HUPO 2021 World Congress

INDUSTRY SEMINARS - LIVE

Live Industry Seminars (60 min)

The following Live Industry Seminars (60 min) are organized by sponsors of HUPO 2021 and will be broadcast live at the day/time mentioned below. Click on the tabs for more details.

  • NOV 15
  • NOV 16
  • NOV 17
  • NOV 19

Thermo Fisher Scientific

Time: 17:15 – 18:15 UTC
Industry Hub Auditorium 2

ISS1 – Roadmap for Translational Proteomics Research and Precision Medicine 

Description

Proteomics has for a long time been expected to shine in the discovery of protein biomarkers in plasma and tissues advancing our understanding of diagnosing diseases such as cancer, monitoring their progression, predicting recurrence and supporting the identification of therapeutic treatment. 

Topics such as longitudinal studies, targeted assays as well as standardization have been at the forefront of discussion, publications, meetings and task forces. In addition, pushing proteomics technologies to demonstrate the value of proteogenomics for defining the molecular signature of human tumors, and translation to other areas of biomedicine and life sciences has been ongoing. 

This session will focus on recent research achievements from leaders in the community that delivers a roadmap for translational proteomics research.

SCEIX

Time: 17:15 – 18:15 UTC
Industry Hub Auditorium 1

ISS2 – Powerful New Proteomic Workflows Enabled by the SCIEX ZenoTOF System

Description

Chair: Dr. Christie Hunter, Director, Application and Technical Marketing, SCIEX

Speakers:

  • Dr. Christie Hunter, Director, Application and Technical Marketing, SCIEX  
  • Professor Jerome Lemoine, Institute of Analytical Sciences at the University of Lyon  
  • Professor Anthony Whetton, Stoller Biomarker Discovery Centre at the University of Manchester 

Join SCIEX for an exciting session highlighting new innovations and proteomics applications made possible using the SCIEX ZenoTOF 7600 system. Dr. Christie Hunter (SCIEX) will provide a short technology overview and introduce the innovations. Then, Professor Jerome Lemoine from the Institute of Analytical Sciences at the University of Lyon and Professor Anthony Whetton from the Stoller Biomarker Discovery Centre at the University of Manchester will share some exciting early results from the platform that highlight the use of the ZenoTOF 7600 system for biomarker research.  

Bioinformatics Solutions BSI

Time: 21:15 – 22:15 UTC
Industry Hub Auditorium 1

ISS3 – Furthering the Understanding of the Human Proteome Using New MS-based Workflows 

Description

Chair: Zac Anderson, MSc., Senior Account Manager, Bioinformatics Solutions Inc.

Speakers: 

  • Curtis McMurtrey, Ph.D., Director of Immunopeptidomics at PureMHC 
  • Dan Maloney, Application Scientist, Bioinformatics Solutions Inc.
  • Zia Rahman, VP of Production, Bioinformatics Solutions Inc.

Time: 17:15 – 18:15 UTC
Industry Hub Auditorium 2

ISS5 – Unearth the Full Potential of DDA Proteomics with SpectroMine 3 

Description

Chair: Maximilian J. Helf (Biognosys) 

  • What’s New in SpectroMine 3

Speaker: Tikira Temu (Biognosys)

Lead developer Tikira Temu is presenting new features in SpectroMine 3, the latest version of our all-in-one software solution for DDA proteomics. Learn how to make the most of your isobaric labeling quantification (ILQ) data, including TMTpro 18-plex experiments. The new PTM workflow makes it easy to extract valuable information about peptide modifications while taking full advantage of Pulsar, our industry-leading search engine. SpectroMine 3 also comes with improved fractionation support, specialized immunopeptidomics functionalities, and dramatically increased processing speed, especially for analyses with multiple variable modifications. 

  • Improving Single Cell Proteomics with Advanced Data Acquisition and Data Analysis

Speaker: Erwin M. Schoof (Technical University of Denmark)

Blood cells are a prime example of complex cellular hierarchy, with Hematopoietic Stem Cells (HSC) as the origin of many cell lineages. The Schoof lab subjected healthy and malignant hematopoietic cells to fluorescence-activated cell sorting (FACS) combined with novel single-cell proteomics (scMS) strategies. Using the latest LC-MS instrumentation with intelligent data acquisition and advanced data analytics provided by Spectromine 3.0, this approach resulted in unprecedented maps of protein expression in individual cells. Furthermore, they developed a computational workflow (SCeptre) for effective MS data post-processing and FACS data integration to extract cell-specific proteins. Results show enrichment of cell-type-specific proteins in various compartments, and protein signatures that clearly distinguish the differentiation stages within their respective hierarchies.

