Research Guides

Department of Chemistry University of Oxford

Professor James McCullagh

Director of the Mass Spectromtry Research Facility and group leader

McCullagh is Associate Professor of Analytical Chemistry and Director of Mass Spectrometry Research Facility which is based in the Chemistry Research Laboratory and houses > £6 million in equipment, providing more than 20 mass spectometer systems and has a dedicated team of permanent research staff to deliver mass spectrometry research services. He is also a Principal Investigator and a group leader focussing on the development of mass spectrometry and separation science methods and applications at the interface between chemistry and other disciplines including biology, physiology and medicine. His research group focusses on developing new analytical approaches to understand small molecule chemistry in complex biological systems.

McCullagh group: Understanding the chemistry of small molecules in complex biological systems.

Our aim is to better understand how small biological molecules function in the context of complex natural systems and what happens when these systems are purturbed.  For example we focus on developing highly efficeint analytical approaches for comprehensive analysis of metabolites in cells, tissue and bio-fluids and applying these to understand how fundamental metabolic processes are altered in disease. We apply a multi-technique approach, including metabolomics, live cell imaging and real-time analysis of metabolism, to focus on comprehensive molecular phenotyping and capturing small molecule interactions at a systems-wide level.


We work highly collaboratively on a wide range of diseases and conditions including diabetes, obesity, heart disease, chronic fatigue syndrome, cancer and inborn errors of metabolism. We are also particularly interested in identifying therapeutic targets and developing a better understanding of changes in metabolism to help in early detection of disease, identifying aetiological trajectories and finding molecular level biomarkers for monitoring the effectiveness of new treatment approaches. If you are interested in a Part II or D.Phil. project or postdoctoral position in the group please contact James McCullagh (

Winter, H.; Kaisaki, P.J.; Harvey, J.; Giacopuzzi, E.; Ferla, M.P.; Pentony, M.M.; Knight, S.J.; Sharma, R.A.; Taylor, J.C.; McCullagh, J.S. Identification of Circulating Genomic and Metabolic Biomarkers in Intrahepatic Cholangiocarcinoma. Cancers 2019, 11, 1895.

Favara, D.M.; Zois, C.E.; Haider, S.; Pires, E.; Sheldon, H.; McCullagh, J.; Banham, A.H.; Harris, A.L. ADGRL4/ELTD1 Silencing in Endothelial Cells Induces ACLY and SLC25A1 and Alters the Cellular Metabolic Profile. Metabolites 2019, 9, 287.

Smith, E.N.; McCullagh, J.S.O.; Ratcliffe, R.G.; Kruger, N.J. Limitations of Deuterium-Labelled Substrates for Quantifying NADPH Metabolism in Heterotrophic Arabidopsis Cell Cultures. Metabolites 2019, 9, 205.

McCullagh et al. Amino acid analysis: Methods and Protocols. 2019, 2nd edition, Springer. (Part of the Methods in Molecular Biology book series (MIMB, volume 2030)

Bailey JD, Diotallevi M, Nicol T, McNeill E, Shaw A, Chuaiphichai S, Hale A, Starr A, Nandi M, Stylianou E, McShane H, Davis S, Fischer R, Kessler BM, McCullagh J, Channon KM, Crabtree MJ. Nitric Oxide Modulates Metabolic Remodeling in Inflammatory Macrophages through TCA Cycle Regulation and Itaconate Accumulation. Cell Reports. 2019 Jul 2;28(1):218-230.e7. doi: 10.1016/j.celrep.2019.06.018.

Cyranka M, Veprik A, McKay EJ, van Loon N, Thijsse A, Cotter L, Hare N, Saibudeen A, Lingam S, Pires E, Larraufie P, Reimann F, Gribble F, Stewart M, Bentley E, Lear P, McCullagh J, Cantley J, Cox RD, de Wet H.Abcc5 Knockout Mice Have Lower Fat Mass and Increased Levels of Circulating GLP-1. Obesity. 2019; 27(8):1292-1304. doi: 10.1002/oby.22521.

James McCullagh and Neil Oldham. Mass Spectrometry.  June 2019, Oxford University Press.

