A fast algorithm and software for analysis of FT-ICR data

In this paper, we present and analyze a fast algorithm that determines the possible molecular formulae corresponding to the resolved peaks in the spectral data obtained from a mass analyzer like an FT-ICR-MS. In contrast to our approach, most known algorithms and software that attempt to solve this important problem are brute-force in nature and consequently, highly prone to combinatorial explosion when dealing with the volume of real data. We also present an object-oriented implementation of our algorithm in a general-purpose, user-friendly, interactive, and easily extensible software tool PG Compound Match Finder. A run-time performance analysis of our software shows that even when dealing with several billion theoretical possibilities matched against tens of thousands of resolved peaks, a complete analysis using today's standard desktop machines can take only a few minutes.