Bruker Daltonics

Time: 17:15 -18:15 UTC
Industry Hub Auditorium 1

ISS4 – Advances in 4D-Proteomics™: Plasma Proteomics and Targeted Quantitative Biology 

Description

Chair: Chris Adams, Bruker Daltonics 

  • prm-PASEF-based Biomarker Discovery in serum from Colon Cancer Patients

Speaker: Prof. Gunnar Dittmar, Head of Quantitative Biology, Luxemburg Institute of Health (LIH) 

Patient serum is a preferred biofluid for diagnostic purposes as it is readily available. The biomarker detection in serum is usually hindered by the enormous dynamic range of protein abundance, making the reliable measurement of lower abundant proteins challenging. Targeted proteomic analysis of selected proteins offers an alternative to dig deeper and detect low abundant protein in this complex matrix. The development of PRM-PASEF combines the advantages of PRM with the additional selectivity of ion-mobility. Using an extensive collection of isotope-labeled reference peptides, we systematically screened patient serum for biomarkers with a high dynamic range in a very short time using fast liquid chromatography. 

  • Toward Comprehensive Plasma Proteomics by Orthogonal Protease Digestion 

Speaker: Asst. Prof. Danielle Swaney, Cellular and Molecular Pharmacology, University California San Francisco (UCSF)

Rapid and consistent protein identification across large clinical cohorts is an important goal for clinical proteomics. Here we apply a simple and accessible tip-based workflow for the generation of DIA spectral libraries to provide a comprehensive overview on the plasma proteome in individuals with and without active tuberculosis (TB). To boost protein coverage, we utilized non-conventional proteases together with the gold standard trypsin, identifying more than 30,000 peptides mapping to 3,309 proteins. Application of this library to quantify plasma proteome differences in TB infection recovered more than 400 proteins in 50 minutes of MS-acquisition, including the direct detection of diagnostic Mycobacterium tuberculosis (Mtb) proteins.

NOVEMBER 17

Time: 17:15 – 18:15 UTC
Industry Hub Auditorium 2

ISS6 – Exploring Molecular Phenotypes of Incident Breast Cancer through Population-based Proteogenomics

Description

Speaker:  Anders Malarstig, Director Target Sciences, Pfizer Worldwide Research, Development & Medical, Stockholm & Senior Researcher, Department of Medical Epdiemiology and Biostatistics, Karolinska Institute, Sweden 

Proteins play key roles in malignant transformation and represent an important hub for oncogenic signaling. Elevated levels of circulating proteins can be identified years before onset of cancer diagnoses. This session will focus on exploring the power of proteomic discoveries at the population scale in breast cancer cohort, and integration of proteogenomics to generate key biological insights into risk prediction of breast cancer that may lead to translational applications for breast cancer prevention.

Time: 17:15 – 18:15 UTC
Industry Hub Auditorium 1

ISS7 – New Insights and Discoveries from Massive Scale Proteomics

Description

Speaker: Dr. Kári Stefánsson, CEO deCode Genetics 

In this 45-minute talk, Dr. Stefánsson will discuss the largest population proteomics study ever performed to help provide more insight on disease and health outcomes. This collaborative research assembled expertise from deCode Genetics and SomaLogic to combine the study of genetic and protein diversity to characterize disease biomarkers in the human population. The data from this type of proteomic study will inform drug discovery and development as well as improvements in health management. 

You will learn about:  

  • The high-throughput technologies (e.g., mass spectrometry) that made this study possible  
  • The application of population proteomics in diagnosis and management of common and rare diseases

Thermo Fisher Scientific

Time: 21:15 – 22:15 UTC
Industry Hub Auditorium 2

ISS8 – Post-translational Modifications – The Third Disruptive Wave in Proteomics 

Description

We have lived through two waves of disruptions in proteomics, the “identification ID” disruption where the large number of identified proteins enabled by LC/MS and bioinformatics. The second wave became “quantitative” enabling 1000’s of proteomes to be quantitatively compared among each other. 

Now, we are about to enter the third disruptive wave, where deciphering protein function is key to push the understanding of biology further. To that end, the study of “post-translational modifications PTMs” is becoming more important due to their contribution to the regulation of protein function and exponentially growing the functional diversity of the proteome and even efforts to generate PTM atlases. 

This session will focus on several approaches to PTM analysis from leaders in the community, on the path for the elucidation of the biological function of proteins or protein groups and classes on a proteome-wide level. to understand the physiological processes by pushing MS approaches and seeing the complete picture of the modified proteome.

Time: 21:15 – 22:15 UTC
Industry Hub Auditorium 1

ISS9 – Advances in Untargeted Plasma Proteomics Analysis with the ProteographTM Product Suite

Description

Chair: Khatereh Motamedchaboki, Seer Inc.

