Targeted quan on the QE part 2!

Yay!  Part 2!

Check out Part 1 here.  The response has been...enthusiastic.  I didn't know so many triple quad users read my blog!

Next on my list is plain old, MS1-ddMS2, with an Inclusion List

Couple of different ways we could process this.  We could quan at the MS1 level, or we could quan on fragment ions at the MS2 level.

Advantages:  Specificity.  We have high resolution accurate mass MS1 to look at and fragment ions to confirm the identity of what we're looking at.  Tons of targets!  We can do an absolute ton of targets here.  How many?  Try 5k.  No joke.  Will we get all 5,000?  Probably not, but that may be more due to the fact that you didn't do a great job making that list of 5,000 ions.  Come on.  You'll do a great job on a list of 10 or 50 or even 100 ions, but you're bound to make a mistake while editing that list of 5,000 ions.  No one can blame you, maybe its 1am and you're sleepy.

Disadvantages:  Sensitivity.  This is the least sensitive way to do our targeted quan.  Now, sensitivity is a relative term.  We're still smoking every Q-TOF on this planet, but not by the margins that we're used to.

Man, I'm beat.  Tomorrow we'll start the sensitive AND specific assays.

Read part 3 here.