Isabelle Alldritt, Beatrice Whitham‐Agut, Miguel Sipin, Jacob Studholme, Angela Trentacoste, Jennifer A. Tripp, Maria Grazia Cappai, Peter Ditchfield, Thibaut Devièse, Robert E.M. Hedges, and James S.O. McCullagh* Metabolomics reveals diet‐derived plant polyphenols accumulate in physiological bone. Scientific Reports. 2019, 29;9(1):8047. doi: 10.1038/s41598-019-44390-1.

Shen X., Voets NL., Larkin SJ., de Pennington N., Plaha P., Stacey R., McCullagh JSO., Schofield CJ., Clare S., Jezzard P., Cadoux-Hudson T., Ansorge O., Emir UE. A Non-invasive Comparison Study between Human Gliomas with IDH1 and IDH2 Mutations by MR Spectroscopy. Metabolites 2019, 9(2), 35

Julie Schulthess, Sumeet Pandey, Melania Capitani, Kevin C. Rue-Albrecht, Isabelle Arnold, Fanny Franchini, Agnieszka Chomka, Nicholas E.Ilott, Daniel G.W. Johnston, Elisabete Pires, James McCullagh, Stephen N.Sansom, Carolina V.Arancibia-Cárcamo, Holm H.Uhlig and Fiona Powrie. The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages. Immunity, 2019, 50(2); 432-445.

Saba Muazzam, Joe Harvey, Thibaut Deviese, Muhammad Farman and James McCullagh. Targeted and Untargeted Metabolite Profiling of the Ethnobotanical Martynia annua L. Identifies Bioactive Compounds with Medicinal Properties. Planta Medica International, 2018.

Alvaro San Millan, Macarena Toll-Riera, Qin Qi, Alex Betts, Richard J Hopkinson, James McCullagh, and R Craig MacLean. Integrative analysis of fitness and metabolic effects of plasmids in Pseudomonas aeruginosa PAO1. Multidisciplinary Journal of Microbial Ecology  2018  (in press).

Mattéa J. Finelli, Teresa Paramo, Elisabete Pires, Brent J. Ryan, Richard Wade-Martins, James McCullagh, Philip C. Biggin, Peter L. Oliver. Oxidation resistance 1 (Oxr1) modulates glycolytic pathways in the cerebellum via an interaction with glucose-6-phosphate isomerase. Molecular Neurobiology  2018 (in press).

Bowen AM, Johnson EOD, Mercuri F, Hoskins NJ, Qiao R, McCullagh JSO, Lovett JE, Bell SG, Zhou W, Timmel CR, Wong LL, Harmer JR. A Structural Model of a P450-Ferredoxin Complex from Orientation-Selective Double Electron-Electron Resonance Spectroscopy. J Am Chem Soc. 2018, 140(7): 2514-2527. doi: 10.1021/jacs.7b11056. Epub 2018 Feb 6.

Katherine E. French, Joe Harvey and James S. O. McCullagh. Targeted and Untargeted Metabolic Profiling of Wild Grassland Plants identifies Antibiotic and Anthelmintic Compounds Targeting Pathogen Physiology, Metabolism and Reproduction. Scientific Reports (2018) 8:1695. DOI:10.1038/s41598-018-20091-z.

Adam Berrington, Natalie L. Voets,  Sarah J. Larkin, Nick de Pennington, James Mccullagh, Richard Stacey, Christopher J. Schofield, Peter Jezzard, Stuart Clare, Tom Cadoux‐Hudson, Puneet Plaha, Olaf Ansorge and Uzay E. Emir. A comparison of 2‐hydroxyglutarate detection at 3 and 7 T with long‐TE semi‐LASER. NMR in Biomedicine. 2018; p 3886.

Thibaut Deviese, Daniel Comeskey, James McCullagh, Christopher Bronk Ramsey and Thomas Higham. New protocol for compound‐specific radiocarbon analysis of archaeological bones. Rapid Commun Mass Spectrom. 2018;32:373–379.

Honarmand Ebrahimi K, Carr SB, McCullagh J, Wickens J, Rees NH, Cantley J, Armstrong FA. The radical-SAM enzyme Viperin catalyzes reductive addition of a 5'-deoxyadenosyl radical to UDP-glucose in vitro. FEBS Letters. 2017 591(16):2394-2405.

