Taking MS spectra from a blank milk blocked membrane may hep you deciding on what to expect from the MS measurements. Depending on the specifics and goals of your experiment, MALDI-TOF MS could be a tool for measuring peptides either directly from the membrane or after rinsing the membrane in MALDI matrix and analyzing the matrix. Best of luck in your work.
It will be very challenge. Peptides from milk protein will interfere with your signal, and usually overwhelm, i.e. after MS, you will only "see" milk protein not your protein.