Hello all - I am new to learning MS and don't have a lot of guidance. I am having a really hard time finding information on what criteria is used to choose the optimal CE for an MRM transition. I have found multiple resources online showing how to do edit ramp functions in my software (Analyst) to obtain an "optimal" CE, but it doesn't explain why that CE was chosen as optimal, so I have no way of knowing for sure that the function worked correctly and that I am choosing the best CE. I have been looking up and down, left and right and cannot get a clear answer. I've also asked multiple people who have all told me different things. I've been told to choose a CE where the parent and daughter ion are about the same intensity; I've been told to choose a CE where the parent ion is 20% the intensity of the daughter ion, and so on. If someone could tell me how they choose their optimal CE I would really appreciate it.
Hello Grace - The usual approach is to choose the CE that gives the highest abundance for maximum sensitivity. With Analyst you can either do this manually by doing a ramp of the CE on the MRM transition or you can use the Compound Optimization app to do this automatically. Don't forget that the CE is only 1 parameter that needs to be optimised. For best sensitivity and repeatability you need to optimise everything including the source parameters.
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