Dr Matt Padula, while being a Senior Lecturer in the School of Life Sciences, also operates the Proteomics Core Facility, the main purpose of which is to provide high level technical support and the instrumentation required for researchers to perform their research projects without having to spend long periods of time learning the complicated techniques and instruments needed to answer the scientific question they want answered. The Core is equipped with the knowledge, expertise and instrumentation to perform almost all proteomic, protein chemistry, lipidomic and metabolomic experiments that could be of use to the faculty’s researchers. In addition, Core staff have built relationships with other institutions and research groups to gain access to instrumentation and expertise not available within UTS. I have 21 years experience in protein chemistry, liquid chromatography, mass spectrometry analysis and characterization of peptides and proteins by liquid chromatography/mass spectrometry (LC/MS), electrophoresis and sample preparation by native and denaturing methodologies. In this time I have performed protein extraction, fractionation and analysis on organisms such as Mycoplasma, bacteria, yeast, mammalian tissue and cells, plant tissue, parasites including Fasciola, Toxoplasma, Eimeria, Haemonchus and Plasmodium, paralysis ticks, coral, snake venom and the pathogenic fungus Cryptococcus. I have expertise in nanoelectrospray mass spectrometric analysis of peptides and proteins, the quantitation of peptides and proteins using mass spectrometry and the determination of de novo peptide sequence from tandem mass spectrometry data. In addition, he has expertise in the fractionation of peptides and proteins by analytical and preparative liquid chromatography and analytical and preparative electrophoresis techniques such as 1D and 2D-PAGE, liquid phase isoelectric focusing and continuous elution electrophoresis. Recently, the focus of my interests has expanded to include lipids and metabolites, specifically developing methods and techniques to extract and fractionate these molecules, subject them to mass spectrometry for identification and quantification, and perform bioinformatic analysis to determine whether changes in abundance in these molecules is significant. There are many opportunities for undergraduate students to gain experience and perform internships within the Core Facility by engaging in small parts of larger projects, all of which are aimed at developing methodologies and techniques that can be further applied to biological problems. A partial list of these projects appears below and a more extensive list can be provided and discussed by contacting me by email. Not all of these projects would be laboratory based but focused on bioinformatic, statistical and interpretative work on previously generated data.

Development of fractionation and analysis techniques for the analysis of proteins, protein expression, post-translational modifications of proteins, and protein complexes in their native and denatured states. These techniques use chromatographic and electrophoretic approaches combined with classical and targeted mass spectrometry techniques. The model wall-less bacteria Mycoplasma, a product of reductive evolution, is used extensively to develop these tecnniques. Internship and other projects. Mapping the ENTIRE E.coli proteome by 2D-PAGE and LC/MS/MS. Software pipelines for proteomics, metabolomics and lipidomics data analysis and visualisation. Improving protein extraction methodologies. Using multiple solvent systems to fractionate and analyse the bacterial lipidome and metabolome. And many more!

