Unravel the in-Source Fragmentation Patterns of Per- and Polyfluoroalkyl Substances during Analysis by LC-ESI-HRMS

In-source fragmentation (ISF) was inevitable during electrospray ionization (ESI) of per- and polyfluoroalkyl substances (PFAS) when analyzed by liquid chromatography coupled with mass spectrometry (LC-MS), resulting in reduced response of molecular ions and misannotation of MS features. Herein, we analyzed 82 PFAS across 12 classes to systematically identify the structures with ISF potentials and reveal the fragmentation pathways. We found up to 100% ISF for 38 PFAS in six classes, which all contain the carboxylate (CO₂^–) headgroup, including perfluoro(di)carboxylates (PF(di)CA), omega H/Cl substituted PFCA (ωH/Cl-PFCA), fluorotelomer carboxylates, and perfluoroalkyl ether carboxylates (PFECA). Seven ISF pathways were identified, including direct cleavage of C–CO₂^–, C–O, and C–C bonds and eliminations of HF/CO₂HF through cyclic transition states by the mechanisms of β-elimination, McLafferty rearrangement, or H···F bridging. We found that the loss of CO₂ is a prerequisite for most other pathways, explaining the absence of ISF for PFAS without a CO₂^– headgroup. The elevated bond dissociation energy of C–CO₂^– explained the reduced ISF for long-chain PFCA and ωH-PFCA. Raising the MS vaporizer and ion transfer tube temperatures significantly aggravated the ISF of most PFAS. These findings provide valuable references to inform the structural identification of PFAS and their degradation products.