  • Enhanced Protein Coverage and Analysis Scale with New Nanoparticle-based Technology for Plasma Proteomics
    Speaker: Daniel Hornburg, Ph.D. Sr. Director of Research and Tech Development, Seer Inc.
    • Current challenges in scaling plasma proteomics
    • Enhanced depth of coverage and throughput with Seer’s Proteograph platform
    • Exploration of physicochemical properties of engineered nanoparticles with protein selectivity enabling deeper proteome coverage
  • Large-Scale, Deep and Untargeted Plasma Proteomics for a Multi-Cancer Biomarker Discovery Study
    Speaker: Bruce E.Wilcox, Ph.D. VP of Proteomics, PrognomiQ
    • The importance of plasma proteomics in multi-omics research and biomarker discovery
    • Advantages of Seer’s Proteograph Product Suite to analyze the plasma proteome at scale
    • Experience with the Proteograph platform for a large-scale plasma proteomics project in multi-cancer clinical research

Visit our content library for more information about Seer and the Proteograph Product Suite: https://seer.bio/library.

Bruker Daltonics

Time: 05:45 -06:45 UTC
Industry Hub Auditorium 1

ISS10 – Advances in 4D-Proteomics™: Single Cell Proteomics and PaSER Real-Time Search 

Description

Chair:  Gary Kruppa, Bruker Daltonics 

  • Single Cell Proteome (SCP) using Glass-Oil-Air-Droplet (GOAD) nano chip device and its application on embryo development 

Speaker: Prof. Catherine C.L. Wong, School of Basic Medical Sciences, Peking University Health Science Center, Center for Precision Medicine Multi-Omics Research

Deep single-cell proteome has great biological significance for understanding cellular heterogeneity. To overcome the barriers along the processes of shotgun SCP, we firstly developed a nanoliterscaled glass-oil-air-droplet (GOAD) chip using miniaturized stationary droplet microreaction and manipulation techniques for multi-step sample pretreatment. We identified more than 1300 protein groups from a 200pg standard cell digest using timsTOF mass spectrometer in parallel-accumulation-serial-fragmentation (PASEF) scanning mode. We further demonstrate the application of GOAD chip device for the first time SCP analysis on embryo development. This method has great potential for achieving ultrasensitive proteomic analysis on single-cell level.

  • PaSER and CCS-aware 4D Informatics 

Speaker: Robin Park, Director of Bioinformatics, Bruker Daltonics

PaSER is a real time GPU-based search engine designed to take advantage of the massive parallelization possible on GPUs to enable real time search.  Real-time database search means that bottom-up shotgun proteomics data can be processed as quickly as it is acquired by the mass spectrometer.  This results in “Run and Done”, meaning that when your sample run is done the database search results are ready and can be used for making real time decisions about the next steps in your sample queue.  PaSER will also implement the use of CCS values obtained with 4D-Proteomics methods for improving the FDR in database searches and in particular to improving de novo peptide identification.  Additional late breaking developments in PaSER portfolio will be discussed.

Time: 17:15 – 18:15 UTC
Industry Hub Auditorium 2

ISS1 – Roadmap for Translational Proteomics Research and Precision Medicine 

Description

Proteomics has for a long time been expected to shine in the discovery of protein biomarkers in plasma and tissues advancing our understanding of diagnosing diseases such as cancer, monitoring their progression, predicting recurrence and supporting the identification of therapeutic treatment. 

Topics such as longitudinal studies, targeted assays as well as standardization have been at the forefront of discussion, publications, meetings and task forces. In addition, pushing proteomics technologies to demonstrate the value of proteogenomics for defining the molecular signature of human tumors, and translation to other areas of biomedicine and life sciences has been ongoing. 

This session will focus on recent research achievements from leaders in the community that delivers a roadmap for translational proteomics research.

Sponsored By: Thermo Fisher Scientific

 

Time: 17:15 – 18:15 UTC
Industry Hub Auditorium 1

ISS2 – Powerful New Proteomic Workflows Enabled by the SCIEX ZenoTOF System

Description

Chair: Dr. Christie Hunter, Director, Application and Technical Marketing, SCIEX

Speakers:

  • Dr. Christie Hunter, Director, Application and Technical Marketing, SCIEX  
  • Professor Jerome Lemoine, Institute of Analytical Sciences at the University of Lyon  
  • Professor Anthony Whetton, Stoller Biomarker Discovery Centre at the University of Manchester 

Join SCIEX for an exciting session highlighting new innovations and proteomics applications made possible using the SCIEX ZenoTOF 7600 system. Dr. Christie Hunter (SCIEX) will provide a short technology overview and introduce the innovations. Then, Professor Jerome Lemoine from the Institute of Analytical Sciences at the University of Lyon and Professor Anthony Whetton from the Stoller Biomarker Discovery Centre at the University of Manchester will share some exciting early results from the platform that highlight the use of the ZenoTOF 7600 system for biomarker research.  

