Industry Supported Seminars
Industry Supported Seminars
The following industry-supported seminars are organized by sponsors of HUPO 2022.
ISS01
Time: 8:00 – 9:00 EST
Room: Gran Cancun 4
Title: Spectronaut® 17: A Groundbreaking Increase in Identifications
Description:
The application of DIA to proteomics has made some extraordinary improvements over the past decade. From the start, Biognosys’ Spectronaut® software has been the gold standard for DIA analysis with numerous improvements throughout the years. None have been as significant as the changes Spectronaut 17 introduces. With the addition of directDIA+, Spectronaut goes beyond what any other DIA analysis software has done before.
During this seminar, you will learn what makes Spectronaut 17 our most groundbreaking release yet. First, Lukas Reiter, Biognosys’ CTO, will introduce directDIA+, what it means for your DIA analysis, and how you can apply it. Then, Jesper Olsen (University of Copenhagen) will present how this new way of processing DIA data enables his team to go significantly deeper into the proteome without the need for a library.
Register here to join us for this exciting seminar: https://survey.biognosys.com/zs/xBRkYY
Speakers
Lukas Reiter, Biognosys
Jesper Olsen, University of Copenhagen
ISS02
Time: 8:00 – 9:00 EST
Room: Gran Cancun 5
Title: Advancing the understanding of the Human Proteome and Immunopeptidome using the latest mass spectrometry technology and PEAKS software
Description: To advance discovery in proteomics and subfields like, immunopeptidomics, we need to harness the latest mass spectrometry technology with advanced data analysis solutions. With the accuracy, sensitivity, and speed of new mass spec instruments, it is pertinent to develop software that is robust, easy to use, high throughput, and can truly take advantage of these new technologies. At BSI, we embrace this mission and continue our efforts by developing the latest data analysis software for discovery proteomics. Here at HUPO 2022, we are proud to announce new versions of PEAKS Studio and PEAKS Online and have two PEAKS users share how they use the software for their research.
For our Industry Sponsored Seminar, we are happy to have Dr. Cristina C Clement, Assistant Professor of Research at Weill Cornell Medicine and Dr. Mayank Srivastava Scientist, Proteomics and Immunopeptidomics at Regeneron share some of their work. Lastly, we have our BSI Applications Manager, Dr. Kyle Hoffman, present our latest workflow, DeepNovo Peptidome, a deep learning-based workflow in PEAKS Online to increase the sensitivity and accuracy of peptide identification.
Speakers
Cristina C Clement, PhD, Assistant Professor of Research, Radiation/Oncology Department, Weill Cornell Medicine
Title: Exploring the proteomes and immunopeptidomes of dendritic cells under physiologically healthy and redox stress mediated metabolic syndrome
Mayank Srivastava, PhD, Scientist, Proteomics and Immunopeptidomics, Regeneron Pharmaceuticals Inc.
Title: Proteogenomic Identification of Hepatitis B virus (HBV) genotype-specific HLA-I restricted peptides from HBV-positive patient liver tissues
Kyle Hoffman, PhD, Applications Manager, Bioinformatics Solutions Inc.
Title: DeepNovo Peptidome: Deep learning-based workflow to increase the sensitivity and accuracy of peptide identification
ISS04
Time: 13:15 – 14:15 EST
Room: Grand Cancun 5
Title: Toward causality in clinical proteomics: advantages and challenges of highly specific tools
Description:
Remarkable advancements in high-plex technology have recently brought proteomics to the forefront for both clinical care and research applications in precision medicine. While this exciting progress has made large-scale population profiling a reality for further development and implementation in clinical contexts, many challenges remain to establish utility of proteomics-based tools in disease treatment and prevention, including for diagnostic, predictive, and prognostic purposes. In this session, leaders from across clinical proteomics fields will share their diverse experiences over the last several years in selecting and utilizing suitable methods that can not only define molecular mechanisms and physiological pathways associated with health and disease states, but also robustly identify protein signatures that accurately and reproducibly reflect clinical phenotypes and predict outcomes. Important factors emerging from previous work in clinical populations related to study design, breadth of platform coverage and sensitivity to protein structure, complementarity of mass spectrometry and affinity-based methods, and analytical and pipeline considerations for model development and validation will also be discussed.
