Not One Method to Rule Them All: A Comparative Study of Chromatographic Platforms (RP-LC-, HILIC-, SFC-, and IC-HRMS) for Water Analysis

Reversed-phase liquid chromatography coupled to high-resolution mass spectrometry (RP-LC-HRMS) is the standard for nontarget screening (NTS) of environmental samples but lacks retention of highly polar contaminants. We compared 12 chromatographic methods across four platforms, RP-LC, anion chromatography (IC), supercritical fluid chromatography (SFC), and hydrophilic interaction chromatography (HILIC), using 127 environmentally relevant compounds (log<i>D</i>_pH7.4 -5.6 to 6.6). Compounds were analyzed in solvent and for a polar subset, in groundwater enriched by vacuum evaporation. Data were collected across four laboratories using 5 RP-LC-, 3 HILIC-, 2 SFC-, and 2 IC-HRMS setups. Feature detection with standard tools yielded more false negatives for SFC and IC. To enable a fair and method-agnostic comparison, an extracted ion chromatogram (EIC)-based workflow was used. Of the 127 compounds, 125 were detected by at least one platform. For log<i>D</i>_pH7.4 > 0, RP-LC covered ∼90%, followed by SFC (∼70%), while IC and HILIC each covered <30%. For very polar compounds (log<i>D</i>_pH7.4 < 0), coverage dropped across all platforms. SFC and HILIC detected up to 60% of polar analytes; IC performed better in negative ionization mode, consistent with anion-exchange separation. Detection frequency declined with polarity, reflecting analytical limitations. Combining RP-LC with either SFC or HILIC increased coverage to 94%. In spiked groundwater, coverage was lower (73%) due to matrix effects and losses during vacuum enrichment. Peak widths were narrowest for SFC (∼2.5 s) and RP-LC (∼4 s) and broadest for HILIC (∼7 s) and IC (∼17 s). Retention times showed limited cross-platform correlation while ionization efficiency was consistent, except for SFC. As no single method provided full coverage, combining RP-LC with one complementary platform (SFC, HILIC, or IC) is required to extend chemical space in environmental NTS.