An algorithm,called searching sequence-specific ions,is proposed here for interpretation of mass spectra of unknown polypeptide.This program is composed of three parts:searching,scoring and merging. The method successfully interpreted some unknown polypeptides’mass spectra. One of the major advantages of this program over algorithms described earlier is its scoring ability which can rank the confidence of every amino acid residues in the interpreted polypeptide.It greatly facilitates the determination of the amino acid sequence and provides a pathway for the application of mass spectra to biology.