Johnson, L, Cameron, M, Waters, L, Padula, MP & Marks, DC 2019, 'The impact of refrigerated storage of UVC pathogen inactivated platelet concentrates on in vitro platelet quality parameters.', Vox sanguinis, vol. 114, no. 1, pp. 47-56.View/Download from: UTS OPUS or Publisher's site Santos, J, Milthorpe, BK & Padula, MP 2019, 'Proteomic Analysis of Cyclic Ketamine Compounds Ability to Induce Neural Differentiation in Human Adult Mesenchymal Stem Cells', INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, vol. 20, no. 3.View/Download from: UTS OPUS or Publisher's site O'Rourke, MB, Smith, CC, De La Monte, SM, Sutherland, GT & Padula, MP 2019, 'Higher Mass Accuracy MALDI-TOF/TOF Lipid Imaging of Human Brain Tissue in Alzheimer's Disease', Current Protocols in Molecular Biology, vol. 126, no. 1.View/Download from: Publisher's site Waters, L, Padula, MP, Marks, DC & Johnson, L 2019, 'Cryopreservation of UVC pathogen-inactivated platelets', Transfusion, vol. 59, no. 6, pp. 2093-2102.View/Download from: Publisher's site Hurtado Silva, M, Berry, IJ, Strange, N, Djordjevic, SP & Padula, MP 2019, 'Terminomics Methodologies and the Completeness of Reductive Dimethylation: A Meta-Analysis of Publicly Available Datasets.', Proteomes, vol. 7, no. 2.View/Download from: UTS OPUS or Publisher's site O'Rourke, MB, Smith, CC, Tse, BCY, Sutherland, GT, Crossett, B & Padula, MP 2019, ''What did i do wrong?' An empirical evaluation of sample preparation methodologies in matrix-assisted laser desorption/ionization-mass spectrometry imaging', Future Science OA, vol. 5, no. 4.View/Download from: Publisher's site O'Rourke, MB, Djordjevic, SP & Padula, MP 2018, 'The Quest for Improved Reproducibility In MALDI Mass Spectrometry', Mass Spectrometry Reviews, vol. 37, no. 2, pp. 217-228.View/Download from: UTS OPUS or Publisher's site Wong, SL, To, J, Santos, J, Allam, VSRR, Dalton, JP, Djordjevic, SP, Donnelly, S, Padula, MP & Sukkar, MB 2018, 'Proteomic Analysis of Extracellular HMGB1 Identifies Binding Partners and Exposes Its Potential Role in Airway Epithelial Cell Homeostasis.', Journal of Proteome Research, vol. 17, no. 1, pp. 33-45.View/Download from: UTS OPUS or Publisher's site O'Rourke, MB, Raymond, BBA, Djordjevic, SP & Padula, MP 2018, 'The Effect of Collimating Lens Focusing on Laser Beam Shape in Matrix Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS)', JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, vol. 29, no. 3, pp. 512-515.View/Download from: UTS OPUS or Publisher's site Waters, L, Cameron, M, Padula, MP, Marks, DC & Johnson, L 2018, 'Refrigeration, cryopreservation and pathogen inactivation: an updated perspective on platelet storage conditions.', Vox sanguinis, vol. 113, no. 4, pp. 317-328.View/Download from: UTS OPUS or Publisher's site Raymond, BBA, Madhkoor, R, Schleicher, I, Uphoff, CC, Turnbull, L, Whitchurch, CB, Rohde, M, Padula, MP & Djordjevic, SP 2018, 'Extracellular Actin Is a Receptor for Mycoplasma hyopneumoniae.', Frontiers in cellular and infection microbiology, vol. 8, no. Feb.View/Download from: UTS OPUS or Publisher's site Main, BJ, Bowling, LC, Padula, MP, Bishop, DP, Mitrovic, SM, Guillemin, GJ & Rodgers, KJ 2018, 'Detection of the suspected neurotoxin β-methylamino-l-alanine (BMAA) in cyanobacterial blooms from multiple water bodies in Eastern Australia.', Harmful algae, vol. 74, pp. 10-18.View/Download from: UTS OPUS or Publisher's site Bogema, DR, Micallef, ML, Liu, M, Padula, MP, Djordjevic, SP, Darling, AE & Jenkins, C 2018, 'Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypes.', BMC genomics, vol. 19, no. 1, pp. 298-298.View/Download from: UTS OPUS or Publisher's site