blood pressure with the always awesome and reliable Protein Prospector. 


  1. Hi:
    We already published this approch one year ago in AC using NTerminal tagging in
    advance ( Sadly not reference to our
    work in JUMP. Thanks for the really nice post!!!

  2. Thanks for the info! I'll request a copy from our library and check it out.