Greetings, and thank you in advance for any help you can provide.

I am using an Agilent LC-MS-QTOF and MassHunter Version 7.0. I am trying to build a quantitation method for a C13 labeled experiment. And I am searching for a way to automate quantitation.

We already have a method and library for our unlabeled compounds. However, we now intend to use a C13-labeled compound in-vivo, to study how it is metabolised. Of course, in an ideal world, it would be doubly C13 labeled so any endogenous amount is <2% at the M+2, but this would require a custom synthesis that is simply cost prohibitive, and any commercially available d-4 compounds are labeled on the reactive sites for metabolism.

So we are using a simple C13 labeled compound. When I go to quantitate samples, I must correct for any endogenous compounds present, as its +1 peak is significant around 20 - 25%. I cannot simply subtract a fixed amount because the endogenous amount will vary, as well as the labeled amount. Ideally, I just quantitate the non-labeled peak, multiply it by the theoretical M+1, and then subtract this amount from the M+1 present;if it is <=0, I simply ignore it, and if it is >0 I attribute this to a product of metabolism from the introduced C13 compound.

So to the point ... IS THERE AN AUTOMATIC WAY TO DO THIS IN MASS HUNTER??? If you know how, can you please share, or even more preferable, send a link to a tutorial / pdf? I cannot be the first to do a C13 labeled experiment in LC-MS!! :) Without success, I have been searching the forums, Google, Agilent presentations, and and our rep doesn't write back.

Thank you again for your time.