I'm using SILAC diet to label mice for 10 days (pulse SILAC) and compare new protein incorporation rates under two different experimental conditions. I want to impute values for those proteins that only contain iBAQ H (fully labeled) and those that only contain iBAQ L(no new synthesis) at any of the 2 experimental conditions. I expect to get a H/L ratio when there is both iBAQ H and iBAQ L for the protein, however there are many cases when the ratio H/L is not reported. I already checked that making the ratio from iBAQ H/iBAQ L doesn't work. MaxQuant uses an algorithm to estimate H/L ratios. Does anyone has an explanation? How can this be approached?