You will learn about:
High-plex proteomics methods used for translational applications in large clinical populations and complementarity with other approaches
Statistical and machine learning approaches for developing protein models that reflect clinical phenotypes to predict outcomes and risk-stratify populations
Moderator: Stephen Williams, MD, PhD – SomaLogic
Speakers:
– Russell Bowler, MD, PhD, Professor of Medicine, National Jewish Health
– Julián Candia, PhD, Staff Scientist, Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health
– Claudia Langenberg, MD, PhD, Professor, Berlin Institute of Health at Charité
– Towia Libermann, PhD, Associate Professor of Medicine, Beth Israel Deaconess Medical Center
ISS05
Time: 13:15 – 14:15 EST
Room: Gran Cancun 4
Title: Increasing sensitivity and speed for the detection of immunopeptide using the timsTOF platform
Moderator: Gary Kruppa, Ph. D., Senior Vice President Strategic Collaborations, Bruker Daltonics
Program
1:15 – 1:20 – Introduction, Gary Kruppa
1:20-1:35 – In-depth sequencing of cancer immunopeptidomes on the Bruker SCP platform enables the discovery of viral antigens in HPV-driven cancer
Prof. Nicola Ternette, University of Oxford
1:35-1:50 – Optimizing deep coverage and high sensitivity immunopeptidomic workflows on the timsTOF Pro2 and SCP platforms
Prof. Stefan Tenzer, W3 Professor for Immunoproteomics, Institute for Immunology, University Medical Center Mainz and Helmholtz Institute for Translational Oncology (HI-TRON) Mainz
Description: 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 – Exploiting trapped ion mobility and PASEF to gain deeper insights into antigen presentation in clinical samples.
Prof Tony Purcell, Monash University, Australia
Description: 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 – Panel Q&A and discussion
ISS06
Time: 13:15 – 14:15 EST
Room: Cozumel
Title: Next generation pan-cancer blood proteome profiling using proximity extension assay
Description: Cancer is a highly heterogeneous disease in need of accurate and non-invasive diagnostic tools. Here, we describe a novel strategy to explore the proteome signature by comprehensive analysis of protein levels using a pan-cancer approach of patients representing the major cancer types. Plasma profiles of 1,463 proteins from more than 1,500 cancer patients representing altogether 12 common cancer types were measured in minute amounts of blood plasma collected at the time of diagnosis and before treatment. AI-based disease prediction models allowed for the identification of a set of proteins associated with each of the analyzed cancers. By combining the results from all cancer types, a panel of proteins suitable for the identification of all individual cancer types was defined. The results are presented in a new open access Human Disease Blood Atlas. The implication for cancer precision medicine of next generation plasma profiling is discussed.
Speaker: Matthias Uhlén, PhD, Professor of Microbiology, Royal Institute of Technology (KTH), Stockholm
Mathias Uhlen focuses on protein science and precision medicine which ranges from basic research to more applied research, including clinical applications in cancer, infectious diseases, cardiovascular diseases, autoimmune diseases and neurobiology. He leads an international effort to systematically map the human proteome creating an open access resource, the Human Protein Atlas (www.proteinatlas.org), with more than 15 million web pages and 10 million annotated bioimages. This resource is now one of the most visited life science databases in the world. His research has resulted in more than 750 publications with more than 80,000 citations and an h-index of 130 (Google Scholar). He is co-founder of 20 biotech companies of which four are publicly traded. He is member of the National Academy of Engineering (NAE) in USA, the Royal Swedish Academy of Science (KVA), the Swedish Academy of Engineering Science (IVA) and the European Molecular Biology Organization (EMBO). He was the Founding Director of the Science for Life Laboratory (SciLifeLab), a Swedish national center for molecular bioscience.
ISS07
Time: 8:00 – 9:00 EST
Room: Gran Cancun 5
Title: Extraordinary Science: Harnessing Novel Workflows in the Pursuit of Advancing Life Science Research
Description:
Please register so that we may provide you breakfast
The evolution of mass spectrometry and rapid enhancements in accurate mass technology have allowed the life sciences field to accomplish remarkable research and enable new workflows previously never thought possible. Join us for breakfast on Tuesday, December 6th to learn about exciting innovations in proteomics. Our esteemed panel of guest speakers will share their latest work and how novel workflows enabled by SCIEX technologies are being used in fields like single cell, biomarker discovery, immunopeptidomics, and high throughput proteomics!
