Since I count the cells before storing and will be lysing the cells using a sonicator before analysis, so is the cryoprotectant required? My concern is that if these chemicals are Mass Spec compatible? and if I store the samples without adding any solvents, will it affect the stability of the metabolites?
I believe that the mentioned solvent and compounds to be used as cryoprotectant will not interfere or react with the metabolites especially at low temperatures. Additionally, the mas spectra of these compounds are known. I suggest that you run an MS for the control (cryoprotectant) in order to enable you to precisely assign the drug and its metabolites.
If you are going to conduct the experiment without cryoprotectant, this might result in yielding unrecognized compounds due to an expected degradation of the pellets.
I suggest you to check also some informations in: Extraction of DNA from Whole Blood and White Blood Cells By Douglas Kitt, 6/6/01, modified for 10ml tubes by AM 2007.