Abstract: A computer program was designed for predicting MS fragments’ mass of peptides or peptide analogs according to known algorithm. It was written by C++ with high transplantability. The output-file of this program can be processed by EXCEL or other electric-table easily. Not only natural occurring peptides but also peptide analogs with unnatural amino acid residue can be processed. MS fragments’ mass of some peptide analogs were predicated by this program. The results show that this program is efficient and dependable. It is convenient and flexible to analysis MS fragments of peptides or peptide analogs supplied by this program.