Quantum Chemical Fragment Precursor Tests: Accelerating de novo annotation of tandem mass spectra

Tandem mass spectrometry is widely used to assign and distinguish chemical structures in proteomics, metabolomics, lipidomics, and many other areas. Spectral annotation remains a major bottleneck. Our "Quantum Chemical Fragment Precursor Tests" (QC-FPT) approach brings the accuracy and generality of modern quantum chemistry to combinatorial-search-based computer-aided spectral annotation. QC-FPT takes as input the dominant fragment peaks from a particular experiment, and one or more chemically reasonable hypotheses for the precursor ion's three-dimensional structure. The algorithm automatically generates possible precursor ion fragmentations matching the target experimental peaks, uses quantum chemistry calculations (geometry optimization with gas-phase semiempirical or density functional theory calculations) to predict each neutral or charged fragment's structure and energy, and reports the thermodynamically feasible predicted fragment assignments. Applications demonstrate that QC-FPT recovers known spectral annotations, can handle multiple ionization and fragmentation methods and adducts, and can capture some fragment rearrangements. We apply QC-FPT to assign previously unassigned peaks in an experimental LC-ESI-MS² spectrum of dimethylarsinothioyl glutathione (Yehiayan et al., Chem. Res. Toxicol. 2014, 27, 754-764), and to a hypothetical experiment distinguishing two isomeric candidates for an "unknown" pesticide's experimental LC-ESI-MS² spectrum. Our results suggest QC-FPT is a practical tool to sharpen and refine the chemical intuition of experimentalists engaged in the laborious process of annotating tandem mass spectra.