Kulkarni A, Mateus M, Thinnes CC, McCullagh JSO, Schofield CJ, Taylor GP and Bangham C. Glucose metabolism and oxygen availability goven reactivation from latency of the human retrovirus HTLV-1. Cell Chemical Biology. 2017 Nov 16; 24(11): 1377–1387.

Riffelmacher , T. Clarke A, Richter FA, Stranks A, Pandey S, Danielli S, Hublitz P, Yu Z, Johnson E, Schwerd T, McCullagh JSO, Uhlig H, Jacobson SE and Simon K. Autophagy-dependent generation of free fatty acids is critical for normal neutrophil differentiation. IMMUNITY, 2017, 47, 466–480.

Jade Bailey, Andrew Shaw, Roman Fischer, Brent J. Ryan, Benedikt M. Kessler, James McCullagh, Richard Wade-Martins, Keith M. Channon, Mark J. Crabtree. A novel role for endothelial tetrahydrobiopterin in mitochondrial redox balance. Free Radical biology and Medicine. 2017, 2014-215.

Hafiza Noreen, Muhammad Farman, James S.O. McCullagh. Bioassay-guided isolation of cytotoxic flavonoids from aerial parts of Coronopus didymus. Journal of Ethnopharmacology 2016;194, 971–9.

Maria Isabel González Sánchez, James McCullagh, Richard H. Guy, Richard G. Compton. Reverse Iontophoretic Extraction of Metabolites from Living Plants and their Identification by Ion-chromatography Coupled to High Resolution Mass Spectrometry. Phytochemical Analysis 2016.

Uche FIDrijfhout FPMcCullagh JRichardson ALi WW. Cytotoxicity Effects and Apoptosis Induction by Bisbenzylisoquinoline Alkaloids from Triclisia subcordata. Phytother Res. 2016; 30(9):1533-9.

Chiara Bardella, Osama Al-Dalahmah, Daniel Krell, Pijus Brazauskas, Khalid Al-Qahtani, Marketa Tomkova, Julie Adam, Sébastien Serres, Helen Lockstone, Luke Freeman-Mills, Inga Pfeffer, Nicola Sibson, Robert Goldin, Benjamin Schuster-Böeckler, Patrick J. Pollard, Tomoyoshi Soga, James S. McCullagh, Christopher J. Schofield, Paul Mulholland, Olaf Ansorge, Skirmantas Kriaucionis, Peter J. Ratcliffe, Francis G. Szele, Ian Tomlinson. Expression of Idh1R132H in the Murine Subventricular Zone Stem Cell Niche Recapitulates Features of Early Gliomagenesis. Cell,  2016, Volume 30, Issue 4, p578–594.

Nicky Huskens, Peadar O'Donohoe, James R. Wickens, James S O McCullagh, Keith J. Buckler, Jaideep J. Pandit. A method for continuous and stable perfusion of tissue and single cell preparations with accurate concentrations of volatile anaesthetics. Journal of Neuroscience Methods (2016) Volume: 258, pp: 87-93.

Adam Berrington, Natalie L. Voets, Puneet Plaha, Sarah J. Larkin, James Mccullagh, Richard Stacey, Muhammed Yildirim, Christopher J. Schofield, Peter Jezzard, Tom Cadoux-Hudson, Olaf Ansorge, and Uzay E. Emir. Improved Localization for 2-Hydroxyglutarate Detection at 3 T Using Long-TE Semi-LASER. Tomography, 2016, Vol2; (2), p94.

Emir U, Larkin S, de Pennington N, Voets N, Plaha P, Stacey R, Al-Qahtani K,  Mccullagh J,  Schofield C, Clare S,  Jezzard P, Cadoux-Hudson T & Ansorge O. Non-invasive quantification of 2-hydroxyglutarate in human gliomas with IDH1 and IDH2 mutations. Cancer Research 2016, 1;76)1):43-9.

Anthony H. Lynch, N. Kruger, Robert E.M. Hedges and James S.O. McCullagh* Variability in the 13C/12C isotope ratios of individual amino acids in plant proteins. Phytochemistry 2016, Vol 125; pp27-34.