Learn about novel innovations in accurate mass analysis delivering both speed and accuracy for large-scale proteomics
Hear about the development of a standardized platform for robust, in-depth high-throughput proteome analysis
Discover the impact of sensitivity gains on the identification and quantification of proteins and peptides
Featured presenters and presentations:
Benjamin C. Orsburn, PhD, Johns Hopkins University School of Medicine
Democratizing single cell proteomics with low-volume suspension trapping, microflow chromatography and time of flight mass spectrometry
Prof. Anthony Purcell, PhD, Monash University
Zeno SWATH DIA and the hunt for cancer antigens on “Ziggy” the ZenoTOF 7600 system
Hugo Gagnon, PhD, PhenoSwitch Bioscience and Allumiqs
High-throughput proteomics in drug development using Zeno SWATH DIA
Dorte Bekker Jensen, PhD, Evosep
Rapid and robust proteomes with standardized methods on the Evosep One powered by Zeno SWATH DIA
ISS08
Time: 8:00 – 9:00 EST
Room: Cozumel
Title: Next Generation of Absolute Protein Quantitation in Biological Matrixes using MRM; faster and higher multiplexed while robust and sensitive
More details coming soon
ISS09
Time: 8:00 – 9:00 EST
Room: Gran Cancun 4
Title: Increasing throughput in proteomics with the high speed and highly robust timsTOF platform
Moderator: Chris Adams, Ph.D., Director of Bioinformatics, Bruker Daltonics Inc.
Program
8:00-8:15 Introduction, PaSER and bioinformatics approaches to real-time processing of large datasets and intelligent acquisition
Chris Adams, Director of Bioinformatics, Bruker Daltonics Inc.
8:15-8:35 Speeding up proteomics using a micro-flow timsTOF HT setup.
Dr. Joanna Tueshaus, TUM School of Life Sciences, Technische Universität München.
Description: 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 Scaling up while Scaling down: Combining High-throughput and Sample-sparing Proteomics Methods.
Prof. Hanno Steen, Associate Professor of Pathology, Harvard Medical School and Director of Proteomics, Boston Children’s Hospital
Description: 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.
ISS10
Time: 13:15 – 14:15 EST
Room: Gran Cancun 4
Title: Unleashing Single Molecule Proteomics at Scale
Agenda:
Incremental and disruptive advances in proteomics
Ruedi Aebersold, PhD, Professor of Systems Biology, Institute of Molecular Systems Biology in ETH Zurich (IMSB)
Comprehensive single-molecule proteomics using Protein Identification by Short-epitope Mapping
Parag Mallick, PhD, Founder and Chief Scientist, Nautilus Biotechnology
Progress toward the analysis of PARP1 protein variants at single-molecule sensitivity
Philip Lorenzi, PhD, Associate Professor, MD Anderson Cancer Center
ISS11
Time: 13:15 – 14:15 EST
Room: Cozumel
Title: Next Generation Proteomics: the future of plasma biomarker discovery with the Proteograph™ Product Suite
Program
Unlocking a New Dimension in Plasma Proteomics Biomarker Discovery with Deep Unbiased Proteomics at Scale
Bruce Wilcox, Ph.D, VP of Proteomics, PrognomiQ Inc.
Evaluation of the Proteograph Product Suite for Analysis of Plateletrich Plasma (PRP); Hidden Gem for Biomarker Discovery
Hugo Gagnon, Ph.D., CSO, PhenoSwitch Bioscience, A division of Allumiqs
A Highly Scaled Proteomic Discovery Study for Prostate Cancer Diagnostic Signatures Using Proteograph Technology with Trapped Ion Mobility Mass Spectrometry
Mark R. Flory, Ph.D, Knight Cancer Institute, CEDAR Center, Oregon Health and Science University
ISS12
Time: 13:15 – 14:15 EST
Room: Gran Cancun 5
Title: Beyond ID – Why High Precision and Accuracy for Quantitative Proteomics is Needed for Biological Insights
Description: There have been significant advances in MS- based protein identifications resulting in the profiling of thousands of proteins from a sample per run. However, a complete picture of biology can only be gained through quantitative proteomics, by having more in-depth level of protein intensities, it’s possible to gain more comprehensive studies of networks and cellular processes.
