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


Spatially resolved molecular analysis of host response to medical device implantation using the 3D OrbiSIMS highlights a critical role for lipids, 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.

Targeted intradermal delivery of alpha-arbutin-loaded dissolving polymeric microneedles visualized by three-dimensional Orbitrap secondary ion mass spectrometry (3D OrbiSIMS), Li Z., Marlow M., Scurr D., Zhu Z., European Journal of Pharmaceutics and Biopharmaceutics196, 114181, 2024.

Toward Comprehensive Analysis of the 3D Chemistry of Pseudomonas aeruginosa Biofilms, 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.

Investigating ApoE4-mediated metabolic alteration of H4 neuroglioma cells of Alzheimer's disease, Lu L., Kotowska A., Kern S., Fang M., Rudd T. R., Alexander M., Scurr D., Zhu Z., Alzheimer's & Dementia19, S24, e082458, 2023.

Sustained Release of Dexamethasone from 3D-Printed Scaffolds Modulates Macrophage Activation and Enhances Osteogenic Differentiation, Majrashi M., Kotowska A., Scurr D., Hicks J. M., Ghaemmaghami A., Yang J., ACS Appl. Mater. Interfaces15, 49, 56623-56638, 2023.

Cannabidiol and fluorinated derivative anti-cancer properties against glioblastoma multiforme cell lines, and synergy with imidazotetrazine agents, Brookes A., Kindon N., Scurr D. J., Alexander M. R., Gershkovich P., Bradshaw T. D., BJC Reports, 2023.

Comparison of Tiling Artifact Removal Methods in Secondary Ion Mass Spectrometry Images, 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.

Label-free Chemical Characterization of Polarized Immune Cells in vitro and Host Response to Implanted Bio-instructive Polymers in vivo using 3D OrbiSIMS, Suvannapruk W., Edney M. K., Fisher L.E., Luckett J. C., Kim D.-H., Scurr D. J., Ghaemmaghami A. M., Alexander M. R., Bio-protocol13, 15, 2023.

Identification of Pseudomonas aeruginosa exopolysaccharide Psl in biofilms using 3D OrbiSIMS, Khateb H., Hook A. L., Kern S., Watts J. A., Singh S., Jackson D., Marinez-Pomares L., Williams P., Alexander M. R., Biointerphases18(3), 031007, 2023.

Dissociative Host-Dopant Bonding Facilities Molecular Doping in Halide Perovskites, 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.

Untargeted Metabolomic Characterization of Glioblastoma Intra-Tumor Heterogeneity Using OrbiSIMS, 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.

Design, Synthesis, and Biological Evaluation of Novel Hybrids Containing Dihydrochalcone as Tyrosinase Inhibitors to Treat Skin Hyperpigmentation, 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.

Development of nanoparticle loaded microneedles for drug delivery to a brain tumour resection site, 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 Biopharmaceutics182, 53-61, 2023.

Identifying new biomarkers of aggressive Group 3 and SHH medulloblastoma using 3D hydrogel models, single cell RNA sequencing and 3D OrbiSIMS imaging, 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 Communications11, 6, 2023.

Single-Cell Metabolic Profiling of Macrophages Using 3D OrbiSIMS: Correlations with Phenotype, Suvannapruk W., Edney M. K., Kim D.-H., Scurr D. J., Ghaemmaghami A. M., Alexander M. R., Analytical Chemistry94, 26, 9389-9398, 2022.

Elucidating the molecular landscape of the stratum corneum, Starr N. J., Khan M. H., Edney M. K., Scurr D. J., PNAS119 (12) e2114380119, 2022. 

Molecular Formula Prediction for Chemical Filtering of 3D OrbiSIMS Datasets, 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 Chemistry94, 11, 4703-4711, 2022.

Efficacy of antimicrobial and anti-viral coated air filters to prevent the spread of airborne pathogens, 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 Reports12, 2803, 2022.

Developing Novel Biointerfaces: Using Chlorhexidine Surface Attachment as a Method for Creating Anti-Fungal Surfaces, 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.

Detection of Label-Free Drugs within Brain Tissue using Orbitrap Secondary Ion Mass Spectrometry as a Complement to Neuro-Oncological Drug Delivery, McCrorie P., Rowlinson J., Scurr D. J., Marlow M., Rahman R., Pharmaceutics14(3), 571, 2022. 

A Multifaceted Ferrocene Interlayer for Highly Stable and Efficient Lithium Doped Spiro-OMeTAD-based Perovskite Solar Cells, 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 Materials12, 26, 2200666, 2022.

The Effect of Temperature on the Molecular Compositions of External and Internal Gasoline Direct Injection Deposits, Edney M. K., Smith E. F., Wilmot E., Reid J., Barker J., Alexander M. R., Snape C. E., Scurr D. J., SAE International, 2021.

A New Particle Mounting Method for Surface Analysis, Dundas A. A., Kern S., Cuzzucoli Crucitti V., Scurr D. J., Wildman R., Irvine D. J., Alexander M. R., Surface and Interface Analysis54, 4, 374-380, 2021.

Residual Polymer Stabiliser causes Anisotropic Electrical Conductivity during Inkjet Printing of Metal Nanoparticles, 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 Materials2, 47, 2021. 

Sequential Orbitrap Secondary Ion Mass Spectrometry and Liquid Extraction Surface Analysis-Tandem Mass Spectrometry-Based Metabolomics for Prediction of Brain Tumor Relapse from Sample-Limited Primary Tissue Archives, 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.

Direct Immobilization of Engineered Nanobodies on Gold Sensors, 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 & Interfaces13(15), 17353-17360, 2021.

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

Internal Diesel Injector Deposit Chemical Speciation and Quantification Using 3D OrbiSIMS and XPS Depth Profiling, 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 Mobility3, 349-364, 2020.

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
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email: nmrcenquiries@nottingham.ac.uk