Tarhonskaya H, Hardy AP, Howe EA, Loik ND, Kramer HB, McCullagh JS, Schofield CJ, Flashman E. Kinetic Investigations of the Role of Factor Inhibiting Hypoxia-inducible Factor (FIH) as an Oxygen Sensor. The Journal of biological chemistry 290 (32):19726-19742 Aug 2015.

Al-Qahtani K,  Jabeen B, Sekirnik R, Riaz N, D.W. Claridge T, J. Schofield C, and. McCullagh J* The Broad Spectrum 2-Oxoglutarate Oxygenase Inhibitor N-oxalylglycine is present in Rhubarb and Spinach Leaves. 2014. Phytochemistry, Sept 2015. 117:456-461.

Valli A, Rodriguez M, Moutsianas L, Fischer R,Fedele V, Huang H, Van Stiphout R, Jones D1, Mccarthy M, Vinaixa M, Igarashi K, Sato M, Soga T, Buffa F, Mccullagh J, Yanes O, Harris AL, and Kessler B. Hypoxia induces a HIF1α-dependent lipogenic phenotype in colorectal cancer cells. 2014. Oncotarget 2014;10;6(4):1920‐41.

Tarhonskaya H, Chowdhury R, Leung IK, Loik ND, McCullagh JS, Claridge TD, Schofield CJ, Flashman E. Investigating the contribution of the active site environment to the slow reaction of hypoxia-inducible factor prolyl hydroxylase domain 2 with oxygen. The Biochemical Journal. 2014; 463(3):363-372 Nov 2014.

Rachel Schiller, Dr. Giuseppe Scozzafava, Dr. Anthony Tumber, Dr. James R. Wickens, Jacob T. Bush, Dr. Ganesha Rai, Dr. Clarisse Lejeune, Dr. Hwanho Choi, Dr. Tzu-Lan Yeh, Mun Chiang Chan, Dr. Bryan T. Mott, Dr. James S. O. McCullagh, Dr. David J. Maloney, Prof. Christopher J. Schofield, Dr. Akane Kawamura. A Cell-Permeable Ester Derivative of the JmjC Histone Demethylase Inhibitor IOX1. ChemMedChem 2014, 9; 566, 566-571.

Gong L, McCullagh JSO*. Comparing ion-pairing reagents and sample dissolution solvents for ion-pairing reversed-phase liquid chromatography/electrospray ionization mass spectrometry analysis of oligonucleotides. Rapid Communications in Mass Spectrometry 2014, 28 (4):339-350.

Tianshu Feng, Atsushi Yamamoto, Sarah E Wilkins, Elizaveta Sokolova, Luke A Yates, Martin Münzel, Pooja Singh, Richard J Hopkinson, Roman Fischer, Matthew E Cockman, Jake Shelley, David C Trudgian, Johannes Schödel, James S O McCullagh, Wei Ge, Benedikt M Kessler, Robert J Gilbert, Ludmila Y Frolova, Elena Alkalaeva, Peter J Ratcliffe, Christopher J Schofield, Mathew L Coleman. Optimal Translational Termination Requires C4 Lysyl Hydroxylation of eRF1. Molecular cell. 2014, 20;53(4):645-54

Feng T, Yamamoto A, Wilkins SE, Sokolova E, Yates LA, Münzel M, Singh P, Hopkinson RJ, Fischer R, Cockman ME, et al. Optimal translational termination requires C4 lysyl hydroxylation of eRF1. Molecular cell 2014, 53(4):645-654.

Chooi KP, Galan SR, Raj R, McCullagh J, Mohammed S, Jones LH, Davis BG. Synthetic phosphorylation of p38α recapitulates protein kinase activity. Journal of the American Chemical Society, 2014, 136(5):1698-1701.

Tarhonskaya H, Rydzik AM, Leung IK, Loik ND, Chan MC, Kawamura A, McCullagh JS, Claridge TD, Flashman E, Schofield CJ. Non-enzymatic chemistry enables 2-hydroxyglutarate-mediated activation of 2-oxoglutarate oxygenases. Nature communications 2014, 5:3423.

