Dear Skyline,

We are in the process of optimising CE for some PRM's we are performing, and we have a question to the user group on what is best practice.

What we have noticed is that we can enhance the sensitivity of our assays 2-3 fold for some peptides however this often results in a lowering of the dotp (dot product) value as we get a different abundance of some fragments (compared to our library spectra) that start to become more dominant. We are wondering what the best practice here is, we have a heavy standard so we can use the idotp for this rather than the library in our final analysis?

Should we regenerate our DDA data with a slope that reflects the optimal energies..?

Any advise is greatly appreciated.

bw,

rob