Mass difference matching crystallizes hidden molecular structures of dissolved organic matter from ultrahigh-resolution tandem mass spectra

Ultrahigh-resolution mass spectrometry has revealed unprecedented detail of natural complex mixtures such as dissolved organic matter (DOM) on a molecular formula level but we lack information on the underlying structural complexity for full-scale identification. We applied a novel approach to decipher DOM’s characteristic chimeric tandem mass (MS2) spectra that represent multiple precursors of the same nominal mass. We calculated mass difference (Δm) matrices from precursor and product ions and matched them with reference Δm’s from 11280 library MS2 spectra and molecular structures. We found 1) indication for the presence of degraded phenolic plant metabolites, unknown N- and S-containing molecules, and missing elements in formula annotation, 2) weak support for postulated Van Krevelen structural domains, 3) multiple significant links between precursor properties, Δm matches, and chemodiversity. Our paper highlights Δm matching by MS2 as a promising tool to reveal novel structural information and molecular ecosystem imprints in complex mixtures like DOM.