CONFIRMED SPONSORS & VIRTUAL SEMINARS

Chair: Aaron Gajadhar, Strategic Marketing Specialist, Thermo Fisher Scientific

Speakers:

• Ryan Bomgarden, Ph.D., Sr. Staff Scientist, Team Leader (Mass Spectrometry Reagents), Thermo Fisher Scientific
• Lars Plate, Assistant Professor of Chemistry and Biological Sciences, Vanderbilt University

1. Providing COVID-19 Clarity Using TMT Reagents for Precision Measurements (Ryan Bomgarden)

   This seminar will highlight recent advances in TMT reagent workflows and their use in recent applications to measure SARS-CoV-2 viral particle expression over time, changes in host cell signaling upon infection, differences in immune responses of mild COVID-19 versus severe cases, and identify potential drug targets and off-targets.

2. TMT-Based Comparative Interactomics of SARS-CoV-2 and Coronavirus Non-Structural Protein Homologs to Identify Shared and Unique Host-Cell Dependencies (Lars Plate)

   Human coronaviruses (hCoV) are an increasing global health threat, as evident by the 2002 SARS epidemic caused by SARS-CoV-1, the 2012 MERS outbreak, and the ongoing COVID-19 pandemic caused by SARS-CoV-2. Despite high protein sequence similarity between SARS-CoV-1 and -2, each strain displays distinctive virulence. A better understanding of the basic molecular mechanisms mediating changes in pathogenicity of different hCoV strains is needed to develop antiviral therapeutics. Here, we profile the virus-host protein-protein interactions of several hCoV non-structural proteins (nsps) that are critical for virus replication. We use tandem mass tag (TMT)-multiplexed quantitative proteomics to sensitively compare and contrast the interactome of nsp2 and nsp4 from three betacoronavirus strains: SARS-CoV-1, SARS-CoV-2, as well as OC43 – a less pathogenic endemic strain associated with the common cold.

For more information, click HERE.

Chair: Stina Lundgren, Pelago Bioscience

Speaker: Tomas Friman, Senior Research Scientist, Pelago Bioscience

CETSA® MS allows for proteome-wide measurement of cellular target engagement using mass spectrometry by generating thermal profiles for 6000−7000 proteins in a single experiment. In contrast to conventional proteomics applications, CETSA MS measures the direct consequences of a drug on both its intended and off targets, as well as the immediate signaling cascade perturbed by the addition of a compound. This assay is free of labels and can be carried out in the live unmodified cells, thereby enabling the discovery of protein targets and pathways that would otherwise not be identified using traditional methods. Further, machine learning algorithms allows for exploration of global patterns and differences as well as extraction of differential proteins or groups of proteins to explore and compare the molecular mode of action of the profiled compounds. Welcome to learn about the CETSA methodology and how the mass spectrometric readout can be used for drug profiling, target deconvolution, biomarker discovery and toxicology safety assessment studies.

Chair: Gary Kruppa, Bruker Daltonics

Speakers:

• Prof. John R. Yates, The Scripps Research Institute, Departments of Molecular Medicine and Neurobiology
• Prof. Gunnar Dittmar, Proteomics of cellular signalling, Luxembourg Institute of Health and Dept. of Life Science and Medicine, University of Luxembourg

1. The Synergies of Mass Spectrometry and Informatics (Prof. John R. Yates)

   Mass spectrometry has always had a powerful synergy with computers. Computers have pushed mass spectrometry forward at key junctures in it’s history from data collection to instrument operation to data analysis. Proteomics was enabled by both tandem mass spectrometry and informatics to rapidly assign amino acid sequences to spectra. As instrumentation has become more powerful informatic capabilities have grown to keep pace with increases in data production and data types. Sophisticated workflows are used to process proteomic experiments that encompass search, quantitation, and statistical processing of data. As new features are added to mass spectrometers like ion mobility this provides additional capability for collecting data and information for interpreting peptides and peptide features. IP2 is a proteomic platform that creates a workflow combining GPU powered search, flexible quantitation, and statistical analysis of data.

2. New prm-PASEF® Method for Highly Multiplexed Targeted Quantitative Proteomics for Clinical Research (Prof. Gunnar Dittmar)

   We developed a prm-PASEF® targeted acquisition method that fully exploits the multiplexing capability of the TIMS-TOF, allowing multiple peptides to be sequentially measured from a single ion mobility scan with no sensitivity loss. We evaluated the performance of this prm-PASEF® method using AQUA peptides spiked in a Hela cell lysate sample. In this update we will discuss the latest developments and results from the prm-PASEF® method in our labs.

For more information and to pre-register, click HERE (note, you will still need to register for HUPO Connect 2020).

Chair: Lukas Reiter, PhD, Biognosys

Speakers:

• Mikhail Savitski, PhD, European Molecular Biology Laboratory
• Erwin Schoof, PhD, Technical University of Denmark

1. Multiplexed Proteomics for Understanding Molecular Biology (Mikhail Savitski)

   An application of multiplexed proteomics for investigating molecular biology will be presented. In particular, examples of how thermal proteome profiling can provide insights into the functional aspects of the proteome will be discussed. The seminar will highlight the benefit of using SpectroMine for these types of experiments.

2. Characterizing Cellular Hierarchies Using Quantitative Single-Cell Proteomics (Erwin Schoof )

   A single-cell proteomics strategy was used to investigate the characteristics of individual cells in acute myeloid leukemia (AML). Taking advantage of the latest advancements in LC-MS instrumentation and data acquisition, the new TMTPro reagents, and SpectroMine 2.0, an unprecedented map of protein expression was built-in individual AML cells. Furthermore, a computational pipeline (SCeptre) was built that effectively processes single-cell proteomics data and permits the extraction of cell-specific proteins. Strong enrichment of stem cell-specific proteins was found in the LSC and progenitor compartments, and protein expression signatures were identified that clearly distinguish cell differentiation stages. This work lays a solid foundation for implementing global single-cell proteomics studies in proteomics labs across the world.

For more information, click HERE.

Chair: Arianna Jones, Global Marketing Manager, Life Science Research, SCIEX

Speakers: 

• Christie Hunter, PhD, Director, SCIEX
• David Boocock, PhD, Nottingham Trent University

The p53 protein is mutated in about 50% of human cancers. The mutant p53 proteins not only lose their normal function but often acquire novel oncogenic functions, a phenomenon termed mutant p53 gain-of-function (GOF). Mutant p53 has been shown to affect the transcription of various genes, as well as by protein–protein interactions with transcription factors and other effectors, however no one has investigated which of these proteins has the potential for being targeted by immunotherapeutic interventions. We therefore investigated the changes occurring after the p53 Null SaOS-2 cells were transfected by conformational p53-mutants R-273 and R-175, examined phenotypic and functional differences using macroscopic observations, proliferation, overall mRNA and proteomic changes alongside immunopeptidome profiling of peptide antigens bound to molecules encoded by the major histocompatibility complex (MHC) and presented on the cell surface. Expression profiling using gene expression microarray, qRT-PCR, and quantitative proteomic mass spectrometry, were employed to identify proteins whose peptide repertoire may be targeted by future immunotherapy/vaccine. The phenotype of SaOS-2-273 and SaOS-175 cells were assessed using colony formation, and proliferation assays. Using OneOmics™ Suite in SCIEX cloud, we identified several candidate markers in both p53 mutant cell lines with differential gene and protein expression from the p53 null control. Cross-comparison with the MHC bound peptides further identified potential targets.