Hosted Workshops

Hosted Workshops

Title: Addressing the analytical rigor of omics measurements for clinical research

Day: Monday Lunchtime

Speakers: Dr. Marten F. Snel, SAHMRI, Head of MS Core Facility

Associate Professor Robert Trengove, Murdoch University, Director Separation Science and Metabolomics Laboratory

Synopsis: The translation of discovery biomarker studies has been plagued with obstacles in the path to clinical utility. Small study sizes, poor experimental reproducibility and inappropriate analytical technique continue to confound the efficient translation from bench to bedside. Waters Corporation continues purposeful innovation in biomedical research with these challenges in mind. SONAR data independent acquisition was developed to improve reproducibility, increase speed of analysis for compatibility with large study cohorts whilst maintaining data quality and quantitative accuracy.

In this lunchtime workshop we will hear from two leading researchers who have been successfully addressing the analytical challenges of protein biomarker discovery in clinical research applications.

Topics: Biomarker Discovery, Translational Research, Reproducibility and accuracy of measurements, SONAR data independent acquisition

Proudly sponsored by Waters

Title: DIA with near 100% Ion Usage: Introducing diaPASEF on the timsTOF Pro

Day: Monday Lunchtime

Speakers: Prof. Dr. Ruedi Aebersold, Head of the Institute of Molecular Systems Biology, ETH, Zurich, Switzerland

Synopsis: The timsTOF Pro with PASEF was introduced as a shotgun proteomics solution at the International HUPO Congress in Dublin in 2017. The unique trapped ion mobility (TIMS) front end of the instrument enables usage of nearly 100% of the ions entering the instrument. However, as in any DDA method the precursor selection is automated, based on the data user adjustable parameters. The precursors that are targeted for MS/MS can vary from run to run due to biological variation and the semi-stochastic nature of the precursor selection process. DIA methods can improve the data completeness by fragmenting all ions in a wider window, but suffer from inefficient usage of the ions as the window must be cycled over the entire mass range of interest. In this workshop the use of a new scan mode called diaPASEF will show how virtually all of the peptide ions can be covered with highly efficient usage of the ions present. Dr. Gary Kruppa will present a brief introduction to the diaPASEF method. Then our featured speaker, Prof. Ruedi Aebersold will present a talk on "SWATH/DIA Proteomics and its Role in Biology".

Topics: DDA and DIA approaches to proteomics; The new diaPASEF approach; The importance of DIA/SWATH methods in biological applications.

Proudly sponsored by Bruker

Title: Advancing Quantitative Proteomics: Multiplexing, Accuracy, and Precision

Day: Monday Lunchtime

Speakers: Khatereh Motamed, Vertical Marketing Specialist (Thermo Fisher Scientific)
Kathryn Lilley, Professor, Department of Biochemistry (University of Cambridge)

Synopsis: Quantitative proteomics strategies using Tandem Mass Tags (TMT) enable precise measurement of protein abundance from multiple samples into a single high-resolution LC-MS analysis. Increasingly, various biological experiments demand higher multiplexing and sample throughput with accurate quantitation. In this workshop, our expert speakers will lay out strategies that combine next generation technologies in multiplexing chemistry, hardware, and software to achieve increased quantitative performance and throughput efficiency on Thermo Scientific Orbitrap Mass Spectrometers. Together, these advances allow for intelligent acquisition methods that improve quantitation accuracy, precision, and proteome depth.

Topics:

  • Quantitative proteomics strategies using Tandem Mass Tags (TMT)
  • Strategies that combine next generation technologies in multiplexing chemistry, hardware, and software to achieve increased quantitative performance and throughput efficiency on Thermo Scientific Orbitrap Mass Spectrometers

Proudly sponsored by Thermo Fisher Scientific

Title: Tools for high productivity proteomics: timsTOF Pro, Evosep One and MaxQuant

Day: Tuesday Breakfast

Speakers: Dr. Nicolai Bache, Head of Applications, Evosep, Denmark.
Prof. Jürgen Cox, PhD, Group Leader of the Computational Systems Biology group at the Max Planck Institute of Biochemistry, Martinsried, Germany.

