I had NO idea that you could even do this. However, this appears to be mostly my ignorance, because these authors have been developing techniques like these for years!
Before I go further, this is the new paper at JPR.
There are a ton of classical genetics techniques for quantifying DNA adducts (essentially DNA that is messed up or altered in some way). Unless a lot of new stuff has popped up since I left JHU, they have:
High false negatives/false positives
Detect adducts that could...be..well...anything... Maybe I'm exaggerating, but I'm not sure that I am. The techniques my department used were fluorescence based and/or gel migration based (sure -- the gels were like 0.5M long, but still...gels...)
I think this paper is an invitation for DNA damage researchers to join us in the 21st century! Check this out:
Yeah -- this method is no joke. I mentioned above that the Turesky lab has been developing mass spec based DNA adduct detection/quantification methods for years, it appears, so they know what they are looking for in terms of mass shifts. However, a classical dd-MS2 method isn't going to cut it here. Honestly, this figure doesn't do this study justice.
At first, I thought this was the first Wi-SIM-DIA paper I'd come across (this is a method on a Tribrid mass spec where the Orbitrap does wide SIM scans while the ion trap does simultaneous small DIA scans. However, to get the level of precision this group needs to detect and identify these adducts, they do all steps in the Orbitrap. This requires a lot of timing because they are eluting digested nucleotides off nano-LC columns and all these Orbitrap scans take time.
Looking at it this way, I immediately wonder if someone could pull this off on a simpler instrument if they had complete hardware control, but then you realize they throw in MS3 as well. Quantification and confirmation of these nasty DNA modification all in one go!