Friday, 7th February 25th Annual Lorne Proteomics Symposium 2020

Confirmed Speakers

Atsuhiko ‘Ash’ Toyama, Shimadzu Corporation, Singapore/Japan

Chris Bowen, Shimadzu Scientific Instruments, Australia

Program

Two presentations will be given covering the following topics:

“Breaking the sensitivity barrier to unravelling the novel roles of lipid mediators in pathophysiology” by Ash Toyama, Ph.D.

 1) A brief overview of Shimadzu’s targeted omics solution portfolio, each addressing the difficulty of the targeted class of compounds by unique approaches.

 2) The recent progress using the LC/MS/MS Lipid Mediators Method Package in a collaborative work with the University of Tokyo, illustrating that method reproducibility is the most critical factor for delivering scientifically meaningful outcome.

 3) Tools to assist data processing and interpretation

“The Q-TOF technologies to reproduce the benefits of targeted workflows in high-resolution analyses” by Chris Bowen

 1) Ultra-fast data acquisition and ion accumulation

 2) UFgrating and iRefTOF – simple ideas made possible by meticulous engineering

 3) Flight tube thermostability for exceptionally stable mass measurement accuracy

 4) DIA capabilities

 5) Nexera Mikros, the microflow solution with great ease

• Plasma proteome profiling to assess human health and disease - Philipp E Geyer
• Precision cancer immunotherapy - can proteomics rise to the challenge? - Anthony Purcell
• Caveolae formation alters intracellular organelle composition and function - Harley Robinson
• Rapid, unbiased identification of protein inclusion components from patient post-mortem brain tissue using Biotinylation by Antibody Recognition (BAR) - Stephanie L Rayner
• Splicing up your sex life - Mark A Baker

• The role of ubiquitylation on the phagosome: a tale of inflammatory responses and vesicle trafficking - Matthias Trost
• Proteogenomic characterization of einkorn wheat cultivars with low celiac disease response - Angela Juhasz
• Multi-omic analysis and functional validation of Campylobacter jejuni grown with intestinal bile salts - Lok Man
• Proteomics tools for medicinal cannabis - Delphine Vincent
• DIGESTIVE PHYSIOLOGY AND PROTEOMICS FOR CONTROLLING AN INVASIVE PEST - Sophia Escobar-Correas
• LC-MS/MS-based multi-omics approach to elucidate developmental adaptations in the parasitic nematode Haemonchus - Tao Wang

• Cellular glycoproteome and proteome during influenza infection - Cassandra Pegg
• “RNA regulons” as potential drivers of Giardia duodenalis stage transition - Balu Balan
• Identification of novel N-glycosylation sites from the bacterium Campylobacter jejuni - Joel Cain
• Understanding glycopeptide antibiotic synthesis by mass spectrometric analysis of polycyclic peptides - Robert JA Goode
• Characterising insult-induced protein-protein crosslinks formed during food processing - Hannah McKerchar
• Multi-omic analysis reveals the pro-inflammatory cytokine IFNγ modulates the immunopeptidome of triple negative breast cancer cells. - Gabriel Goncalves

