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Group

Biological Mass Spectrometry & Proteomics

Unit(s) of assessment: Allied Health Professions, Dentistry, Nursing and Pharmacy

Research theme: Health and Wellbeing

School: School of Science and Technology

Overview

The Mass Spectrometry & Proteomics group is run by Dr’s David Boocock and Clare Coveney and is part of the “omics”/biomarker discovery umbrella including Professor Graham Ball’s bioinformatics group in in the John van Geest Cancer Research Centre.

The group analyses samples such as protein extracts from cancer cells, cells with knocked out genes, tissues, blood and other body fluids and interrogates these data sets to find critical differences in the cellular pathways involved in cancer and other diseases. Proteins are large complex molecules that play many critical roles in the body. They are the “machines” of the cells that allow them to function. Proteins are made up of large numbers of smaller units called amino acids which join together to form long chains which we term “proteins”.

The human body is estimated to contain over a million different forms of proteins. The complex profile of proteins within an organism is very dynamic, it changes due to many factors such as stress, disease, therapy. This complement of proteins in the body is known as the “proteome” and the study of it, and its changes, is known as “proteomics”. Mass Spectrometry is a technique, using very specialised instrumentation, that accurately measures the weights and abundance of molecules – for example, proteins and fragments of proteins (peptides).

Being able to know the molecular weight of a protein allows us to decipher its identity by breaking it up into its constituent amino acids and modern methodologies such as Data Independent Acquisition (DIA) allow precise quantitation across thousands of proteins per sample.

Collaboration

Dr Csaba Matta, University of Debrecen, Hungary

Professor Tim Johnson, Director, Immunology Therapeutic Are,a UCB Pharma, Slough UK

Rob Layfield, Professor of Protein Biochemistry, Universty of Nottingham, UK

Dr Elizabeth Marsh, Senior lecturer in Cellular and Molecular Biology, University of Derby UK

Dr Gillian Knight, Associate Dean for Learning & Teaching in the School of Engineering & Applied Science, Aston University, UK

Dr. Vincenzo Desiderio Assistant Professor Medical Histology and Embryology University of Campania "Luigi Vanvitelli", Naples, Italy

Publications

Alterations in the chondrocyte surfaceome in response to pro-inflammatory cytokines. Bernadette Jeremiasse, Csaba Matta, Christopher R. Fellows, David J. Boocock, Julia R. Smith, Susan Liddell, Floris Lafeber, Willem E. van Spil & Ali Mobasheri. BMC Mol and Cell Biol 21, 47 (2020)

Neurite outgrowth inhibitory levels of organophosphates induce tissue transglutaminase activity in differentiating N2a cells: evidence for covalent adduct formation. Ibtesam S. Almami, Maha A. Aldubayan, Shatha G. Felemban, Najiah Alyamani, Richard Howden, Alexander J. Robinson, Tom D. Z. Pearson, David Boocock, Alanood S. Algarni, A. Christopher Garner, Martin Griffin, Philip L. R. Bonner & Alan J. Hargreaves. Arch Toxicol (2020)

Exercise Training in Obese Rats Does Not Induce Browning at Thermoneutrality and Induces a Muscle-Like Signature in Brown Adipose Tissue. Peter Aldiss, Jo E. Lewis, Irene Lupini, Ian Bloor, Ramyar Chavoshinejad, David J. Boocock, Amanda K. Miles, Francis J. P. Ebling, Helen Budge and Michael E. Symonds. Frontiers in Endocrinology/. 11. p 97. (2020)

β2-Adrenergic Signalling Promotes Cell Migration by Upregulating Expression of the Metastasis-Associated Molecule LYPD3. Michael Gruet, Daniel Cotton, Clare Coveney, David J. Boocock, Sarah Wagner, Lucie Komorowski, Robert C. Rees, A. Graham Pockley, A. Christopher Garner, John D. Wallis, Amanda K. Miles, and Desmond G. Powe. Biology. 9:2. (2020)

Silica bound co-pillar[4+1]arene as a novel supramolecular stationary phase. Subbareddy Mekapothula, Matthew A. Addicoat, David J. Boocock, John D. Wallis, Peter J. Cragg and Gareth W. V. Cave. Chemical Communications. 12. (2020)

Molecular phenotyping of the surfaceome of migratory chondroprogenitors and mesenchymal stem cells using biotinylation, glycocapture and quantitative LC-MS/MS proteomic analysis. Csaba Matta, David J. Boocock, Christopher R. Fellows, Nicolai Miosge, James E. Dixon, Susan Liddell, Julia Smith & Ali Mobasheri. Scientific Reports 9, 9018. (2019)

