The M1 protein of influenza virus is a highly hydrophobic polypeptide that is resistant to enzyme cleavage during incubation in water solutions. We show here that the M1 protein that is immobilized on an insoluble activated support (thiopropyl Sepharose-6B) by means of a thiol-disulfide exchange reaction acquires sensitivity to trypsin. After tryptic digestion noncysteine-containing peptides of M1 were removed by washing the support, while cysteine-containing ones were detached from the support by reduction. As a result, 24 unique tryptic peptides of M1 protein were clearly separated by reversed-phase high-performance liquid chromatography. The described method opens a new way to the investigation of functional properties of distinct domains of viral thiol proteins.