Publications

Key publications from the lead investigators since 2009

Review articles

Dunn, WB Erban A, Weber RJM, Creek DJ, Brown M, Breitling R, Hankemeier T, Goodacre R, Neumann S, Kopka J and Viant MR. Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics. Metabolomics, 2013, 9, S44-66.

Dunn WB, Wilson ID, Nicholls AW and Broadhurst D. The importance of experimental design and QC samples in large-scale and MS-driven untargeted metabolomic studies of humans. Bioanalysis. 2012, 4, 2249-64.

Dunn WB, Broadhurst DI, Atherton HJ, Goodacre R and Griffin JL. Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy. Chem. Soc. Rev. 2011, 40, 387-413.

Technology and Method Development

Davidson RL, Weber RJ, Liu H, Sharma-Oates A, Viant MR. Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data. Gigascience, 2016, 5, 10.

Hao J, Liebeke M, Sommer U, Viant MR, Bundy JG, Ebbels TM. Statistical Correlations between NMR Spectroscopy and Direct Infusion FT-ICR Mass Spectrometry Aid Annotation of Unknowns in Metabolomics. Anal Chem. 2016, 88, 2583-9.

Mullard G, Allwood JW, Weber R,  Brown M, Begley P, Hollywood KA, Jones M, Unwin RD, Bishop PN, Cooper GJS. and Dunn, WB. . A new strategy for MS/MS data acquisition applying multiple data dependent experiments on Orbitrap mass spectrometers in non-targeted metabolomic applications. Metabolomics, 2015, 11, 1068-80.

Bradbury J. Genta-Jouve G., Allwood JW, Dunn WB, Goodacre R, Knowles JD, He S. and Viant MR. MUSCLE: Automated closed loop multi-objective evolutionary LC-MS/MS method optimisation for targeted analysis. Bioinformatics, 2015, 31, 975-7.

Zhou J, Weber RJM, Allwood JW, Mistrik R, Zhu Z, Ji Z, Chen S, Dunn WB, He S. and Viant MR. HAMMER: Automated operation of Mass Frontier to construct in-silico mass spectral fragmentation libraries. Bioinformatics, 2014, 30, 581-3

Kirwan JA, Broadhurst DI, Davidson RL and Viant MR. Characterising and correcting batch variation in an automated direct infusion mass spectrometry (DIMS) metabolomics workflow. Anal. Bioanal. Chem. 2013, 405, 5147-57.

Kotze HL, Armitage EG, Sharkey KJ, Allwood JW, Dunn WB, Williams KJ and Goodacre R. A novel untargeted metabolomics correlation-based network analysis incorporating human metabolic reconstructions. BMC Systems Biology, 2013, 7, 107.

Weber RJM, Li E, Bruty J, He S and Viant MR. MaConDa: a publicly accessible Mass spectrometry Contaminants Database. Bioinformatics, 2012, 28, 2856-57.

Vaughan AA, Dunn WB, Allwood JW, Wedge DC, Blackhall FH, Whetton AD, Dive C and Goodacre R. Liquid chromatography-mass spectrometry calibration transfer and metabolomics data fusion. Anal. Chem. 2012, 84, 9848-57.

Ludwig C, Easton JM, Lodi A, Tiziani S, Manzoor S, Southam AD, Byrne JJ, Bishop LM, He S, Arvanitis TN, Günther UL and Viant MR. Birmingham Metabolite Library: A publicly accessible database of 1-D 1H and 2-D 1H J-resolved NMR spectra of authentic metabolite standards (BML-NMR). Metabolomics, 2012, 8, 8-18.

Wedge DC, Allwood JW, Dunn WB, Vaughan AA, Simpson K, Brown M, Priest L, Blackhall FH, Whetton AD, Dive C and Goodacre, R. Is serum or plasma more appropriate for intersubject comparisons in metabolomic studies? An assessment in patients with small-cell lung cancer. Anal. Chem. 2011, 83, 6689-97.