PYK2 promotes HER2-positive breast cancer invasion. Shaymaa IK. Al-Juboori, Jayakumar Vadakekolathu, Sarra Idri, Sarah Wagner, Dimitrios Zafeiris, Joshua RD. Pearson, Rukaia Almshayakhchi, Michele Caraglia, Vincenzo Desiderio, Amanda K. Miles, David J. Boocock, Graham R. Ball and Tarik Regad. Journal of Experimental & Clinical Cancer Research. 38:210. (2019)

Interscapular and Perivascular Brown Adipose Tissue Respond Differently to a Short-Term High-Fat Diet. Peter Aldiss, Jo E. Lewis, David J. Boocock, Amanda K. Miles, Ian Bloor, Francis J. P. Ebling, Helen Budge and Michael E. Symonds. Nutrients 11(5), 1065. (2019)

Monoamine oxidase-A promotes protective autophagy in human SH-SY5Y neuroblastoma cells through Bcl-2 phosphorylation. Aslihan Ugun-Klusek, Theodosis Theodosi, Ellen Billett, Christoph Ufer, David Boocock, Florence Burté, Julia C. Fitzgerald, Patrick Yu-Wai-Man, Lynn Bedford. Redox Biology. 20 Jan. (2019)

The Vitamin D Binding Protein axis modifies disease severity in Lymphangioleiomyomatosis. Suzanne Miller, Clare Coveney, Janice Johnson, Aliki-Eleni Farmaki, Nishant Gupta, Martin D. Tobin, Louise V. Wain, Francis X. McCormack, David J. Boocock, Simon R. Johnson. European Respiratory Journal 52: 1800951 (2018)

A new inhibitor of glucose-6-phospate dehydrogenase blocks pentose phosphate pathway and suppresses malignant proliferation and metastasis in vivo. Michele Caraglia, Luigi Mele, Francesca Paino, Federica Papaccio, Tarik Regad, David Boocock, Paola Stiuso, Angela Lombardi, Davide Liccardo, Gabriella Aquino, Antonio Barbieri, Claudio Arra, Clare Coveney, Marcella La Noce, Gianpaolo Papaccio, Virginia Tirino, and Vincenzo Desiderio. Cell, Death and Disease. 9, Article number: 572. (2018)

Proteomic profiling reveals the transglutaminase-2 externalization pathway in kidneys post-UUO. Furini G, Schroeder N, Huang L, Boocock DJ, Coveney C, Tonoli E, Ramaswamy R, Ball G, Verderio C, Johnson TS, Verderio EAM. Journal of the American Society of Nephrology. 29 (3) 880-905. (2018)

Identification and characterisation of Nanog+/ Oct4 high/Sox2+ doxorubicin-resistant stem-like cells from transformed trophoblastic cell lines. Balahmar RM., Boocock DJ., Coveney C., Vadakekolathu J., Ray S., Regad T., Ali S and Sivasubramaniam S. Oncotarget. Vol. 9, (6), 7054-7065. (2018)

Related projects

Recent grant/contract capture:

Motor Neurone Disease Scotland, “Exploring neuronal extracellular vesicle proteomes -implications for ALS”. Co-Investigator with The University of Nottingham. £141,012, 2021-2023.

The Oracle Cancer Trust “The pathogenesis of HPV within oropharyngeal cancer”  £102,234 co-investigator with Derby and Aston University. 2021-2024.

Investigation of the plasma and urine proteome in patients with different rates of Chronic Kidney Disease (CKD) progression to identify stable and progressive disease fingerprints. £105,740. UCB

Biopharma Spr. Co-Investigator at NTU. 2017-2018. Cancer and Polio Research Fund. Investigation of NNMT as a key regulator of cancer metastasis and identification of new therapeutic targets. £4,611. Principle Investigator. 2017-2018.

The LAM Foundation. “Discovery of serum markers of disease activity for LAM”. £22,241. Co-investigator with The University of Nottingham. 2015-2016.

Facilities

The Biological Mass Spectrometry & Proteomics Group currently houses two Sciex TripleTOF instruments utilising SWATH (Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra, a form of DIA) for quantitation, connected to Eksigent NanoLC 400 chromatography systems, and a Bruker UltrafleXtreme MALDI-TOF. We have access within the John van Geest Cancer Research Centre to instrumentation to facilitate multi-omic analyses including gene expression micro-array, Nanostring platform, cell sorting/flow cytometry, laser capture microdissection.