Compare concentrations using LC/MS Suppose I run a reaction and then pass the results through LC/MS to find the conversion. One idea could be to compare the peaks of the reactants to the peak of the product. But:


MS peak will depend on the levels of ionization of each of the compounds
UV spectra depends on the molar extinction coefficient of the compounds


So it looks like I can't compare the peaks. Is this right and if so what are the possible ways of finding the conversion?
You can indeed find the conversion (not the absolute concentrations), even without calibrating the system.

At time t = 0, take an exactly measured volume of reaction mixture (e.g. 1 mL) and dilute it in a volumetric flask with water and/or acetonitrile to an exact volume (e.g. 100 mL).

Inject an exact volume (e.g. 50 uL) of the diluted solution in the LCMS and note down the (UV-based) peak area of the limiting reagent. This is your ${A_0 = \epsilon \cdot C_0 \cdot k}$, where ${C_0}$ is the concentration of your limiting reagent at this time, and ${k}$ is a constant related to the sample size and dilutions.

At any time t, do exactly the same as above, and you get an area ${A_t = \epsilon \cdot C_t \cdot k}$. Under these conditions, ${k}$ is the same, and of course so is ${\epsilon}$.

As you know, the conversion is ${y = 1 - \frac {C_t}{C_0}  = 1 - \frac {A_t}{A_0} }$.