Roediger, B, Lee, Q, Tikoo, S, Cobbin, JCA, Henderson, JM, Jormakka, M, O'Rourke, MB, Padula, MP, Pinello, N, Henry, M, Wynne, M, Santagostino, SF, Brayton, CF, Rasmussen, L, Lisowski, L, Tay, SS, Harris, DC, Bertram, JF, Dowling, JP, Bertolino, P, Lai, JH, Wu, W, Bachovchin, WW, Wong, JJ-L, Gorrell, MD, Shaban, B, Holmes, EC, Jolly, CJ, Monette, S & Weninger, W 2018, 'An Atypical Parvovirus Drives Chronic Tubulointerstitial Nephropathy and Kidney Fibrosis.', Cell, vol. 175, no. 2, pp. 530-543.e24.View/Download from: UTS OPUS or Publisher's site O'Rourke, MB & Padula, MP 2017, 'A new standard of visual data representation for imaging mass spectrometry.', PROTEOMICS - Clinical Applications, vol. 11, no. 3-4.View/Download from: UTS OPUS or Publisher's site Aili, SR, Touchard, A, Petitclerc, F, Dejean, A, Orivel, J, Padula, MP, Escoubas, P & Nicholson, GM 2017, 'Combined Peptidomic and Proteomic Analysis of Electrically Stimulated and Manually Dissected Venom from the South American Bullet Ant Paraponera clavata', JOURNAL OF PROTEOME RESEARCH, vol. 16, no. 3, pp. 1339-1351.View/Download from: UTS OPUS or Publisher's site Kumar, M, Padula, MP, Davey, P, Pernice, M, Jiang, Z, Sablok, G, Contreras-Porcia, L & Ralph, PJ 2017, 'Proteome Analysis Reveals Extensive Light Stress-Response Reprogramming in the Seagrass Zostera muelleri (Alismatales, Zosteraceae) Metabolism.', Frontiers in Plant Science, vol. 7, pp. 1-19.View/Download from: UTS OPUS or Publisher's site Stroud, LJ, Slapeta, J, Padula, MP, Druery, D, Tsiotsioras, G, Coorssen, JR & Stack, CM 2017, 'Comparative proteomic analysis of two pathogenic Tritrichomonas foetus genotypes: there is more to the proteome than meets the eye', INTERNATIONAL JOURNAL FOR PARASITOLOGY, vol. 47, no. 4, pp. 203-213.View/Download from: UTS OPUS or Publisher's site O'Rourke, MB, Raymond, BBA & Padula, MP 2017, 'The Characterization of Laser Ablation Patterns and a New Definition of Resolution in Matrix Assisted Laser Desorption Ionization Imaging Mass Spectrometry (MALDI-IMS).', Journal of The American Society for Mass Spectrometry, vol. 28, no. 5, pp. 895-900.View/Download from: UTS OPUS or Publisher's site Padula, MP, Berry, IJ, O Rourke, MB, Raymond, BBA, Santos, J & Djordjevic, SP 2017, 'A Comprehensive Guide for Performing Sample Preparation and Top-Down Protein Analysis.', Proteomes, vol. 5, no. 2.View/Download from: UTS OPUS or Publisher's site Jiang, Z, Kumar, M, Padula, MP, Pernice, M, Kahlke, T, Kim, M & Ralph, PJ 2017, 'Development of an Efficient Protein Extraction Method Compatible with LC-MS/MS for Proteome Mapping in Two Australian Seagrasses Zostera muelleri and Posidonia australis.', Frontiers in Plant Science, vol. 8, pp. 1-14.View/Download from: UTS OPUS or Publisher's site Santos, J, Milthorpe, BK, Herbert, BR & Padula, MP 2017, 'Proteomic Analysis of Human Adipose Derived Stem Cells during Small Molecule Chemical Stimulated Pre-neuronal Differentiation.', International journal of stem cells, vol. 10, no. 2, pp. 193-217.View/Download from: UTS OPUS or Publisher's site Berry, IJ, Jarocki, VM, Tacchi, JL, Raymond, BBA, Widjaja, M, Padula, MP & Djordjevic, SP 2017, 'N-terminomics identifies widespread endoproteolysis and novel methionine excision in a genome-reduced bacterial pathogen.', Scientific Reports, vol. 7, no. 1, pp. 1-17.View/Download from: UTS OPUS or Publisher's site Widjaja, M, Harvey, KL, Hagemann, L, Berry, IJ, Jarocki, V, Raymond, BBA, Tacchi, JL, Gründel, A, Steele, JR, Padula, MP, Charles, IG, Dumke, R & Djordjevic, SP 2017, 'Elongation factor Tu is a multifunctional and processed moonlighting protein.', Scientific Reports, vol. 7, no. 1, pp. 1-17.View/Download from: UTS OPUS or Publisher's site Waters, L, Padula, MP, Marks, DC & Johnson, L 2017, 'Cryopreserved platelets demonstrate reduced activation responses and impaired signaling after agonist stimulation', TRANSFUSION, vol. 57, no. 12, pp. 2845-2857.View/Download from: UTS OPUS or Publisher's site