Secondary Ion Mass Spectrometry
3D OrbiSIMS
The 3D OrbiSIMS facility was set up with a £2.5m EPSRC Strategic Equipment Award ‘3D OrbiSIMS: Label free chemical imaging of materials, cells and tissues’ 2017-2023 (). Its capability has grown from this initial investment, now including a second ToF SIMS instrument and employing 3 members of staff to manage the facility and its userbase, undertake data acquisition, researcher supervision, training and respond to external enquiries. Morgan Alexander and David Scurr are Director and co-Director of the 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
Publications
Healthcare
, Kim K.-S., Wong K. F. C., Jo A., Martínez-Jarquín S., Jha R., Kotowska A. M., Kim H. J., Kim D.-H., Cho J.-Y., Analytica Chimica Acta, 1381, 344803, 2026.
, Kotowska A. M., Hiramatsu F., Alexander M. R., Scurr D. J., Lightfoot J. W., Chauhan V. M., Journal of the American Chemical Society, 147, 8, 6439-6449, 2025.
, Crucitti, V. C., Hajiali H., Dundas A. A., Jayawarna V., Tomolillo D., Francolini I., Vuotto C., Salmeron-Sanchez M., Dalby M. J., Alexander M. R., Wildman R. D., Rose F. R. A. J., Irvine D. J., Journals of Materials Chemistry B, 13, 15, 4657-4670, 2025.
, Kotowska A. M., Fay M., Watts, J. A., Gilmore, I. S., Scurr D. J., Howe A., Capka V., Perez C. E., Doud D., Patel S., Communications Chemistry, 8, 1, 160, 2025.
, Romero M., Luckett J., Dubern J.-F., Figueredo G. P., Ison E., Carabelli A. M., Scurr D. J., Hook A. L., Kammerling L., da Silva A. C., Nature Communications, 16, 1, 5295, 2025.
, Lu L., Kotowska A. M., Kern S., Fang M., Rudd T. R., Alexander M. R., Scurr D. J., Zhu Z., Anal. Chem., 96, 11760–11770, 2024.
, Suvannapruk W., Fisher L. E., Luckett J. C., Edney M. K., Kotowska A. M., Kim D.-H., Scurr D. J., Ghaemmaghami A. M., Alexander M. R., Advanced Science, 2306000, 2024.
, Li Z., Marlow M., Scurr D., Zhu Z., European Journal of Pharmaceutics and Biopharmaceutics, 196, 114181, 2024.
, Kotowska A. M., Zhang J., Carabelli A., Watts J., Aylott J. W., Gilmore I. S., Williams P., Scurr D. J., Alexander M. R., Anal. Chem. 95, 49, 18287-18294, 2023.
, Lu L., Kotowska A., Kern S., Fang M., Rudd T. R., Alexander M., Scurr D., Zhu Z., Alzheimer's & Dementia, 19, S24, e082458, 2023.
, Majrashi M., Kotowska A., Scurr D., Hicks J. M., Ghaemmaghami A., Yang J., ACS Appl. Mater. Interfaces, 15, 49, 56623-56638, 2023.
, Brookes A., Kindon N., Scurr D. J., Alexander M. R., Gershkovich P., Bradshaw T. D., BJC Reports, 2023.
, Suvannapruk W., Edney M. K., Fisher L.E., Luckett J. C., Kim D.-H., Scurr D. J., Ghaemmaghami A. M., Alexander M. R., Bio-protocol, 13, 15, 2023.
, Khateb H., Hook A. L., Kern S., Watts J. A., Singh S., Jackson D., Marinez-Pomares L., Williams P., Alexander M. R., Biointerphases, 18(3), 031007, 2023.
, Suvannapruk W., Edney M. K., Fisher L.E., Luckett J. C., Kim D.-H., Scurr D. J., Ghaemmaghami A. M., Alexander M. R., Bio-protocol, 13, 15, 2023.
, Khateb H., Hook A. L., Kern S., Watts J. A., Singh S., Jackson D., Marinez-Pomares L., Williams P., Alexander M. R., Biointerphases, 18(3), 031007, 2023.
, He W., Edney M. K., Paine S. M. L., Griffiths R. L., Scurr D. J., Rahman R., Kim D.-H., Anal.Chem. 95, 14, 5994-6001, 2023.
, Xue S., Li Z., Ze X., Wu X., He C., Shuai W., Marlow M., Chen J., Scurr D., Zhu Z., Xu J., Xu S., J. Med. Chem., 66, 7, 5099-5117, 2023.
, Muresan P., McCrorie P., Smith F., Vasey C., Taresco V., Scurr D. J., Kern S., Smith S., Gershkovich P., Rahman R., Marlow M., European Journal of Pharmaceutics and Biopharmaceutics, 182, 53-61, 2023.
, Linke F., Johnson J. E. C., Kern S., Bennett C. D., Lourdusamy A., Lea D., Clifford S. C., Merry C. L. R., Stolnik S., Alexander M. R., Peet A. C., Scurr D. J., Griffiths R. L., Grabowska A. M., Kerr I. D., Coyle B., Acta Neuropathologica Communications, 11, 6, 2023.
, Suvannapruk W., Edney M. K., Kim D.-H., Scurr D. J., Ghaemmaghami A. M., Alexander M. R., Analytical Chemistry, 94, 26, 9389-9398, 2022.
, Starr N. J., Khan M. H., Edney M. K., Scurr D. J., PNAS, 119 (12) e2114380119, 2022.
