Approaches for GC-HRMS Screening of Organic Microcontaminants: GC-APCI-IMS-QTOF versus GC-EI-QOrbitrap

This study explores the capabilities of GC-APCI-IMS-QTOF MS and GC-EI-QOrbitrap MS in screening applications and different strategies for wide-scope screening of organic microcontaminants using target suspect and nontarget approaches. On one side, GC-APCI-IMS-QTOF MS excels at preserving molecular information and adds ion mobility separation, facilitating screening through the list of componentized features containing accurate mass, retention time, CCS, and fragmentation data. On the other side, the extensive and robust fragmentation of GC-EI-QOrbitrap MS allows the application of different strategies for target and nontarget approaches using the NIST library spectra. Our findings revealed that GC-EI-QOrbitrap MS is more sensitive in target approaches. Automated workflows for suspect screening in GC-APCI-IMS-QTOF MS minimize false annotations but face challenges with false negatives due to in-source fragmentation and limitations when using in silico fragmentation tools. Conversely, a nontarget approach in GC-EI-QOrbitrap MS can reliably identify unknowns but results in more false annotations in complex matrices. This work highlights the strengths and limitations of each system and guides for their optimal application for wide-scope screening in environmental and food safety applications.