HUPO

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., 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

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.