In LCMS the most important is the selection of stationary phase of the LC component and then the mobile phase. Simple things like partition coefficient makes a big difference in the selection of mobile phase.

Dear Dong,

The intensity of the compound is related to the concentration of the analyte not with the mobile phase. however, the symmetry of peak is somehow related to the mobile phase. The retention time depends upon the Pka value of the particular analyte so if you are using any mobile phase or buffer solution, pH value 2 units above or below to the Pka value can completely ionized or will maintain the un-ionized form of analyte that will affect its retention because ionized form elutes early as compared to un-ionized form.   

I fully agree with Nilesh, and thats what I am emphasizing the importance of mobile phase selection along with a matching stationary phase.

Dear Jai and Nilesh,

Generally,   the retention behaviors  of compound are along with a matching stationary phase. However, when the stationary phase is identified, the change of moble phase, such as ACN-water, 1% FA ACN-water, ACN-1% FA water, at constant flow rate and ratio, will affect the retention behaviors and intensity of the compounds. How?

This is based on the adsorption coefficients of the compounds to be identified. This is to answer your question in brief.