Monday 18th September
Methods and instrumentation for a quantum leap in proteomics performance
“ timsTOF with PASEF : improvement in speed and sensitivity for data dependent shotgun proteomics”
Oliver Räther, Bruker Daltonik GmbH, R&D Manager, Germany
“The promise of PASEF in clinical proteomics”
Prof. Matthias Mann, Max Planck Institute of Biochemistry, Germany
Introduction to CRISPR-Cas9 genome engineering and its potential application in proteomic research
Laura Carleton, PhD:
• Introduction to CRISPR-Cas9 genome engineering
• Useful tools and on-line resources to determine your genotype faster
• Generation of reporter and fluorescently labelled cell lines as tools for my research
• Applying CRISPR-Cas9 to my proteomic research
Biomarkers in Ovarian Cancer from SWATH maps of clinical samples
Robert Graham Ph.D., Sr Lecturer in Clinical Proteomics, Deputy Director Stoller Biomarker Discovery Centre, University of Manchester
Improved Workflows for Structural Proteomics: Studying Protein Interactions
Christoph Borchers, Ph.D.: Director, UVic-Genome BC Proteomics Centre
Recent development in structural proteomics: From “de-novo” elucidation of protein structures to in-depth characterization of “in-vivo” proteome-wide interaction networks
Richard Scheltema, Ph.D.:Junior Assistant Professor, Utrecht University
Chemical crosslinking for the masses; a user friendly approach to analyzing complex data
Applying Waters DIA workflows in disease research
David Heywood:Senior Manager Omics Business Development
David has 25 years of experience in the mass spectrometry business and has performed many roles including technical and software support, sales and marketing and has helped commercialize many of Waters successful high resolution mass spectrometry solutions for discovery omics. David is now responsible for global marketing strategies of these platforms.
Ion mobility-enhanced data independent acquisitions enabling the understanding of brain disorders
Prof. Daniel Martins-de-Souza, PhD:Daniel is PhD in Biochemistry and Professor of Biochemistry at the University of Campinas (UNICAMP), Brazil and Affiliated Member of the Brazilian Academy of Sciences. Neuroproteomics was the subject of his PhD thesis, which he continued to study during his postdoctoral training in the Max Planck Institute of Psychiatry and also in the University of Cambridge. He headed a Neuroproteomics Unit at the Ludwig Maximilians University (LMU) before returning to Brazil in 2014, where he founded the Laboratory of Neuroproteomics. Daniel´s lab employs proteomic tools to investigate molecular mechanisms involved in psychiatric disorders and the identification of potential
Tuesday 19th September
Metabolomics Analysis for Confirmation of Proteomics Insights
From proteomics results, many researchers know pathways perturbed in their experimental biological system. Metabolomics offers a different perspective on biology as metabolites are closer to the phenotype. Metabolomics samples can be analyzed on the same LC/Q-TOF system used for proteomics analysis thus facilitating collection of multi-omics data. Using pathways discovered from proteomics analysis, a target list of metabolites can be used to mine metabolomics data to confirm proteomics observations. Triple quadrupole-based targeted metabolomics for large scale studies will also be discussed..
Christine Miller: Agilent Technologies
Jennifer Van Eyk: PhD, Cedars-Sinai
The Future of High-Throughput Human Plasma Proteomics
Proteins from the blood circulatory system are indicative of the health status of an individual. Blood plasma is the most frequently used biological sample in clinical research and routine laboratory diagnostics. Changes in composition of proteins and/or their quantities in the blood can be correlated to disease onset or therapy response. Only monitoring the levels of major blood proteins simultaneously makes it possible to recognize the “Big Picture” and explain the ongoing pathological processes in the body.
Mass spectrometry based proteomics is an established technology for quantitative monitoring of plasma proteins. Recent advancements in mass spectrometry technology enable the quantification of plasma proteomes in a high-throughput mode of hundreds or even thousands of samples.
This lunch symposium will be focused on applications of different proteomics workflows for large-scale plasma sample studies.
Prof. Manuel Mayr, King’s College London: Plasma Proteomics in Epidemiology: are we really measuring the correct apolipoproteins for cardiovascular disease risk assessment?