Dunn WB, Broadhurst D, Begley P, Zelena E, Francis-McIntyre S, Anderson N, Brown M, Knowles JD, Halsall A, Haselden JN, Nicholls AW, Wilson ID, Kell DB, Goodacre R. and the Human Serum Metabolome (HUSERMET) Consortium. Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nature Protocols, 2011, 6, 1060-83.

Brown M, Wedge DC, Goodacre R, Kell DB, Baker PN, Kenny LC, Mamas MA, Neyses L and Dunn WB Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets. Bioinformatics 2011, 27, 1108-12.

Weber RJM and Viant MR. MI-Pack: Increased confidence of metabolite identification in mass spectra by integrating accurate masses and metabolic pathways. Chemometrics and Intelligent Laboratory Systems, 2010, 104, 75-82.

Begley P, Francis-McIntyre S, Dunn WB, Broadhurst DI, Halsall A, Tseng A, Knowles J,, HUSERMET Consortium, Goodacre R and Kell DB. Development and Performance of a Gas Chromatography-Time-of-Flight Mass Spectrometry Analysis for Large-Scale Nontargeted Metabolomic Studies of Human Serum. Analytical Chemistry, 2009, 81, 7038-46.

Zelena E, Dunn WB, Broadhurst D, Francis-McIntyre S, Carroll KM, Begley P, O'Hagan S, Knowles JD, Halsall A, HUSERMET Consortium, Wilson ID and Kell DB. Development of a Robust and Repeatable UPLC-MS Method for the Long-Term Metabolomic Study of Human Serum. Analytical Chemistry, 2009, 81, 1357-64.

Brown M, Dunn WB, Dobson P, Patel Y, Winder CL, Francis-McIntyre S, Begley P, Carroll K, Broadhurst D, Tseng A, Swainston N, Spasic I, Goodacre R and Kell DB. Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics. Analyst, 2009, 134, 1322-32.

Research applications

Zhang J, Abou-Elwafa Abdallah M, Williams TD, Harrad S, Chipman JK and Viant MR. Gene expression and metabolic responses of HepG2/C3A cells exposed to flame retardants and dust extracts at concentrations relevant to indoor environmental exposures. Chemosphere, 2016, 144, 1996-2003.

Southam AD, Khanim FL, Hayden RE, Constantinou JK, Koczula KM, Michell RH, Viant MR, Drayson MT and Bunce CM. Drug Redeployment to Kill Leukemia and Lymphoma Cells by Disrupting SCD1-Mediated Synthesis of Monounsaturated Fatty Acids. Cancer Res., 2015, 75, 2530-40.

Dunn WB, Lin W, Broadhurst D, Begley P, Brown M, Zelena E, Vaughan AA, Halsall A, Harding N, Knowles JD, Francis-McIntyre S, Tseng A, Ellis DI, O’Hagan S, Aarons G, Benjamin B, Chew-Graham S, Moseley C, Potter P, Winder CL, Potts C, Thornton P, McWhirter C, Zubair M, Pan M, Burns A, Cruickshank JK, Jayson GC, Purandare N, Wu FCW, Finn JD, Haselden JN, Nicholls AW, Wilson ID, Goodacre R. and Kell DB. Molecular phenotyping of a UK population: defining the human serum metabolome. Metabolomics, 2015, 11, 9-26.

Drury NE, Howell NJ, Calvert MJ, Weber RJ, Senanayake EL, Lewis ME, Hyde JA, Green DH, Mascaro JG, Wilson IC, Graham TR, Rooney SJ, Viant MR, Freemantle N, Frenneaux MP and Pagano D. The effect of perhexiline on myocardial protection during coronary artery surgery: a two-centre, randomized, double-blind, placebo-controlled trial. Eur J Cardiothorac Surg., 2015, 47, 464-72.

Drogan D, Dunn WB,  Lin W, Buijsse B, Schulze MB, Langenberg C,  Brown M, Floegel A, Dietrich S, Rolandsson O, Wedge DC, Goodacre R, Forouhi NG, Sharp SJ, Spranger J, Wareham NJ and Heiner H. Untargeted metabolic profiling identifies altered serum metabolites of type 2 diabetes mellitus in a prospective, nested case-control study. Clinical Chemistry, 2014,. 61, 487-97.

