HUPO

December 4 - 8, 2022

Cancun, Mexico

Introduction

Introduction

Join us at HUPO in Cancun at the Cancun Convention Center from December 4 - 8 and listen to our two seminars about the timsTOF platform. Our Monday lunch seminar covers the detection of immunopeptides and our Tuesday breakfast seminar is about increasing throughput in proteomics. Both seminars will be held in Gran Cancun 4 room.

 

Don't forget to come by our Booth #401.

Monday Lunch Seminar

Increasing sensitivity and speed for the detection of immunopeptides using the timsTOF platform
Monday, December 5, 2022, 1:15 - 2:15 pm

1:15 - 1:20 pm Introduction
Gary Kruppa, Ph.D., Senior Vice President Strategic Collaborations, Bruker Daltonics

1:20 - 1:35 pm In-depth sequencing of cancer immunopeptidomes on the Bruker SCP platform enables the discovery of viral antigens in HPV-driven cancer
Prof. Nicola Ternette, Ph.D., Associate Professor Antigen Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom

1:35 - 1:50 pm Optimizing deep coverage and high sensitivity immunopeptidomic workflows on the TimsTOF Pro2 and SCP platforms
Prof. Stefan Tenzer​, Ph.D., W3 Professor for Immunoproteomics, Head of Mass Spectrometry Core Facility, University Medical Center and Helmholtz Institute for Translational Oncology (HI-TRON) Mainz, Germany

Abstract: Mass spectrometry (MS)-based immunopeptidomics,  the analysis of the major-histocompatibility complex (MHC) associated peptide (MAP) ligand repertoire, has become an integral part of personalized immunotherapy research. We systematically optimized DDA and novel DIA acquisition methods for reproducibility and immunopeptidome coverage. Notably, the increased sensitivity of the timsTOF SCP instrument platform resulted in more than 2.5-fold higher peptide numbers for 8-12-mers and 1.9-fold higher number of proteins covered compared to the timsTOF Pro2, enabling deeper immunopeptidomic analyses. Our fully optimized method allowed the identification of approx.10,000 peptides from an equivalent of less than 7 million cells of which more than 85% were predicted to bind human MHC class I with low- or high-affinity.

1:50-2:05 pm Exploiting trapped ion mobility and PASEF to gain deeper insights into antigen presentation in clinical samples
Prof. Tony Purcell, Ph.D., Biochemistry & Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia

Abstract: The analysis of clinical biopsies on the timsTOF Pro 2 has provided unprecedented depth for immunopeptidomics studies across a range of indications including duodenal biopsies from celiac disease patients and tumour biopsies. I will showcase some examples of how workflows on this instrument are advancing translational research at the Monash Biomedicine Discovery Institute. 

2:05-2:15 pm Panel Q&A and discussion

Gary Kruppa, Ph.D., Senior Vice President Strategic Collaborations, Bruker Daltonics

Prof. Nicola Ternette, Ph.D., Associate Professor Antigen Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom

Prof. Stefan Tenzer​, Ph.D., W3 Professor for Immunoproteomics, Head of Mass Spectrometry Core Facility, University Medical Center and Helmholtz Institute for Translational Oncology (HI-TRON) Mainz, Germany

Prof. Tony Purcell, Ph.D., Biochemistry & Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia

Tuesday Breakfast Seminar

Increasing throughput in proteomics with the high speed and highly robust timsTOF platform
Tuesday, December 6, 2022, 8:00 - 9:00 am

8:00 - 8:15 am Introduction, PaSER and bioinformatics approaches to real-time processing of large datasets and intelligent acquisition
Chris Adams​, Ph.D., Business Development Director, Global Bioinformatics, Life Science Mass Spectrometry, Bruker Daltonics, USA

8:15 - 8:35 am Speeding up proteomics using a micro-flow timsTOF HT setup
Johanna Tueshaus, Ph.D., Postdoc, Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technische Universität München, Munich, Germany

Abstract: Deep proteomic profiling of FFPE brain tissue using a highly powerful combination of micro-flow LC with a timsTOF HT setup

8:35 - 8:55 am Scaling up while Scaling down: Combining High-throughput and Sample-sparing Proteomics Methods
Prof. Hanno Steen, Ph.D., Associate Professor of Pathology, Harvard Medical School, Director of the Proteomics Center, Boston Children’s Hospital, Boston, MA, USA 

Abstract: Meaningful biomarker studies that account for genetic, environmental and lifestyle variation require large cohorts – too large for the current proteomics platforms. Our recent involvement in NIAID-funded immunophenotyping studies on understanding COVID-19’s impact on the immune system and the efficacy of vaccination required the analysis of thousands of plasma samples, highlighted the importance of increasing throughput while simultaneously decreasing the sample volumes. To this end, the Steen Lab has been developing a high throughput proteomics platform that allows for the robust processing and analysis of such large numbers of a wide range of body fluid samples bringing us closer to truly personalized medicine.

Chris Adams​, Ph.D., Business Development Director, Global Bioinformatics, Life Science Mass Spectrometry, Bruker Daltonics, USA

Johanna Tueshaus, Ph.D., Postdoc, Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technische Universität München, Munich, Germany

Prof. Hanno Steen, Ph.D., Associate Professor of Pathology, Harvard Medical School, Director of the Proteomics Center, Boston Children’s Hospital, Boston, MA, USA 

Hanno Steen, Ph.D., is an Associate Professor of Pathology at Harvard Medical School, Principal Investigator in the Department of Pathology at Boston Children’s Hospital (BCH) and its Director of Proteomics. He is a member of the Neurobiology Program at BCH, the Precision Vaccines Program at BCH, the NIAID-funded Human Immunology Project Consortium (HIPC), the NCI/NIDDK-funded Consortium for the Study of Chronic Pancreatitis, Diabetes, and Pancreatic Cancer (CPDPC) and the NIAID-funded Immunophenotyping Assessment in a Covid-19 Cohort (IMPACC). After studying chemistry in Freiburg/Germany, Manchester/UK (UMIST) and Zurich/Switzerland (ETH), he received his Ph.D. from the University of Southern Denmark (Odense/Denmark) under the supervision of Dr. Matthias Mann. After postdoctoral training in proteomics and quantitative biology in the laboratories of Drs. Steve Gygi and Marc Kirschner at Harvard Medical School, he joined the faculty at BCH in 2004. At BCH, he established a state-of-the-art proteomics laboratory dedicated to developing and applying quantitative proteomics methods to identify disease-relevant biomarkers in primary human specimens. His laboratory is currently focused on developing high-throughput and sample proteomics methods for detecting biomarkers in small amounts of systemic body fluids such as urine or blood for various inflammatory, infectious and neurodegenerative diseases. He has published more than 170 papers in international peer-reviewed journals which have been cited more than 23,000 times.

 

For Research Use Only. Not for use in clinical diagnostic procedures.