Sponsored Lunch Symposiums

Monday 18th September


Decyphering the Proteome complexity

Tracking proteome changes for the purpose of fundamental biology or candidate biomarker discovery is enhanced by going beyond the identification and relative quantitation of gene expression products. As most of these genes can be translated into a variety of proteoforms, out of which only a subpart will be responsible for the targeted biological activity, being able to distinguish between those proteoforms and to fully characterize them is another challenge of today’s proteomics. Discover how Bruker users benefited from our solutions to profile proteoforms or glycopeptides and perform in-depth protein characterization.


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

Richard Scheltema, Ph.D.:Junior Assistant Professor, Utrecht University


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


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


Methods and instrumentation for a quantum leap in proteomics performance

Bruker is proud to introduce new workflows that will boost the performance of its proteomics solution beyond what has been possible in recent years using the most sophisticated instrumentation.
As an outcome of 8 years of development, the next-generation UHR-Q-TOF platform enables Parallel Accumulation Serial Fragmentation providing for an up to 10-fold increase in MS/MS data acquisition rate with no sensitivity or resolution loss : it simply sets new standards for routine high-performance proteomics workflows.
This new platform as well as more routine existing platforms will benefit from the latest methods and software advances, providing a boost to both identification and relative quantitation performance thanks to a new DIA workflows that allow spectral database free identifications.


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

Gyorgy Marko-Varga, Ph.D.: Associate professor, Lund University

Wednesday 20th September


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

Kathryn Lilley, Ph.D.:Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge

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