Combining mass spectrometry (MS) with ion mobility (IM) provides a powerful approach for characterizing biomolecules. IM adds an additional “gas-phase chromatography” dimension, in which ions are separated not only by mass and charge, but also by their size and shape. This enables the distinction of isomers and provides an additional structural descriptor: the rotationally averaged collision cross section (CCS).

Figure: Schematic of IM separation, where analytes are separated based on their size, charge and shape.

We are interested in understanding the fundamentals of IM-MS, including theoretical CCS prediction benchmarking, energy calibration and deconvolution of IM-MS data. We are part of the Marie Skłodowska-Curie Actions Doctoral Network “Mobilitrain”, which is a consortium of 21 partners in academia and industry addressing fundamental questions of IM-MS.

 Our group primarily uses IM-MS for the structural characterization of metabolites, glycans and self-assembling peptide assemblies. Because glycans exhibit extensive regio- and stereochemical complexity, conventional MS – even when combined with liquid chromatography and tandem MS – often cannot fully resolve all isomeric forms. Our goal is to develop IM-MS workflows capable of differentiating these closely related glycan isomers and to apply these methods to analyze glycan and glycosylation patterns in clinical patient samples as part of larger glycomics studies.

Figure: IM separation of glycans gives different and discriminatory CCS values of N-glycans

Downloads

• Excel spreadsheet to estimate CCSs from traveling wave ion mobility mass spectrometry data. See file for further details and literature.
• pdf with step-by-step description of the instrument optimization and calibration procedure.

Related Publications on Fundamentals of IM-MS

• Plate-height model of ion mobility-mass spectrometry
  Grabarics, M.; Lettow, M.; Kirk, A.T.; von Helden, G.; Causon, T.J. & Pagel, K. Analyst. 2020 

Related Publications on Applications of IM-MS

• Ion mobility–mass spectrometry of palytoxin-like compounds produced by Ostreopsis cf. ovata
  Medina-Pérez, N.I.; Peralta-Moreno, M.N.; Rubio-Martinez, J.; Bechtella, L.; Polewski, L.; Szekeres, G.P.; Berdalet, E.; Moyano, E. & Pagel. K.  Anal. Bioanal. Chem. 2025 
• Ion Mobility Mass Spectrometry-Based Disaccharide Analysis of Glycosaminoglycans 
  Polewski, L.; Moon, E.; Zappe, A.; Götze, M.; Szekeres, G.P.; Roth, C. & Pagel, K. Chem. Eur. J. 2024
• Determination of Sialic Acid Isomers from Released N-Glycans Using Ion Mobility Spectrometry
  Manz, C.; Mancera-Arteu, M.; Zappe, A.; Hanozin, E.; Polewski, L.; Giménez, E.; Sanz-Nebot, V. & Pagel, K. Anal. Chem. 2022
• Shotgun Ion Mobility Mass Spectrometry Sequencing of Heparan Sulfate Saccharides
  Miller, R.L.; Guimond, S.E., Schwörer, R.; Zubkova, O.V.; Tyler, P.C.; Xu, Y.; Liu, J.; Chopra, P.; Boons, G.J.; Grabarics, M.; Manz, C.; Hofmann, J.; Karlsson, N.G.; Turnbull, J.E.; Struwe, W.B. & Pagel, K. Nat. Commun. 2020
• Glycan Analysis by Ion Mobility-Mass Spectrometry
  Hofmann, J.; Pagel, K., Ang. Chem. lnt. Ed. 2017, 56, 8342–8349.
• Ion mobility separation of deprotonated oligosaccharide isomers - evidence for gas-phase charge migration 
  Struwe, W.B.; Baldaug, C.; Hofmann, J.; Rudd, P.M. & Pagel, K. Chem. Commun. 2016 
• Identification of carbohydrate anomers using ion mobility–mass spectrometry
  Hofmann, J.; H. S. Hahm, P. H. Seeberger; Pagel, K.; Nature. 2015
• Estimating collision cross sections of negatively charged N-glycans using traveling wave ion mobility-mass spectrometry
  Hofmann, J.; Struwe, W.B.; Scarff, C.A.; Scrivens, J.H.; Harvey, D.J.; Pagel, K.; Anal. Chem. 2014