Synopsis: With the trend toward clinical research and translational proteomics, the measurement of ever larger sample cohorts is needed for e.g. biomarker validation. Other emerging research areas, such as single cell proteomics, require running large numbers of samples. These trends place increasing demand on not just speed and sensitivity, of instrumentation, but also robustness and reproducibility. Since its introduction in 2017, the timsTOF Pro has proven to be not only an exceptionally fast and sensitive instrument for shotgun proteomics, but has also proven to have exceptional robustness. The combination of high sample throughput with robustness, and computational tools to get the most out of the acquired data, yields what we term "high productivity" proteomics.
In this workshop the combination of the Evosep One, a highly robust microflow LC system with the timsTOF Pro will be presented by Dr. Nicolai Bache of Evosep, with the title, "High productivity proteomics with the timsTOF Pro and Evosep One". Then Prof. Juergen Cox of the Max Planck Institute in Martinsried, Germany will present on recent developments for getting the most out of such data, with the title, "Unlocking the power of the fourth dimension: MaxQuant for timsTOF pro".

Topics: Trapped ion mobility coupled to a QTOF for shotgun proteomics. Robust LC operation at microflow rates using a combination of high flow sample preparation and injection, followed by microflow chromatography. Computational methods for efficiently analyzing 4-dimensonal shotgun proteomics.

Proudly sponsored by Bruker

Title: Adapting EasyPep™ MS Sample Preparation and TMT labeling for higher throughput and larger volume formats

Day: Tuesday Lunchtime

Speakers: Ryan Bomgarden, Sr. Staff Scientist (Thermo Fisher Scientific)

Synopsis:Advances in mass spectrometry (MS) instrumentation have enabled routine analysis of complex protein samples. However, sample preparation methods are not standardized with many protocols taking 8-24hrs in addition to suffering from low peptide yields, poor digestion efficiency and limited scalability. Recently, we developed a new, simplified sample prep kit containing pre-formulated reagents and a standardized protocol for processing 10µg to 100µg protein samples in less than 2 hours. In this study, we adapted our chemistry to use an automated liquid handling system for sample preparation, TMT labeling, and a 96-well filter plate for peptide clean up.

Topics:

  • Introduce a new, simplified sample prep kit containing pre-formulated reagents and a standardized protocol
  • Using an automated liquid handling system for sample preparation, TMT labeling, and a 96-well filter plate for peptide clean up

Proudly sponsored by Thermo Fisher Scientific 

Title: Integrative Structural Biology, The Next Frontier of MS-Based Proteomics

Day: Tuesday Lunchtime

Speakers: Ruedi Aebersold, Professor, Department of Biology, Institute of Molecular Systems Biology (University of Zurich)

Synopsis: To understand protein functioning in the cellular environment, it is essential that researchers determine protein complex assembly and structure beyond that of individual proteins. Solving the structure of large dynamic complexes often requires integrating several complementary mass spectrometry techniques—an approach known as integrative structural biology. Thermo Fisher Scientific leads the way in accelerating protein structure-function studies with its Integrative Structural Biology solutions. In this workshop, our expert speaker will share new approaches for structural proteomics workflows.

Topics:

  • To understand protein functioning in the cellular environment
  • Solving the structure of large dynamic complexes
  • Sharing new approaches for structural proteomics workflows

Proudly sponsored by Thermo Fisher Scientific 

Title: Driving personalized medicine through targeted protein biomarker discovery - taking proteomics beyond mass spectrometry

Day: Tuesday Lunchtime

Speakers: Professor Matthias Uhlén (Royal Institute of Technology, Stockholm). Other speakers to be confirmed.

Synopsis: As proteomics takes an increasingly central role in driving precision medicine forwards, many new technologies are coming through to complement mass spectrometry, and in some cases, broaden the possibilities for protein biomarkers in this area. Olink has developed one such enabling technology for protein biomarker discovery, providing high throughput, sensitive analysis of multiple proteins direct from very small volumes of plasma/serum without the need for further sample preparation. Olink technology has been used widely in both the pharma-biotech and clinical research sectors in Europe and the U.S., generating around 90 million protein measurements from over a million samples, and resulting in over 250 peer-reviewed publications. These studies cover many types of applications, from the search for novel drug targets, to protein profiles for patient stratification and risk assessment, as well as to gain invaluable pathophysiological insights across a broad range of disease areas. As Olink expands into the wider Asia region, we are delighted to arrange this workshop at HUPO 2019 in Australia, and to have the opportunity to present a few examples of the many successful protein biomarker studies that have been carried out to date in both wellness and disease. Please come and join the discussion.

