Conformational Ordering of Biomolecules in the Gas Phase: Nitrogen Collision Cross Sections Measured on a Prototype High Resolution Drift Tube Ion Mobility-Mass Spectrometer

TLDR

Ion mobility‑mass spectrometry provides gas‑phase collision cross‑section data that reveal intrinsic folding forces without solvent and serve as reproducible metrics for identifying and characterizing molecules. The study uses a prototype platform featuring a uniform‑field drift tube flanked by electrodynamic ion funnels and linked to a high‑resolution quadrupole time‑of‑flight mass spectrometer. We measured 594 nitrogen‑derived CCS values with ±0.5 % precision across quaternary ammonium salts, lipids, peptides, and carbohydrates, showing nitrogen CCSs are systematically larger than helium values yet preserve class‑separation trends, highlighting the need for caution when calibrating nitrogen data with helium standards.

Abstract

Ion mobility-mass spectrometry measurements which describe the gas-phase scaling of molecular size and mass are of both fundamental and pragmatic utility. Fundamentally, such measurements expand our understanding of intrinsic intramolecular folding forces in the absence of solvent. Practically, reproducible transport properties, such as gas-phase collision cross-section (CCS), are analytically useful metrics for identification and characterization purposes. Here, we report 594 CCS values obtained in nitrogen drift gas on an electrostatic drift tube ion mobility-mass spectrometry (IM-MS) instrument. The instrument platform is a newly developed prototype incorporating a uniform-field drift tube bracketed by electrodynamic ion funnels and coupled to a high resolution quadrupole time-of-flight mass spectrometer. The CCS values reported here are of high experimental precision (±0.5% or better) and represent four chemically distinct classes of molecules (quaternary ammonium salts, lipids, peptides, and carbohydrates), which enables structural comparisons to be made between molecules of different chemical compositions for the rapid "omni-omic" characterization of complex biological samples. Comparisons made between helium and nitrogen-derived CCS measurements demonstrate that nitrogen CCS values are systematically larger than helium values; however, general separation trends between chemical classes are retained regardless of the drift gas. These results underscore that, for the highest CCS accuracy, care must be exercised when utilizing helium-derived CCS values to calibrate measurements obtained in nitrogen, as is the common practice in the field.