Dr. Roland Bruderer, Biognosys AG:High throughput, single shot plasma proteome profiling on a robust capillary flow setup
Decyphering the Proteome complexity
“Clinical proteomics: beyond peptide profiling”
Hans Wessels, Ph.D., Radboud University, Medical Center, Netherlands
” Peptides to Proteoforms: Maximising UHR QTOF data for Biomarker Discovery”
Andrew Webb, Ph.D., Walter and Eliza Hall Institute, Australia
Robust Front-End Solutions for Clinical Proteomics
Evosep develops new solutions to make clinical proteomics 100 times more robust and 10 times faster. We are targeting the growing need for throughput with robust solutions for clinical and large-scale proteomics.
Matthias Mann: Perspectives of clinical proteomics for precision medicine and the resulting demands on front-end separation for mass spectrometric analysis.
Proteome Profiling for the Cancer Moonshot Program: From Basic Research to Large Scale Analyses
Aaron Gajadhar, Ph.D.: Strategic Marketing Specialist, Thermo Fisher Scientific
Pushing the leading edge in protein quantitation: Integrated, precise, and reproducible proteomic workflows
Gyorgy Marko-Varga, Ph.D.: Associate professor, Lund University
The Cancer MoonShot Centre, Lund.
Wednesday 20th September
Improving high-throughput proteomics research
As discovery and targeted proteomics research has matured, researchers have been looking for new ways to overcome the limitations of conventional approaches. Agilent’s innovations for proteomics will be covered including a data independent approach using ion mobility mass spectrometry and supporting software workflows for transforming protein information into a biological context. Agilent’s unique Jet Stream proteomics solution using standard flow UHPLC will be discussed. This approach was used to improve throughput for a targeted plasma proteomics epidemiology study investigating cardiovascular disease.
Rudi Grimm: Agilent Technologies
Prof Manuel Mayr: MD, PhD, King’s College London
Quantitative analysis of two cancer signaling pathways using multiplex-immunoprecipitation and targeted mass spectrometry
The AKT/mTOR and RAS/ERK pathways represent key mechanisms for cells to regulate cell survival, proliferation, and motility. These two pathways extensively engage in cross-talk to positively and negatively regulate each other. The lack of rigorously verified reagents and a reliance on semi-quantitative immunoassays limit the accurate quantitative analysis of these pathway proteins. Immunoprecipitation coupled with mass spectrometry (IP-MS) enables assessment of antibody specificity and identification of low-abundant pathway targets. Multiplexed IP with magnetic beads using a Kingfisher instrument followed by targeted MS (mIP-tMS) can quantitate multiple proteins of interest, PTMs, and interacting partners in a single MS run. mIP-tMS assays were developed and optimized for absolute quantitation of targets in these pathways and benchmarked with western blot (WB). mIP-tMS assays allowed absolute quantitation of multiple total and phosphorylated targets from both pathways in low to sub-nanogram concentrations across two unstimulated, IGF-1 stimulated, and LY294002 treated cell lysates. The benchmarking of mIP-tMS assays with Protein A/G and Streptavidin magnetic beads showed low correlation for quantitation of total and phosphorylated targets relative to WB. This lower correlation may be due to differences in the specificity of antibodies used for each assay technique.
John Rogers, Senior R&D Manager, Thermo Fisher Scientific: John Rogers is a Senior R&D Manager at Thermo Scientific where he manages the development of new reagents and kits for protein mass spectrometry research. John has an undergraduate degree in Biochemistry and Computer Science and a Ph.D in Pharmacology from the University of Washington. John managed a bioinformatics group at Parke-Davis/Pfizer and a proteomics group at Abbott before joining Thermo Fisher Scientific in 2007. Since joining Thermo, John has led the development of new protein sample preparation reagents, MS standards and calibrants, reagents for quantitative proteomic analysis, and new workflows for antibody verification using immunoprecipitation with mass spectrometry.
Advances in Accurate, High-Throughput Quantitative Proteomics
James Duncan, Ph.D.:Assistant Professor Fox Chase Cancer Center
Exploring the “Dark” Kinome in Cancer Using Chemical Proteomics
Kathryn Lilley, Ph.D.:Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge
Approaches to explore the spatial translatome