Targeted quan on the Q Exactive -- Which method to use when? Part 1

One of the many things the Q Exactive is good (great?) at is targeted quan.  But it can be a little tricky.  You have a ton of different methods to choose from for doing targeted quan and each has advantages /disadvantages over the others.  Having too many options is a great problem to have, but if you aren't using the best one for your particular experiment, it might still be a problem.  I'm going to have a little monologue (tirade) about each one and where the ideal experiment for each.  Now, this ain't doctrine or nothin.  Please refer to the Disclaimer statement.

Number 1:  Targeted SIM.

Also called HRAM-SIM; HR-SIM, so on and so on.  In this method the QE gets a list of targets we filter in the quadrupole in a very focused mass range and are read out for quan in MS1 using the XIC in Pinpoint or Skyline.

Advantage:  Sensitivity!  Crank up the fill time and I don't care how low your peptide signal is, if its ionizing you are going to find it.  My personal belief (feel free to scoff, triple quad people):  Using this function I can hit triple quad level sensitivity -- on a limited number of targets.  Yes, a Quantiva is more sensitive than a QE, in general, but I can allow the C-trap to fill for 3 seconds if I want.  This gives me QQQ or better sensitivity, but it isn't practical to do on more than a few targets.
Disadvantage:  Cycle time, cycle time, cycle time.  Each scan is an Orbitrap scan.  Even at 17,500 resolution, we're talking 64ms.  More if you crank up your fill time to get those super low abundance targets.  Even if we schedule all of our T-SIMS, we have a finite number that we can look at due to the length of time it takes to get one scan.  Possible disadvantage.  In extremely complex mixtures, higher resolution may be necessary to really separate your ion of interest from similar co-eluting peaks.  Specificity suffers at higher speed.

Number 2:  Targeted Multiplex SIM

MSX

Lets take a whack at the disadvantages T-SIM has by using the quad on the Q E to collect multiple targets sequentially.  We can do as many as ten at once.  Is 6ms per target possible?  Heck yeah it is!

Advantage:  Sensitivity, though not as sensitive as regular T-SIM.  Better cycle time.  We've traded more targets for less sensitivity.

Disadvantage:  Cycle time can still be a bit an issue on big lists.  As you'll see, each method has a compromise.  We're at 10 times more targets, but a QQQ can still do more.  We're still much more sensitive than other methods on the list.  We still may have the specificity issues that the regular T-SIM has on extremely complex lists.  Higher resolution (which we have, in abundance!) is the solution, but that will decrease our number of targets.


Wow.  I'm getting sleepy.  Time to put a "Part 1" in the title.
Read part 2 here.