Collision cross‐section measurements of small molecules via transient decay profiles observed in Orbitrap mass analyzers

Collision cross section (CCS) of organic compounds can be measured via Fourier transform-based mass spectrometry (MS) by modeling the decay rate of transient signals in the analyzer. Deriving CCS values of low-mass molecules (mass < 2000 Da and CCS < 500 Ų) with Orbitrap MS is challenging due to their high axial frequencies and small absolute variances in cross-sectional profiles. Here, we acquired mass spectra of progressively more complex low-mass analytes using commercial Orbitrap mass spectrometers. The transient signals were processed using Fast Fourier transform (FFT) and short-time Fourier transform (StFFT) to derive decay constants of multiple select ionic species from a single MS full-scan experiment. Decay constants were translated into CCS values using at least two internal standards in the same mass spectrum. Our results suggest target ionic species should have high S/N in order to derive CCS values with ≤0.5% uncertainty. Limitations in the precision of CCS measurements reflect local space charge effects that disturb ion motion in the analyzer. The derived CCS values of polymer like fragments of Ultramark 1621 and small molecules such as individual protonated amino acids can achieve average ±1% error with selection of internal standards across a wide mass range. Future studies need to optimize the strategy to select internal standards in order to improve the precision and accuracy of CCS measurements for small molecules via Orbitrap MS.