Fast Graphically Inspired Algorithm for Assignment of Molecular Formulae in Ultrahigh Resolution Mass Spectrometry

This study focuses on the deterministic task of assigning molecular formulae to exact masses that are generated by ultrahigh resolution mass spectrometry. A new algorithm based on low-mass moieties (LMMs) such as CH₄O_–1 and C₄O_–3 completely replaces conventional computational loops that explore a user-defined range of C, H, and O when searching for molecular formulae that have a given exact mass. The LMM-based algorithm has been coupled with a combinatorial algorithm that uses nested loops for N, P, S, and ¹³C to assign molecular formulae. The resulting program is more than 1700 times faster than its brute-force counterpart that uses nested loops for all elements, and both programs yield identical output files. The new LMM-based program is 1050 times faster than the open-source program HR2, 60 times faster than Molecular Formula Calculator, and 3.6 times faster than MassCalc/FormCalc.