HUPO 2024

4D-Proteomics™ Innovation: Multiomics in the post-genomic era

The timsTOF mass spectrometer portfolio continues to drive advancements in proteomic analysis. Leveraging cutting-edge technologies such as Trapped Ion Mobility Spectrometry (TIMS) and Parallel Accumulation Serial Fragmentation (PASEF), timsTOF instruments offer enhanced sensitivity, speed, and dynamic range for comprehensive proteomic characterization. Additionally, the integration of 4D-Proteomics™ methodologies further refines protein identification and quantification accuracy. Join us as we explore the transformative potential of timsTOF mass spectrometers in unraveling the complexities of the proteome across a variety of different applications.

10:30 - 11:00 Registration

11:00 - 11:10 What's new at Bruker
Daniel Hornburg, Ph.D., Vice President Biomarker and Precision Medicine, Bruker Scientific LLC, San Jose, CA, USA

11:10 - 11:35 Exploring the Sweet Side of Cells
Guinevere Lageveen-Kammeijer, Ph.D., Assistant Professor, Analytical Biochemistry Group of the Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Groningen, Netherlands

11:35 - 12:00 Precision Proteomics in human disease
Roman Fischer, Ph.D., Associate Professor and Head of Discovery Proteomics Facility, University of Oxford, Oxford, United Kingdom

12:00 - 12:30 Lunch break

12:30 - 12:55 Comprehensive phosphoproteome analysis using midia-PASEF
Stefan Tenzer, Ph.D., Professor for Immunoproteomics, Institute for Immunology, University Medical Center Mainz, Helmholtz Institute for Translational Oncology (HI-TRON) Mainz, Germany

12:55 - 13:20 Scalable and sensitive phosphoproteomics
Florian Meier-Rosar, Ph.D., Junior Professor, Functional Proteomics, Jena University Hospital, Jena, Germany

13:20 - 13:35 Detection of cytokines by g-DIA PASEF
Gunnar Dittmar, Professor, Ph.D., Dipl.-Ing., Luxembourg Institute of Health, Luxembourg

13:35 - 14:00 Single-cell and spatial proteomics workflows – pushing mass spectrometry acquisition for in-depth tissue mapping
Claudia Ctortecka, Ph.D., Post Doctoral Associate, Broad institute of MIT and Harvard, Cambridge, MA, USA

Unlocking High Sensitivity: Advancements in Single Cell Proteomics with the timsTOF Ecosystem

Join us for a scientifically engaging lunch seminar focused on the high sensitivity achieved with timsTOF technology, particularly in single cell proteomics. Christoph Krisp, Ph.D., will present the Bruker solution portfolio, showcasing how our advancements enable significant biological discoveries from minimal sample material. We'll explore two key concepts: discover how the group of Christine Carapito, Ph.D., Research Director at the LSMBO in Strasbourg, handles larger single cell cohorts as well as immunopeptides, and secondly, how Fabian Coscia, Ph.D., combines imaging techniques to select disease-relevant regions of interest, demonstrating the potential of spatial proteomics workflows. In the context of multiomics in the post-genomic era, learn how integrating imaging and proteomics leads to more informed decisions and deeper biological insights.

12:15 - 12:25 Where sensitivity matters - Ultra-high sensitivity Single Cell mass spectrometry on the timsTOF Ultra 2
Christoph Krisp, Ph.D., Application Development Scientist, Bruker Daltonics, Bremen, Germany

12:25 - 12:50 Spatially resolved tissue proteomics with single-cell sensitivity 
Fabian Coscia, Ph.D., Group Leader, Spatial Proteomics, Max Delbrück Center for Molecular Medicine, Berlin, Germany

12:50 - 13:00 timsTOF Ultra to explore where the very small matters very much: Immunopeptidomics and single cell proteomics explorations
Pauline Perdu-Alloy, Ph.D. Student, BioOrganic Mass Spectrometry Laboratory (LSMBO-IPHC), CNRS and University of Strasbourg, Strasbourg, France

Jeewan Babu Rijal, Post-doctoral fellow, BioOrganic Mass Spectrometry Laboratory, CNRS and University of Strasbourg, France

Maximize the Potential of Your Data: Scalable Bioinformatics to Access Meaningful Results

In the modern landscape of mass spectrometry proteomics, bioinformatics has become a cornerstone for generating, managing, and interpreting data efficiently and effectively. Our lunch seminar will delve into this critical aspect, showcasing how scalable bioinformatics solutions can prevent data analysis bottlenecks and ensure rapid, versatile results. Hear from our head of research for Bruker ProteoScape™ (BPS), Jonathan Krieger Ph.D., about our strategies to provide impactful solutions, followed by an insightful talk on rescoring MS2 data to maximize its value by members of the CompOmics group run by Prof. Lennart Martens at the University of Ghent. Finally, we will join Lukas Reiter, Ph.D., CTO at Biognosys, to discover the enhanced capabilities of Spectronaut 19, specifically optimized for timsTOF data, and see how it can elevate your proteomics research. 

