This is a SBIR Phase I project. The goal of the project is to develop an improved method of protein sequencing based on the capillary high performance liquid chromatography and tandem mass spectrometry. Specifically, the project involves the development of a probabilistic model for peptide fragmentation and ionization that is consistent with actual data, and the development of a prototype algorithm that finds the peptide wit the maximum likelihood of yielding a given spectrum. The commercial potential of this work is the development of a software system which would analyze peptide fragment mass spectroscopy data to yield protein sequence data. If successful such a product could be provided as a stand alone system or it could be integrated into the software packages that are provided with mass spectrometers.