Nanoscale and Microscale Research Centre

Secondary Ion Mass Spectrometry

OrbiSIMS image

3D OrbiSIMS  Facility



A Time of Flight Secondary Ion Mass Spectrometer (ToF-SIMS) with hybrid OrbiTrapTM functionality, the '3D OrbiSIMS' is the first of its kind in an academic setting. Based on the prototype at the National Physical Laboratory (NPL) the instrument combines the function of the two hybridised components to facilitate an unprecedented level of mass spectral molecular analysis for a range of materials (hard and soft matter, biological cells and tissues). The dual functionality of this hybrid system underpins spatial and mass resolution improvements in chemical identification and imaging that revolutionize mass spectrometry imaging. Most notably the capacity to identify unknown organic species in complex solid samples is dramatically improved. Importantly, the facility is complemented by high pressure freezing cryo-preparation facilities that enable biological samples to be maintained close to their native state. Complemented by the more commonly applied (but more disruptive) freeze drying and sample fixation the 3D OrbiSIMS facility is ideally targeted at soft matter analyses and enables label free molecular analysis. However when the exceptional surface sensitivity (1-3nm) and high mass/spatial resolution are combined with a depth profiling sputtering beam, the instrument becomes an extremely powerful tool for 3D chemical analysis on a multitude of sample types.

Key Features

  • High mass resolution spectrometry (>240,000 and 11,000 amu for the OrbiTrap and the ToF, respectively.
  • High spatial resolution chemical imaging (<70 nm).
  • Gas cluster ion beam sputtering for controlled depth profile analysis of organics.
  • Cryogenic sample preparation facility, including high pressure freezing, freeze drying, cryo-ultramicrotomy and more.
  • Category 2 preparation facilities for cell/tissue analysis.




Research Highlights 

3D MS imaging using dual beam and dual spectrometer (mode 10) of single rat alveolar macrophage cell incubated in media with the drug amiodarone


(a) Sequence of 30 keV Bi3+ (~300-nm resolution) ToF-SIMS images of total ion counts at ~400-nm depths as the cell is sputtered away. (b) As in a, color overlay of phosphocholine marker (m/z 184), gray, nuclear marker (m/z 157), magenta and amiodarone [M+H]+ (m/z 646), green (c) 3D rendering of the cell with phosphocholine marker, (m/z 184, gray, opacity 0.40), nuclear marker (m/z 157, magenta) and amiodarone [M+H]+ (m/z 646), green.

The 3D OrbiSIMS - Label-Free Metabolic Imaging with Sub-cellular Lateral Resolution and High Mass Resolving Power, Passarelli et al., Nature Methods, DOI 10.1038/nmeth.4504


The use of nanovibration to discover specific and potent bioactive metabolites that stimulate osteogenic differentiation in mesenchymal stem cells, Hodgkinson T., Tsimbouri P. M., Llopis-Hernandes V., Campsie P., Scurr D., Childs P. G., Phillips D., Donnelly S., Wells J. A., O'Brien F. J., Salmeron-Sanchez M., Burgess K., Alexander M., Vassalli M., Oreffo R. O. C., Reid S., France D. J., Dalby M. J., Science Advances7(9), eabb7921, 2021

Protein Identification by 3D OrbiSIMS to Facilitate in situ Imaging and Depth Profiling, Kotowska A. M., Trindade G. F., Mendes P. M., Williams P. M., Aylott J. W., Shard A. G., Alexander M. R., Scurr D. J., Nature Communications11(5832), 2020

Mechanisms of Lipid Preservation in Archaeological Clay Ceramics Revealed by Mass Spectrometry Imaging, Hammann S., Scurr D. J., Alexander M. R., Cramp L. J. E., Proceedings of the National Academy of Sciences of the United States of America (PNAS)117(26), 14688-14693, 2020

Immune Modulation by Design: Using Topography to Control Human Monocyte Attachment and Macrophage Differentiation, Vassey M. J., Figueredo G. P., Scurr D. J., Vasilevich A. S., Vermeulen S., Carlier A., Luckett J., Beijer N. R. M., Williams P., Winkler D. A., de Boer J., Ghaemmaghami A. M., Alexander M. R., Advanced Science7(11), 2020

Cryo-OrbiSIMS for 3D Molecular Imaging of a Bacterial Biofilm in its Native State, Zhang J., Brown J., Scurr D. J., Bullen A., MacLellan-Gibson K., Williams P., Alexander M. R., Hardie K. R., Gilmore I. S., Rakowska P. D., Analytical Chemistry92(13), 9008-9015, 2020

Spatially Resolved Molecular Compositions of Insoluble Multilayer Deposits Responsible for Increased Pollution from Internal Combustion Engines, Edney M. K., Lamb J. S., Spanu M., Smith E. F., Steer E., Wilmot E., Reid J., Barker J., Alexander M. R., Snape C. E., Scurr D. J., ACS Applied Materials & Interfaces12(45), 51026-51035, 2020



Nanoscale and Microscale Research Centre

Cripps South building
University of Nottingham
University Park
Nottingham, NG7 2RD

telephone: +44 (0) 115 748 6340
email: nmrcenquiries@nottingham.ac.uk