Anderson, S.G., Dunn, W.B., Banerjee, M., Brown, M., Broadhurst, D.I., Goodacre, R., Cooper, G.J.S., Kell, D.B. and Cruickshank, J.K. Evidence That Multiple Defects in Lipid Regulation Occur before Hyperglycemia during the Prodrome of Type-2 Diabetes. PloS One, 2014, e103217

Lodi A, Tiziani S, Khanim FL, Günther UL, Viant MR, Morgan GJ, Bunce CM, Drayson MT. Proton NMR-based metabolite analyses of archived serial paired serum and urine samples from myeloma patients at different stages of disease activity identifies acetylcarnitine as a novel marker of active disease. PLoS One. 2013, 8, e56422.

Thiele I, Swainston N, Fleming RMT et al. A community-driven global reconstruction of human metabolism. Nature Biotechnology, 2013, 31, 419-25.

Young SP, Kapoor SR, Viant MR, Byrne JJ, Filer A, Buckley CD, Kitas GD and Raza K. The impact of inflammation on metabolomic profiles in patients with arthritis. Arthritis Rheum., 2013, 65, 2015-23.

Dunn WB, Brown M,Worton SA, Davies K, Jones RL, Kell DB and Heazell, AEP. The metabolome of human placental tissue: investigation of first trimester tissue and changes related to preeclampsia in late pregnancy. Metabolomics, 2012, 8, 579-97. 

Dunn WB, Summers A. Brown M, Goodacre R, Lambie M, Johnson T, Wilkie M, Davies S, Topley N and Brenchley P. Proof-of-principle study to detect metabolic changes in peritoneal dialysis effluent in patients who develop encapsulating peritoneal sclerosis. Nephrol. Dial. Transplant. 2012, 27, 2502-10.

Ugarte M, Brown M, Hollywood KA, Cooper GJ, Bishop P and Dunn WB. Metabolomic analysis of rat serum in streptozotocin-induced diabetes and after treatment with oral triethylenetetramine (TETA). Genome Med. 2012, 4, 35.

Lodi A, Tiziani S, Khanim FL, Drayson MT, Günther UL, Bunce CM and Viant MR. Hypoxia triggers major metabolic changes in AML cells without altering indomethacin-induced TCA cycle deregulation. ACS Chem. Biol., 2011, 6, 169-75.

Soydemir F, Kuruvilla S, Brown M, Dunn WB, Day P,, Crocker IP, Baker PN, Sibley CP and Brownbill P. Adapting in vitro dual perfusion of the human placenta to soluble oxygen tensions associated with normal and pre-eclamptic pregnancy. Lab. Invest., 2011, 91, 181-89.

Horgan RP, Broadhurst DI, Walsh SK, Dunn WB, Brown M, Roberts CT, North RA, McCowan LM, Kell DB, Baker PN and Kenny LC. Metabolic profiling uncovers a phenotypic signature of small for gestational age in early pregnancy. J. Proteome Res. 2011, 10, 3660-73.

Kenny LC, Broadhurst DI, Dunn WB, Brown M, North RA, McCowan L, Roberts C, Cooper GJS, Kell DB. and Baker PN. Robust early pregnancy prediction of later preeclampsia using metabolomic biomarkers. Hypertension, 2010, 56, 741-49.

Horgan R, Broadhurst DI, Dunn WB, Brown M, Heazell AE, Kell DB, Baker PN and Kenny LC. Changes in the Metabolic Footprint of Placental Villous Explant-Conditioned Medium cultured in different oxygen tensions from placentas of Small for Gestational Age and normal pregnancies. Placenta, 2010, 31, 893-901.

Khanim FL, Hayden RE, Birtwistle J, Lodi A, Tiziani S, Davies NJ, Ride JP, Viant MR, Gunther UL, Mountford JC, Schrewe H, Green RM, Murray JA, Drayson MT and Bunce CM. Combined bezafibrate and medroxyprogesterone acetate: potential novel therapy for acute myeloid leukaemia. PLoS One. 2009, 4, e8147.