Don't miss this opportunity to learn how advanced bioinformatics can influence your project's success.

12:00 - 12:10 Maximize the Potential of Your Data: Scalable Bioinformatics to Access Meaningful Results
Jonathan Krieger, Ph.D., Head of Research, Bruker ProteoScape, Bruker Daltonics, Toronto, Canada

12:10 - 12:35 From raw to refined: Always get more out of your data with TIMSRescore
Robbin Bouwmeester, Ph.D. Postdoctoral Researcher, Research Foundation - Flanders (FWO), Ghent, Belgium

Robbe Devreese, MSc, VIB-UGent Center for Medical Biotechnology & Department of Biomolecular Medicine, Ghent University, Ghent, Belgium

12:35 - 13:00 Advancing DIA data processing: pushing the boundaries and tackling current field challenges
Lukas Reiter, Ph.D., Chief Technology Officer (CTO), Biognosys, Zurich, Switzerland

diaPASEF^® analysis with Spectronaut^® in a Linux High Performance Computing Environment – Experience and Applications 

With the advent of high throughput data acquisition methods producing increasing complex and high dimensional data in proteomics we now face the challenge of increasing data volume and analysis needs. Many academic labs have access to high performance computing (HPC) capabilities via their university or via national facilities that could increase their data processing potential. However, these facilities generally run Linux operating systems with job scheduling and are therefore less accessible for some analysis pipelines. Recently Linux support has been introduced in Spectronaut enabling the possibility of running on Linux-based HPC environments. 

Our lab has recently established a pipeline for the analysis of diaPASEF^® data at scale with Spectronaut using the Northern Ireland High Performance Computing Centre hosted at Queen’s University Belfast. The workflow leverages Spectronaut’s capability to store results in saved experiment files (.SNE) such that computationally intensive signal processing steps are carried out on the compute cluster, but data visualization and post-processing can be performed on local machines in the Spectronaut GUI environment.

In this talk I aim to first describe our experience with this mode of data analysis and, second, to describe some applications in the space of quantitative interaction proteomics and/or targeted protein degradation.

Ben Collins
Professor, School of Biological Sciences, Queen’s University Belfast, Belfast, UK

Advanced Multiplex DIA: Quantifying Protein Turnover Impacted by Gene Copy Number Alterations

In this presentation, we will discuss the experimental and bioinformatic advancements of a multiplex DIA-MS workflow. This new workflow leverages a false discovery rate (FDR) control algorithm with various options supported by the latest version of Spectronaut^®, including channel-specific FDR and deep-learning-based selection of heavy and light transitions.

We will show the extensive validation of this enhanced multiplex workflow for dynamic or pulse SILAC experiments, designed to determine proteome-wide turnover rates. We will demonstrate how different Spectronaut options influence experimental performance and how this workflow reveals selective protein turnover in response to genome/gene dosage imbalances that are relevant to genetic syndromes and cancer drug resistance.

Yansheng Liu
Ph.D., Associate Professor, Department of Pharmacology and Department of Biomedical Informatics and Data Science, Yale University School of Medicine, New Haven, CT, USA

iST-automation goes 96! PreOmics launches the Automated Protein Prep 96 (APP96) at HUPO World 2024 in Dresden.

The APP96 is a compact and easy-to-set-up automation platform for proteomics sample preparation. It features a unique in-tip stationary phase-based workflow, eliminating the need for large centrifuges and complex pressure systems. Working on a 96-well plate format, the APP96 enables iST-based automated processing of up to 96 samples per day or overnight. Experience high-quality, reliable LC-MS sample preparation processing for large sample sets with confidence.

Want to have an exclusive look at the APP96? Then join the PreOmics booth #6 or visit their HUPO World 2024 information page.

Come and visit us at booth No. 5 in the exhibition and get the chance to talk to our experts. Also our partners Biognosys No. 7 and PreOmics No. 6 will be with us.