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19th Human Proteome Organization World Congress

  • About
    • Welcome Message
    • About the Human Proteome Organization
    • HUPO Virtual Organizing Committee
    • HUPO Awards
    • Early Career Researchers
    • Pre-Congress Webinar Series
      • July Pre-Congress Webinar: Impact of Proteomics on COVID
      • August Pre-Congress Webinar: Impact of Proteomics on Precision Medicine
      • September Pre-Congress Webinar: New Innovations in Proteomics
    • Bruker’s User Meeting at HUPO Connect
    • Contact Us
  • Registration
    • On-Demand Webinar Registration
    • Main Congress Registration
  • HUPO Connect 2020
    • Scientific Program
      • Pre-Congress Training
      • Bioinformatics Hub
      • Main Program
    • ECR Manuscript Competition
    • HUPO PhD Poster Competition
    • Meet the Speakers
    • Abstracts
    • Virtual Congress FAQs
  • Sponsorship
    • Sponsorship Opportunities
    • Confirmed Sponsors & Virtual Seminars
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HUPO Connect 2020 would like to thank the following companies for their support:

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Virtual Seminars during HUPO Connect 2020

 

Monday, October 19
15:15-16:00 UTC
Accelerating COVID Proteomics Research Using Tandem Mass Tags

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.

Monday, October 19
15:15-16:00 UTC
Explore the Proteome Using CETSA MS

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.

Tuesday, October 20
15:15-16:00 UTC
Advance in 4D-Proteomics™: Bioinformatics and prm-PASEF®

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).

Wednesday, October 21
15:15-16:00 UTC
Exploring Multiplexed Proteomics in Complex Applications with SpectroMine

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.

Wednesday, October 21
15:15-16:00 UTC
Multi-omic Analysis of Two Common p53 Mutations: Proteins Regulated by Mutated p53 as Potential Targets for Immunotherapy

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.

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Virtual Seminars Available on Demand

  • Biognosys
    Raising Standards for DDA Data Analysis with SpectroMine 2
    Chair: Maximilian J. Helf, PhD, Biognosys
    Speakers: Lynn Verbeke, MSc, Biognosys and Fabia Simona, PhD, Biognosys
    SpectoMine 2 integrates the state-of-the-art Pulsar search engine, now offering full support for ion mobility technologies (e.g., FAIMS and PASEF) and achieving more identifications thanks to deep learning augmentation. In this seminar, you will receive insights into how the software works internally, and how you can easily analyze ILQ data (e.g. TMTpro) with SpectroMine 2.
     
  • Bioinformatics Solutions Inc. (BSI)
    High-Throughput Immunopeptidomics: Discovery and Validation
    Chair: Katherine Tran, Bioinformatics Solutions Inc.
    Speakers: Robert Salzler, PhD, Regeneron Pharmaceuticals, Inc., and Jonathan Krieger, PhD, Bioinformatics Solutions Inc.
    The use of cancer immunotherapy has become increasingly popular due to their precision and efficacy compared to other cancer treatments. To develop effective cancer immunotherapy treatments, of which the goal is the generation of adaptive immune responses and long-term immune memory, patient-specific tumor antigens need to be identified. Mass spectrometry (MS)-based workflows have been demonstrated to have great potential to identify HLA-peptide targets, an ideal target for tumor-specific antigens.
     
  • Covaris
    Reproducible, Hands-Free Protein Sample Preparation with Covaris AFA®
    Chair: Dr Nicolas Autret, Covaris
    Speakers: Dr Nicolas Autret, Covaris; Dr Fabian Coscia, Center for Proteomics Research, Copenhagen; and Prof. Jeroen Krijgsveld, DKFZ, Heidelberg
    This presentation intends to introduce how Covaris Adaptive Focused Acoustics has been used for sample preparation, introducing the technology and presenting the main results achieved with Covaris AFA, including published data as well as unpublished results from collaborations with Mass Spectrometry leading laboratories.
     
  • PharmaFluidics
    Practical Applications of µPAC™ Column Technology Using Data-Independent Acquisition for Clinical Proteomics
    Chair: Ali Pervez, Senior Business Development US West-Coast, PharmaFluidics
    Speakers: Geert Van Raemdonck, Global Field Support Expert, PharmaFluidics; Jan Muntel, Senior Scientist, Biognosys AG; and Simion Kreimer, Project Scientist, Cedar Sinai Medical Center
    This seminar will include the following three presentations:

    • micro Pillar Array Column (µPAC) technology (by PharmaFluidics)
    • Development and optimisation of DIA workflow (by Biognosys)
    • Proteome analyses of clinical samples (by Cedar Sinai)

     

  • Phenomenex
    Miniaturized Separations and Increased Sensitivity – What to Expect When Moving to Micro and Nano Scale HPLC
    Chair & Speaker: Jason A. Anspach, PhD
    As modern mass spectrometers (MS) have become ever increasingly more sensitive the limiting factor of the relative ionization efficacy has remained a constraint. The limit to any mass spectrometer’s sensitivity is the amount of sample that gets ionized and subsequently introduced into the MS. In this talk, we will discuss some of the tools that are now available in terms of new column technologies, injection modes (trap and elute), and separation condition strategies, and even connection systems that can help with the miniaturization of analytical scale separations to micro and nano scale.
     
  • Quanterix
    High-Definition Simoa® Biomarker Detection for Precision Monitoring of Disease Progression
    Chair: Kevin Hrusovsky, Quanterix
    Speakers: Kevin Hrusovsky, Quanterix; Sharel Figueredo, PhD, Quanterix; and Paula Perin, PhD, Quanterix
    This discussion will include an overview of the Quanterix mission to promote precision healthcare and unlock proteomics potential through advancements in digital biomarker detection. Attendees will learn how Simoa technology is being used to monitor health and disease progression in the fields of neurology and infectious disease, including COVID-19. We will share data that demonstrate how our immunoassay platforms provide vastly increased sensitivity as compared to alternative multiplex assay technologies.
     
  • Seer
    Unbiased, Deep, Rapid and Scalable Proteomics with the Proteograph™ – an Integrated Solution for Unlocking the Proteome
    Chair: Juan Cruz Cuevas, PhD, Seer, Inc.
    Speakers: John Blume, PhD, Seer, Inc.; Daniel Hornburg, PhD, Seer, Inc.; and Mark Flory, PhD, Oregon Health Sciences University
    For decades, a critical limiting factor in proteomics has been the inability to access the proteome in an unbiased, deep manner, rapidly and at the scale necessary to survey and understand its diversity. To create a more transformative view of the proteome, we had to create a new technology; one that provides a new lens on the proteome, enabling researchers to see the breadth, depth and dynamic nature of proteome diversity across populations and time.
     
  • Thermo Fisher Scientific
    Enabling Quantitative Proteomics by Improved Peptide Identifications
    Chair: Claire Dauly, Manager Sales Support LSMS ‘OMICS’ Europe, Thermo Fisher Scientific
    Speakers: Khatereh Motamedchaboki, Thermo Fisher Scientific; and Prof. Dr. Bernhard Küster, Technical University of Munich
    These presentations will describe some of the latest developments to advance proteomics research using innovative Orbitrap mass spectrometry Hardware and Prosit Software Solutions. The latest Thermo Scientific™ Orbitrap Exploris™ 240 mass spectrometer offers leading performance with compact, simplicity and intelligent data acquisition. Posit is a deep neural network developed by the Kuster Lab at TUM to predict iRT values and MS2 spectra for given peptide sequences leading to improved identifications and lower false discovery rates.
     

 



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