, Edney M. K., Kotowska A. M., Spanu M., Trindade G. F., Wilmot E., Reid J., Barker J., Aylott J. W., Shard A. G., Alexander M. R., Snape C. E., Scurr D. J., Analytical Chemistry, 94, 11, 4703-4711, 2022.
, Watson R., Oldfield M., Bryant J. A., Riordan L., Hill H. J., Watts J. A., Alexander M. R., Cox M. J., Stamataki Z., Scurr D. J., de Cogan F., Scientific Reports, 12, 2803, 2022.
, Bryant J. A., Riordan L., Watson R., Nikoi N. D., Trzaska W., Slope L., Tibbatts C., Alexander M. R., Scurr D. J., May R. C., de Cogan F., Global Challenges, 2100138, 2022.
, McCrorie P., Rowlinson J., Scurr D. J., Marlow M., Rahman R., Pharmaceutics, 14(3), 571, 2022.
, Meurs J., Scurr D. J., Lourdusamy A., Storer L. C. D., Grundy R. G., Alexander M. R., Rahman R., Kim D.-H., Analytical Chemistry, 2021.
, 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 Advances, 7(9), eabb7921, 2021.
, 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 Communications, 11(5832), 2020
, 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 Science, 7(11), 2020
, 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 Chemistry, 92(13), 9008-9015, 2020
Analytical Method Development
, Milne L. K., D/O Ajayakumar A. A., Holyland I. L., Kotowska A. M., Hogwood J., Gray E., Mulloy B., Merry C. L. R., Hook A. L., Carbohydrate Polymers, 371, 124415, 2026.
, Meurs J., Nasir A., Figueredo G. P., Burroughs L., Abdelrazig S. A., Denning C., Winkler D. A., Barrett D. A., Kim D.-H., Alexander M. R., Analytical Chemistry, 97, 24, 12776-12785, 2025.
, Kandanaarachchi S., Gardner W., Alexander D. L. J., Muir B. W., Chouinard P. A., Crewther S. G., Scurr D. J., Halliday M., Pigram P. J., Anal. Chem., 95, 47, 17384-17391, 2023.
, Edney M. K., Kotowska A. M., Spanu M., Trindade G. F., Wilmot E., Reid J., Barker J., Aylott J. W., Shard A. G., Alexander M. R., Snape C. E., Scurr D. J., Analytical Chemistry, 94, 11, 4703-4711, 2022.
, Dundas A. A., Kern S., Cuzzucoli Crucitti V., Scurr D. J., Wildman R., Irvine D. J., Alexander M. R., Surface and Interface Analysis, 54, 4, 374-380, 2021.
, Simões B., Guedens W. J., Keene C., Kubiak-Ossowska K., Mulheran P., Kotowska A. M., Scurr D. J., Alexander M. R., Broisat A., Johnson S., Muyldermans S., Devoogdt N., Adriaensens P, Mendes P. M., ACS Applied Materials & Interfaces, 13(15), 17353-17360, 2021.
, Melissa K Passarelli, Alexander Pirkl, Rudolf Moellers, Dmitry Grinfeld, Felix Kollmer, Rasmus Havelund, Carla F Newman, Peter S Marshall, Henrik Arlinghaus, Morgan R Alexander, Andy West, Stevan Horning, Ewald Niehuis, Alexander Makarov, Colin T Dollery & Ian S Gilmore Nature Methods 14, 1175–1183, 2017.
Anthropology
, 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.
Energy and Engineering
, Nyman P., Björklund P., Yaghini N., Lu L., Hopper E. R., Hunt G., J. Tribol., 147(5), 051111, 2025.
, Lanzetta L., Gregori L., Huerta Hernandez L., Sharma A., Kern S., Kotowska A. M., Emwas A.-H., Gutiérrez-Arzaluz L., Scurr D. J., Piggott M., Meggiolaro D., Haque Md A., De Angelis F., Baran D., ACS Energy Lett., 8, 7, 2858-2867, 2023.
, Webb T., Liu X., Westbrook R. J. E., Kern S., Sajjad M. T., Jenatsch S., Imalka Jayawardena K. D. G., Hashini K. Perera W., Marko I. P., Sathasivam S., Li B., Yavari M., Scurr D. J., Alexander M. R., Macdonald T. J., Haque S. A., Sweeney S. J., Zhang W., Advanced Energy Materials, 12, 26, 2200666, 2022.
, Lamb J. S., Barker J., Wilmot E., Scurr D. J., Snape C. E., Smith E. F., Alexander M. R., Reid J.,SAE International Journal of Advances and Current Practices in Mobility, 3, 349-364, 2020.
, Edney M. K., Kotowska A. M., Spanu M., Trindade G. F., Wilmot E., Reid J., Barker J., Aylott J. W., Shard A. G., Alexander M. R., Snape C. E., Scurr D. J., Analytical Chemistry, 94, 11, 4703-4711, 2022.
, Edney M. K., Smith E. F., Wilmot E., Reid J., Barker J., Alexander M. R., Snape C. E., Scurr D. J., SAE International, 2021.
, Trindade G. F., Wang F., Im J., He Y., Balogh A., Scurr D., Gilmore I., Tiddia M., Saleh E., Pervan D., Turyanska L., Tuck C. J., Wildman R., Hague R., Roberts C. J., Communications Materials, 2, 47, 2021.
, Edney M. K., Smith E. F., Wilmot E., Reid J., Barker J., Alexander M. R., Snape C. E., Scurr D. J., SAE International, 2021.
, 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 & Interfaces, 12(45), 51026-51035, 2020.