• Towards the generation of a comprehensive proteome map for Phytophthora cinnamomi, the causal agent of native dieback - Christina Andronis
• Interaction of Common Antibiotics with Human Serum Albumin as Determined by Hydrogen Deuterium Exchange and Chemical Cross Linking Mass Spectrometry - Ching-Seng Ang
• Investigating proteome changes between primary and metastatic cutaneous squamous cell carcinoma using SWATH mass spectrometry - Ali Azimi
• Expression of SCN2A protein in different mouse models of SCN2A encephalopathy and after antisense oligonucleotide treatment - Todd Blackburn
• SWATH-MS proteomics reveals time-dependent acid stress response in Campylobacter jejuni  - Utpal Bose
• A High Throughput approach to identifying compound inhibitors of mRNA processing and export - Kirstyn Carey
• The E3 ubiquitin ligase SCF^(cyclin-F) complex regulates caspase-3, a key executor of the apoptotic cell death program - Flora Cheng
• MASS SPECTROMETRY IMAGING STUDY OF LIPID METABOLITES IN THE ADULT MOUSE TESTIS - Emmanuelle Claude
• Chronic obstructive pulmonary disease: is autoimmunity a contributing factor? - Penelope V Dalla
• Measurement of protein losses during sample preparation - Chris Desire
• High-confidence identification of protein methylation in Giardia duodenalis, a neglected gastrointestinal parasite - Samantha J Emery-Corbin
• OMIC Investigation of Chondrocytes’ Response to varying mechanical load – Assessment of aging and impact stress - Lee A Gethings
• Insights into the proteomics of abiotic stresses in rice - Fatemeh Habibpourmehraban
• Crosstalk between protein methylation and phosphorylation in yeast and human - Joshua Hamey
• Proteome response to drought stress of three species of rice from different geographic regions - Sara Hamzelou
• A draft map of the Rice plant proteome - Karthik Kamath
• Quantitative proteomic analyses of molecular response to the RNA polymerase I transcription inhibitor CX-5461 in olaparib-resistant ID8 mouse ovarian cancer cells   - Jian Kang
• Cell wall and whole cell proteomes define flocculation and fermentation behaviour of yeast - Edward EDK Kerr
• New Stemsation: Proteomic Characterisation of Human Adipose Stem Cells - Naomi Koh Belic
• Redox modifications of cysteine in the liver of type 2 diabetes mellitus - Desmond K Li
• Association of post-translational modifications in the evolution of diabetic nephropathy in a rodent model of type 2 diabetes mellitus - Shivanjali J. Lingam
• PromarkerD: A novel test for predicting rapid decline in renal function in type 2 diabetes  - Richard Lipscombe
• Molecular profiling of fermented dairy products using mass spectral fingerprinting technologies - Evelyne Maes
• Kinetic mass spectrometry imaging to study cytosolic ribosomes remodeling in plants - Federico Martinez-Seidel
• Cotton reproduction: SWATH-MS reveals stage-specific proteins involved in cotton pollen development - Matthew J McKay
• Prevalence and mechanisms of diastaticus-like phenotypes and genotypes in Saccharomyces cerevisiae brewing strains - Pippa E Mckinstry

Dissecting the roles of glycosylation on bacterial proteins within the Burkholderia genus

Dr Nichollas Scott

Department of Microbiology and Immunology, The University of Melbourne

Bio: Dr Scott completed his PhD at the University of Sydney (2007 to 2012) on the development of MS approaches for the study of bacterial protein modifications. The key focus of his doctorate was the establishment of a protocol for enriching bacterial glycopeptides irrespective of glycan composition. In 2012 with the aid of a NHMRC Early Career Fellowship he moved to the University of British Columbia to undertake a postdoc with Prof Leonard Foster. Within the Foster lab Dr Scott began applying quantitative proteomics approaches to study protein interactions and bacterial glycosylation systems at a systems level. From 2012 to 2015 Dr Scott spearheaded projects to characterise bacterial glycosylation systems across Gram-negative pathogens including, Acinetobacter baumannii, Burkholderia cenocepacia and Ralstonia solanacearum. In 2016 Dr Scott returned to Australia where he completed a second postdoc in the laboratory of Prof Elizabeth Hartland, developing novel enrichment approaches to track Arginine-glycosylation. In 2017, on the back of two national awards from the Australasian Proteomics Society (the 2016 International Early Career Award & the 2017 Ken Mitchelhill Award), NHMRC and ARC funding Dr Scott established his independent research group in the Department of Microbiology and Immunology at the University of Melbourne. Since 2017 Dr Scott’s lab has sought to identify and track microbial glycosylation events to understand the role of glycosylation in microbial pathogenesis. In 2019 in recognition of his contribution to the field of glycoconjugate research Dr Scott was awarded the 2019-IGO Young Glycoscientist Award from the International Glycoconjugate Organization.

Abstract: Protein glycosylation, the chemical addition of sugars to proteins, is an important but poorly understood aspect of bacterial physiology. Recently we identified that multiple human pathogens of the Burkholderia genus possess a conserved O-linked glycosylation system. High-throughput screening studies have shown the inhibition of glycosylation profoundly impacts virulence in Burkholderia, yet little is known about the underlying mechanism. Using the Cystic fibrosis pathogen B. cenocepacia as a model we have sought to improve our understanding of the role of glycosylation within Burkholderia species. Using state of the art proteomics approaches we have now identified >70 proteins are glycosylated at over 110 sites across strains of B. cenocepacia. Mutagenesis studies have shown that the loss of glycosylation leads to profound effects on the proteome with quantitative proteomics/degradomics revealing that a subset of glycoproteins require glycosylation for stability. Using thermal proteomics, we have also begun to track the effect of glycosylation on protein stability within the proteome. Our quantitative proteomics, degradomics and thermal proteomics results support that glycosylation plays multiple roles in the biology of B. cenocepacia. By understanding how glycosylation contributes to B. cenocepacia protein function this work will improve our ability to harness bacterial glycosylation to create bespoke glycoconjugates.