Nalawade-Chavan S, McCullagh J, Hedges R. New hydroxyproline radiocarbon dates from Sungir, Russia, confirm early mid upper palaeolithic burials in Eurasia. PLoS One 2014; 9 (1):e76896

Nalawade-Chavan S, Hedges R, Ramsey CB, Higham T, McCullagh J, Bonsall C, Boroneanţ A. Compound-specific radiocarbon dating of essential and nonessential amino acids: Towards determination of dietary reservoir effects in humans. Radiocarbon, 2013, 55(2-3):709-719.

Anat Marom, James S O McCullagh, Thomas F G Higham, Robert E M Hedges. Hydroxyproline dating: Experiments on the 14C analysis of contaminated and low collagen bones. RADIOCARBON, Vol 55, Nr 2–3, 2013, p 698–708

Yang M, Hardy AP, Chowdhury R, Loik ND, Scotti JS, McCullagh JS, Claridge TD, McDonough MA, Ge W, Schofield CJ. Substrate Selectivity Analyses of Factor Inhibiting Hypoxia-Inducible Factor. Angew Chem Int Ed Engl. 2013.

Elena M Sanchez-Fernandez, Hanna Tarhonskaya, Khalid Al Qahtani, Richard J Hopkinson, James S.O. McCullagh, Christopher J Schofield, Emily Flashman. Investigations on the Oxygen Dependence of a 2-Oxoglutarate Histone Demethylase. Biochemical Journal. 2013; 449, 491-6.

Marom A, Higham TFG, Sinitsyn AA, REM HedgesMcCullagh JSO.* Single amino acid radiocarbon dating of Upper Palaeolithic modern humans. Proceedings of the National Academy of Sciences. 18th April 2012.

Mantri M, Webby CJ, Loik ND, Hamed RB, Nielsen ML, McDonough MA, McCullagh JSO, Boettger A, Schofield CJ, Wolf A. Self-hydroxylation of the splicing factor lysyl hydroxylase, JMJD6. MedChemComm 2012, 3(1):80-85.

Tripp JA and McCullagh JS. Preparative HPLC separation of underivatized amino acids for isotopic analysis. 828: 339-350. In Method in Molecular Biology Series 828: Amino acid analysis, eds Alterman MA and Hunziker P. Springer 2012.

Wei Ge, Alexander Wolf, Tianshu Feng, Chia-hua Ho, Rok Sekirnik, Adam Zayer, Nicolas Granatino, Matthew E. Cockman , Christoph Loenarz1 , Nikita D.Loik , Adam P. Hardy , Timothy D.W. Claridge, Mukram M. Mackeen, James S. Mccullagh, Yuliya Gordiyenko, Armin Thalhammer, Atsushi Yamamoto, Ming Yang, Yi Liu, Zhihong Zhang, Marion Schmidt-Zachmann, Benedikt M. Kessler, Peter J. Ratcliffe, Gail M. Preston, Mathew L. Coleman and Christopher J. Schofield. Oxygenase catalysed Ribosome Hydroxylation is conserved from Prokaryotes to Humans. Nature Chemical Biology. 2012; 8, 960-2.

Sanchez-Fernandez EM, Tarhonskaya H, Al-Qahtani K, Hopkinson J, McCullagh JSO, Candela-Lena JI, Schofield CJ, Flashman E. Kinetic investigations on the reaction of a 2-oxoglutarate dependent histone demethylase with oxygen. FEBS JOURNAL. 2012, 279:478-478.

Honch NV, McCullagh JS, Hedges REM. Variation of bone collagen amino acid δ13C values in archaeological humans and fauna with different dietary regimes: developing frameworks of dietary discrimination. Am. J. Phys. Anthropol. 2012; 148 (4): 495-511.

Jean-Philippe Godin & James S. O. McCullagh.*Current applications and challenges for liquid chromatography coupled to isotope ratio mass spectrometry (LC/IRMS). Rapid Communications in Mass Spectrometry. 2011, 25, 3019–3028.

Anthony H. Lynch, James S. O. McCullagh*, and Robert E. M. Hedges. Liquid chromatography/isotope ratio mass spectrometry measurement of δ13C of amino acids in plant proteins. Rapid Communications in Mass Spectrometry. 2011, 25, 2981–2988.

