Dissolved organic matter (DOM) is an ultracomplex mixture that plays a central role in global biogeochemical cycles. Despite its importance, DOM remains poorly understood at the molecular level. Over the last decades, significant efforts have been made to decipher the chemical composition of DOM by high-resolution mass spectrometry (HR-MS) and liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS). Yet, the complexity and high degree of nonresolved isomers still hamper the full structural analysis of DOM. To address this challenge, we developed an offline two-dimensional (2D) LC approach using two reversed-phase dimensions with orthogonal pH levels, followed by MS/MS data acquisition and molecular networking. 2D-LC-MS/MS reduced the complexity of DOM, enhancing the quality of MS/MS spectra and increasing spectral annotation rates. Applying our approach to analyze coastal-surface DOM from Southern California (USA) and open-ocean DOM from the central North Pacific (Hawaii), we annotated in total more than 600 structures via MS/MS spectrum matching, which was up to 90% more than that in iterative 1D LC-MS/MS analysis with the same total run time. Our data offer unprecedented insights into the molecular composition of marine DOM and highlight the potential of 2D-LC-MS/MS approaches to decipher the chemical composition of ultracomplex samples.

Bigelow Laboratory for Ocean Sciences 60 Bigelow Drive East Boothbay Maine 94544 United States

Department of Biochemistry University of California Riverside 169 Aberdeen Dr Riverside California 92521 United States

Department of Environmental Analytical Chemistry Helmholtz Centre for Environmental Research Leipzig 04318 Germany

Helmholtz Institute for Functional Marine Biodiversity Carl von Ossietzky University Oldenburg Oldenburg 26129 Germany

Institute for Chemistry and Biology of the Marine Environment Carl von Ossietzky University Oldenburg Oldenburg 26382 Germany

Institute of Organic Chemistry and Biochemistry of the CAS Praha 6 Prague 166 10 Czech Republic

Interfaculty Institute of Microbiology and Medicine University of Tuebingen Auf der Morgenstelle 24 Tuebingen 72076 Germany

Scripps Institution of Oceanography University of California San Diego 8622 Kennel Way La Jolla California 92037 United States

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