With several techniques available for quantitative proteomics, this workshop will briefly describe the attributes of “high quality quantitation” with examples of how these techniques are chosen to answer that biological question.
Speakers:
Lilian Heil, University of Washington
Jesper Olsen, Novo Nordisk Foundation Center for Protein Research
ISS13
Time: 18:15 – 19:15 EST
Room: Gran Cancun 4
Title: Recent Advances in Glycoproteomics
Speakers:
Albert Heck, University of Utrecht – The uniqueness of our glycoproteome; insights from high resolution native mass spectrometry
Stacy Malaker, Yale University – Mucinomics as the next frontier of mass spectrometry
Karen Abbott, Florida Intnl University – The Impact of Notch Glycosylation on Ovarian Cancer Growth
Nicki Packer, Macquarie University – Are we there yet? – glycoproteomics analysis of complex samples
ISS14
Time: 18:15 – 19:15 EST
Room: Gran Cancún 5
Title: The Proteomics of Aging: Drug Discovery
Small molecule discovery has found a new home in human proteomics. A two year Big Data study of the proteomics of aging compared to the proteomics of youth yielded a human peptide that would be a potential super drug for infectious disease – but it was unstable due to protease degradation in vivo. Maxwell used a patented stabilization technology to synthesize flexible small molecules that mimic the never before mimicked functions of peptides. Come learn how the future of small molecule discovery has found a new home in human proteomics.
ISS15
Time: 8:00 – 9:00 EST
Room: Gran Cancun 4
Title: En Route to Confident Results – One Plate Sample Preparation of Proteins from Complex Biological Matrices
Description:
Understanding the complex role that the proteome plays in different diseases is paramount to the development of next generation treatment modalities and being able to accurately monitor protein biomarkers is essential for patient care. Large scale application of proteomics in clinical research and testing requires robust, reproducible, and fast sample preparation methods that result in high quality purified protein samples.
While the end-detection analytical tools (such as liquid chromatography (LC) coupled to Mass Spectrometry (MS)) have undergone significant advancements in the last decade and half, technology involved in the preparation of samples compatible with these instruments has not experienced the same progress. Adaptive Focused Acoustics® (AFA®) Technology has been the gold standard for DNA shearing in almost every Next Generation Sequencing (NGS) laboratory and is now gaining unprecedented popularity as the sample preparation technology for a host of Proteomics and protein analysis workflow.
This workshop will highlight the application of AFA to clinical proteomics sample preparation workflows resulting in robust, fast, scalable, high throughput extraction of protein from complex biological matrices including FFPE tissue and fresh cells. A scalable FFPE sample preparation method utilized for a targeted assay for the relative quantitation of immunoglobulins in FFPE bone marrow biopsies will be discussed. Additionally, a workflow developed for the lysis of fresh white blood cells, extraction of protein, and rapid digestion will be shown. The workflows discussed can be easily implemented to enhance reproducibility of sample preparation for LC-MS analysis. This in turn significantly decreases turnaround time of results. In addition, AFA based workflows can be used for supporting high throughput automatable pre-analytical processes.
Confident results depend upon reliable sample preparation processes whether the goal is to better understand signaling pathways in model systems or determining pharmacokinetic and pharmacodynamic properties of a biotherapeutic. The presentations in this workshop will demonstrate the capabilities of AFA for development of robust, reliable, and confident workflows for protein extraction and LC-MS compatible sample preparation from complex biological matrices.
Speakers:
– Deb Bhattacharyya, PhD, Covaris, LLC, Woburn, MA, US
– Jessica R Chapman, PhD, Memorial Sloan Kettering Cancer Center
ISS18
Time: 13:15 – 14:15 EST
Room: Gran Cancun 5
Title: Single Cell Proteomics for Biological Insights – Going beyond one cell at a time for high throughput with no compromise
Description: Gaining comprehensive biological insights requires the ability to analyze a statistically significant number of cells. This means optimizing each step of the single cell proteomics workflow for throughput, and sensitivity for maximum identifications and quantification.
This workshop will focus on sample preparation from cell sorting to multiplexed single cell digestion and labeling that enable running hundreds of cells per day with quantitative data, leading to real impactful biological insights across life science research. We will also discuss future developments in advanced chromatography and separations that deliver high quality and high sensitivity for single cell proteomics
Speakers:
Anjali Seth, Cellenion
Ryan Kelly, Brigham Young University