A.M. Pollard, P. Ditchfield, J.S.O. McCullagh, T.G. Allen, M. Gibson, C. Boston, S. Clough, N. Marquez-Grant, and R.A. Nicholson. ‘‘These Boots Were Made For Walking’’: The Isotopic Analysis of a C4 Roman Inhumation From Gravesend, Kent, UK. American Journal of Physical Anthropology. (2011): 146:446–456.

McCullagh J*, Godin JP, Schierbeek H, Preston T. Liquid Chromatography-Isotope Ratio Mass Spectrometry Review. Rapid communications in mass spectrometry, 2011, 25(20):2969-2970.

Lingzhi Gong and James S.O. McCullagh.* Analysis of oligonucleotides by hydrophilic interaction liquid chromatography coupled to negative ion electrospray ionization mass spectrometry. Journal of Chromatography A, 1218 (2011) 5480-5486.

Gaye-Siessegger, Focken, U. J., McCullagh J.S.O.* The effect of dietary amino acid abundance and isotopic composition on the growth rate, metabolism and tissue d13C of rainbow trout. British Journal of Nutrition (2011), doi:10.1017/S0007114510005696

McCullagh J.S.O.*, (2010) Mixed mode chromatography isotope ratio mass spectrometry. Rapid Communications in Mass Spectrometry. (2010) 24; 483-494.

Monica Mantri, Nikita D. Loik, Refaat B. Hamed, Timothy D. W. Claridge, James S. O. McCullagh, Christopher J. Schofield. The 2-Oxoglutarate Dependent Oxygenase JMJD6 Catalyses Oxidation of Lysine Residues to give 5S-Hydroxylysine Residues. ChemBioChem, (2011), 12, 531-534.

McCullagh J.S.O, Marom A and Hedges R.E.M. Radiocarbon dating of individual amino acids from archaeological bone collagen. Radiocarbon. vol 52, Nr 2-3, 2010, p 620-634.

Raghavan, M., McCullagh J.S.O and Hedges R.E.M. Amino acid δ13C analysis of hair keratin using liquid chromatography/isotope ratio mass spectrometry: Palaeodietary implications from intra-individual comparisons with bone collagen. Rapid Communications in Mass Spectrometry. (2010) 24; 541-548.

Schneider R, Jensen SA, Whitman P, McCullagh JSO, Redfield C and Handford PA. Biophysical Characterisation of Fibulin-5 Proteins Associated with Disease. J Mol Biol. 2010;401(4):605-17.

McCullagh J.S.O. Mass Spectrometry. Chapter 13 in ‘The organic Chemist’s Handbook’ (2nd edition).

James McCullagh, Julia Gaye-Siessegger and Ulfert Focken. Determination of underivatized amino acid d13C by liquid chromatography/isotope ratio mass spectrometry for nutritional studies: the effect of dietary non-essential amino acid profile on the isotopic signature of individual amino acids in fish. Rapid Commun. Mass Spectrom. 2008; 22: 1817–1822

McCullagh, J.S.O and Hedges REM. ‘The Spectrometry Handbook’. Invited contribution (Chapter 33: Mass Spectrometry in Archaeology).

McCullagh J.S.O. (2007) Isotopic Analysis at the Molecular Level: A Frontier in Palaeodietary Reconstruction. In Crossing Frontiers, OUP, Monograph, Oxford.

James S.O. McCullagh,* Dieter Juchelka and Robert E. M. Hedges. Analysis of amino acid 13C abundance from humanand faunal bone collagen using liquid chromatography/isotope ratio mass spectrometry. Rapid Commun. Mass Spectrom. 2006; 20: 2761–2768.

Tripp, J.A., McCullagh, J.S.O. and Hedges, R.E.M., Preparative separation of underivatized amino acids for compound-specific stable isotope analysis and radiocarbon dating of hydrolyzed bone collagen. Journal of Separation Science, (2006) 29(1), 41-48.

McCullagh, J.S.O., Tripp, J.A. and Hedges, R.E.M., Carbon isotope analysis of bulk keratin and single amino acids from British and North American hair. Rapid Communications in Mass Spectrometry, (2005) 19(22). 3227-3231.