|Using Skyline for target-directed DCC analysis||antoine lacour||2021-08-04|
I am looking to use Skyline to speed up the analysis of a target directed DCC run. For those not familiar with the experiment, you take a library of reagents (in this case aldehydes and hydrazides) which react to form a library of products (here acylhydrazones). The reaction is an equilibrium which can be modified by Le Chatelier's principle, in this case by the addition of an enzyme. The idea is to find the products in the equilibrium which are amplified by adding the enzyme, which indicate potential binders to the target in question. See the following article for an example : https://pubs.rsc.org/en/content/articlelanding/2021/sc/d1sc00330e#!
I am wondering if I can use Skyline to help with the analysis of the data coming from these runs. We run a blank experiment with no enzyme and one with enzyme and compare the formation of the products in both.
I created a transition list (M to M+H (not sure if this is what I should be inputting but it seems to work as I intend)) with all possible products of the equilibrium, and imported the LC-MS data from both the blank run and enzyme run. Using this I can easily figure out the retention time of the product and compare its presence or absence in each run.
However I Have the following issues/questions
I attached a sample picture of the extracted chromatograms with all the compounds shown.
Thanks in advance for your help, and I apologise in advance for any incorrect terminology I use, MS is not my strong suit.