Comparative evaluation of positive and negative LC-MS modes for DOM profiling

Dissolved organic matter (DOM) in marine environments is critical for nutrient cycling and carbon storage, forming a fundamental part of the ocean's biogeochemical cycles. Traditionally, DOM analysis has utilized negative electrospray ionization (ESI-) mass spectrometry, yet positive electrospray ionization (ESI+) mode has recently gained traction. However, few studies have compared ESI+ and ESI- to understand how these modes impact the overall DOM profiling results. This study investigates DOM profiles from the Sansha Yongle Blue Hole (SYBH)-the world's deepest blue hole-using HPLC-Orbitrap-MS/MS in both ESI+ and ESI- modes. Results show that ESI+ detects a broader range of DOM ions, with a significant correlation in ion counts between the two modes across different depths. ESI+ is more effective for detecting nitrogen-rich compounds (CHN, CHON, CHONS), while ESI- is better for sulfur-rich compounds (CHOS), especially in anoxic layers. Both modes identify similar levels of carbohydrates, carboxyl-rich alicyclic molecules (CRAM), and unsaturated aliphatic compounds (UA), but ESI+ detects more highly unsaturated compounds (HU), peptides, and polyphenols. Correlations in ion counts for carbohydrates, CRAM, and UA across depths indicate consistency between modes, while differences for HU, peptides, and polyphenols suggest lower ionization efficiency in ESI-. Both modes distinguish oxic, chemocline, and anoxic layers, but molecular parameters like double bond equivalents (DBE), modified aromaticity index (AImod), and H/C ratios correlate between modes, while O/C ratios do not. These discrepancies suggest that using only one ionization mode may bias DOM interpretation. Future studies should employ multi-mode ionization to enhance DOM profiling and understanding across marine environments.