Direct measurement of protein translation and degradation rates In vivo at proteomic scales in the clinic and beyond; new approaches to stable isotope metabolic labelling and analysis

Dr Owen Duncan

School of Molecular Sciences, The University of Western Australia

Bio: Dr Duncan is a Post-doctoral Research Fellow working in Harvey Millar's laboratory at the University of Western Australia. His main area of work is the development of mass spec based data acquisition and processing focusing on metabolic incorporation of stable isotopes for measuring flux at the protein level (protein synthesis and degradation rates). His PhD studies were supervised by Prof. Ryan Lister and Jim Whelan where he used early QTOF instruments combined with an intricate free flow electrophoresis based subcellular fractionation workflow to establish the mitochondrial outer membrane proteome in higher plants. He has since worked with nanoflow proteomics daily and have recently been involved in the establishment and commissioning of the Western Australian Proteomics core facility established with NCRIS funding in December 2019 which is focused on the delivery of flux proteomics to researchers nationally.

Abstract: Protein abundances are established by the combination of synthesis and degradation; the direct measurement of which has been complex and time consuming for individual proteins and simply not possible at scale. Advances at the University of Western Australia using stable isotope labelling combined with mass spectrometry has allowed the parallel measurement of synthesis and degradation rates of hundreds to thousands of protein species in a single sample. In collaboration with researchers at the Fiona Wood Foundation we've refined the use of heavy hydrogen in the form of deuterium oxide (²H₂O) coupled to skin biopsies and mass spectrometry to measure the synthesis and degradation rates of various isoforms of collagen in human burns patients over time in scar vs non scar skin with the aim of both determining when the most effective times are to apply drug based interventions in scar formation and to measure their efficacy. The second part of this talk will cover experimental design and other examples of protein flux measurements.

• To be provided - Judit Villen
• New tools to study protein ubiquitination - David Komander
• Deciphering irreversible cysteine redox post-translational modifications in myocardial ischemia / reperfusion injury - Stuart Cordwell
• HNF4A sumoylation is regulated by fasting.   - Dylan J Harney
• Protein TAILS tell remarkable tales: Positional proteomics reveals diverse N-Terminomes and proteolytic landscapes in disease - Chris Overall

• Challenges in Visualization and Analysis of Mass Spectrometry Imaging Experiments - Kylie Bemis

• MassOmics: An R package of a cross-platform data processing pipeline for large-scale GC-MS untargeted metabolomics datasets. - George GUO
• MHCpLogics: a machine learning-based tool for unsupervised data visualisation and cluster analysis of immunopeptidomes - Mohammad Shahbazy
• OmixLitMiner - Tool for fast evaluation of knowledge and importance of regulated individual proteins derived from differential proteomics - Hartmut Schlüter
• CiteFuse enables multi-modal analysis of CITE-seq data - Hani Jieun Kim

• Stimulomics: large-scale mapping of signalling networks downstream of major cell surface receptors - Sean J Humphrey
• Precision phosphoproteomics reveals kinase targets enhancing muscle insulin sensitivity - Elise J. Needham
• Analytical guidelines for co-fractionation mass spectrometry obtained through global profiling of gold standard Saccharomyces cerevisiae protein complexes - Gene Hart-Smith
• Lipidomic Mapping, Localization and Characterization in Tissues by MALDI- Imaging Mass Spectrometry - Anjaneyaswamy Ravipati

• Multi-Omics Analysis of the Intermittent Fasting Response - Mark Larance
• Using genomics and proteomics to understand the antibiotic resistance capabilities of a bacterial pathogen - Stephanie E L Town
• Protein coding potential of annotated non-coding RNAs encoded by the human genome - Hitesh Kore
• Integrating Multiple Technologies - Steve Binos

• The Hitchhiker’s Guide to the Yeast Interactome - Ignatius Pang
• Identification of aggressive prostate cancer through in-depth proteomics of tissues and urines - Thomas Kislinger
• LFQ-Analyst, an interactive web-platform to analyse quantitative proteomics data - Ralf Schittenhelm
• Deciphering the stage-specific glycoprotein signatures of colorectal cancer using integrated mass spectrometry-based omics - Rebeca Kawahara Sakuma

• Interactive visualisation, and reproducibility in bioinformatics - David Powell