Evaluating Ion Mobility Data Acquisition, Calibration, and Processing for Small Molecules: A Cross-Platform Assessment of Drift Tube and Traveling Wave Methodologies

As ion mobility spectrometry (IMS) separations continue to be added to analytical workflows due to their power in environmental and biological sample analyses, harmonization and capability understanding between existing and newly released instruments are desperately needed. Developments in IMS platforms often exhibit focus on increasing resolving power (R_p) to better separate molecules of similar structure. While the additional separation capacity is advantageous, ensuring these developments coincide with appropriate data extraction and analysis methods is imperative to ensure routine adoption. Herein, we assess the performance of the MOBILion MOBIE in relation to a commercially available drift tube IMS-MS, the Agilent 6560, and evaluate feature extraction and analysis pipelines. Both instruments were operated using matched conditions when possible, and performance metrics of scan speed, R_p, limits of detection (LOD), and propensity for isomer separation via LC-IMS-MS were evaluated. Similar scan speeds pertaining to IMS-MS frame generation were noted for both platforms, and collision cross section (CCS) values for the MOBIE were generally within ≤ 1% difference from previously reported drift tube values. Both platforms were also able to generate quantitative data (comparable limits of detection) in experiments with perfluoroalkyl substances (PFAS) mixtures in a cell-based model (both medium and cell lysates), as demonstrated in Skyline with adjusted mobility filtering parameters. Higher R_p was, however, noted on the MOBIE in comparison to the 6560 (200-300 vs 45-60 CCS/ΔCCS without data processing), allowing the detection of more PFAS isomers and indicating promise toward future applications in chemical exposomics studies and biomarker discovery when molecules exhibit similar structures.