High concentrations of urea and guanidine hydrochloride are commonly used for the denaturation of protein, which was digested by enzymatic proteolysis for the identification by MS analysis. The presence of these contaminants seriously suppresses the ion signal of analytes in MALDI-TOF MS analysis. Herein, a novel MALDI matrix, 3, 4-diaminobenzophenone (DABP), has been found with high tolerance for these contaminants in MALDI MS analysis. The ion signal of analyte insulin can be detected in the presence of 2 M guanidine hydrochloride and 1.5 M urea using DABP as matrix. The tryptic digest of BSA (400 fmol) in 1 M guanidine hydrochloride or 1 M urea was successfully analyzed without any pretreatment prior to MS analysis. Furthermore, it has been found that this matrix can also effectively suppress the cation ion adduction of the peptides in the presence of high concentrations of metal ions in sample solution.