Topics: Professor Uhlén will describe how he has utilized Olink protein analysis in a major longitudinal wellness study.

Proudly sponsored by Olink

Title: Clinical Research Applications of the timsTOF Pro

Day: Tuesday Lunchtime

Speakers: Catherine CL Wong, Ph. D., Director, Center for Precision Medicine Multi-omics Research, and Associate Professor, Health Science Center, Peking University, China.
Prof. Andrew Webb, Ph. D., Laboratory Head in the Advanced Technology and Biology Division of the Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.

Synopsis: The timsTOF Pro with PASEF was introduced as a shotgun proteomics solution at the International HUPO Congress in Dublin in 2017. The unique trapped ion mobility (TIMS) front end of the instrument enables usage of nearly 100% of the ions entering the instrument. This leads to superb sensitivity when combined with the time and space focusing provided by the TIMS device. When used with the PASEF scan method, very high MS/MS speeds >100 Hz also become routine. Since its introduction, the speed, sensitivity and robustness of the timsTOF Pro have proven attractive to researchers working in clinical proteomics research. After a brief introduction to the unique features of the timsTOF Pro with PASEF, by Dr. Gary Kruppa, Prof. Catherine Wong will present a talk on "Mapping the Q-glycoproteome Using the timsTOF Pro". Following this Prof. Andrew Webb will speak on, "High throughput Proteomics on the timsTOF Pro: Applications to clinical research and beyond".

Topics: Unique features and principles of operation of the timsTOF Pro with TIMS and PASEF. Clinical research proteomics applications of the timsTOF Pro. Glycoproteomics applications of the timsTOF Pro.

Proudly sponsored by Bruker

Title: HIGH-THROUGHPUT PROTEOMICS WITH EVOSEP ONE

Day: Wednesday Lunchtime

Speakers: Dr Nicolai Bache, Head of Application, Evosep

Synopsis: Evosep aims to improve quality of life and patient care by radically innovating protein based clinical diagnostics. Making sample preparation and separation before MS analysis 10 times faster and 100 times more robust will enable truly large cohort studies for biomarker validation and provide the foundation for precision medicine.

This will be highligthed in the talk: “Increasing throughput with DIA and diaPASEF: from pre-clinical models to protein complexes”

Topics: Clinical proteomics, large cohort studies, DIA, diaPASEF, protein complexes, high throughput, robust proteomics

Proudly sponsored by Evosep

Title: The Next Era in Pathway Proteomics – Towards Turnkey Targeted Quantitation Workflows

Day: Wednesday Lunchtime

Speakers: Emily Chen, Senior Director (Thermo Fisher Scientific)
Lauren Stopfer, PhD Student (Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology)

Synopsis: Accurate monitoring of cell signaling pathway proteins has proven challenging due to the low cellular abundance of these targets and lack of standardized targeted proteomic methodologies and reagents. In this workshop, our expert speakers will share the latest advances and newest technologies in targeted peptide quantitation and pathway analysis, including our panel of Thermo Scientific SureQuant multiplex immunoprecipitation targeted mass spectrometry kits. They will also introduce the novel SureQuant internal standard triggered parallel reaction monitoring (IS-PRM) methodology for more reproducible and sensitive quantitation on Thermo Scientific Orbitrap mass spectrometers.

Topics:

  • Sharing the latest advances and newest technologies in targeted peptide quantitation and pathway analysis
  • Panel of Thermo Scientific SureQuant multiplex immunoprecipitation targeted mass spectrometry kits
  • Introduce the novel SureQuant internal standard triggered parallel reaction monitoring (IS-PRM) methodology

Proudly sponsored by Thermo Fisher Scientific