Sponsored By: SCEIX

 

 

Time: 21:15 – 22:15 UTC
Industry Hub Auditorium 1

ISS3 – Furthering the Understanding of the Human Proteome Using New MS-based Workflows 

Description

Chair: Zac Anderson, MSc., Senior Account Manager, Bioinformatics Solutions Inc.

Speakers: 

  • Curtis McMurtrey, Ph.D., Director of Immunopeptidomics at PureMHC 
  • Dan Maloney, Application Scientist, Bioinformatics Solutions Inc.
  • Zia Rahman, VP of Production, Bioinformatics Solutions Inc.

Sponsored By:   Bioinformatics Solutions BSI

Time: 17:15 – 18:15 UTC
Industry Hub Auditorium 2

ISS5 – Unearth the Full Potential of DDA Proteomics with SpectroMine 3 

Description

Chair: Maximilian J. Helf (Biognosys) 

  • What’s New in SpectroMine 3

Speaker: Tikira Temu (Biognosys)

Lead developer Tikira Temu is presenting new features in SpectroMine 3, the latest version of our all-in-one software solution for DDA proteomics. Learn how to make the most of your isobaric labeling quantification (ILQ) data, including TMTpro 18-plex experiments. The new PTM workflow makes it easy to extract valuable information about peptide modifications while taking full advantage of Pulsar, our industry-leading search engine. SpectroMine 3 also comes with improved fractionation support, specialized immunopeptidomics functionalities, and dramatically increased processing speed, especially for analyses with multiple variable modifications. 

  • Improving Single Cell Proteomics with Advanced Data Acquisition and Data Analysis

Speaker: Erwin M. Schoof (Technical University of Denmark)

Blood cells are a prime example of complex cellular hierarchy, with Hematopoietic Stem Cells (HSC) as the origin of many cell lineages. The Schoof lab subjected healthy and malignant hematopoietic cells to fluorescence-activated cell sorting (FACS) combined with novel single-cell proteomics (scMS) strategies. Using the latest LC-MS instrumentation with intelligent data acquisition and advanced data analytics provided by Spectromine 3.0, this approach resulted in unprecedented maps of protein expression in individual cells. Furthermore, they developed a computational workflow (SCeptre) for effective MS data post-processing and FACS data integration to extract cell-specific proteins. Results show enrichment of cell-type-specific proteins in various compartments, and protein signatures that clearly distinguish the differentiation stages within their respective hierarchies.

Sponsored By:

 

Time: 17:15 -18:15 UTC
Industry Hub Auditorium 1

ISS4 – Advances in 4D-Proteomics™: Plasma Proteomics and Targeted Quantitative Biology 

Description

Chair: Chris Adams, Bruker Daltonics 

  • prm-PASEF-based Biomarker Discovery in serum from Colon Cancer Patients

Speaker: Prof. Gunnar Dittmar, Head of Quantitative Biology, Luxemburg Institute of Health (LIH) 

Patient serum is a preferred biofluid for diagnostic purposes as it is readily available. The biomarker detection in serum is usually hindered by the enormous dynamic range of protein abundance, making the reliable measurement of lower abundant proteins challenging. Targeted proteomic analysis of selected proteins offers an alternative to dig deeper and detect low abundant protein in this complex matrix. The development of PRM-PASEF combines the advantages of PRM with the additional selectivity of ion-mobility. Using an extensive collection of isotope-labeled reference peptides, we systematically screened patient serum for biomarkers with a high dynamic range in a very short time using fast liquid chromatography. 

  • Toward Comprehensive Plasma Proteomics by Orthogonal Protease Digestion 

Speaker: Asst. Prof. Danielle Swaney, Cellular and Molecular Pharmacology, University California San Francisco (UCSF)

Rapid and consistent protein identification across large clinical cohorts is an important goal for clinical proteomics. Here we apply a simple and accessible tip-based workflow for the generation of DIA spectral libraries to provide a comprehensive overview on the plasma proteome in individuals with and without active tuberculosis (TB). To boost protein coverage, we utilized non-conventional proteases together with the gold standard trypsin, identifying more than 30,000 peptides mapping to 3,309 proteins. Application of this library to quantify plasma proteome differences in TB infection recovered more than 400 proteins in 50 minutes of MS-acquisition, including the direct detection of diagnostic Mycobacterium tuberculosis (Mtb) proteins.

Sponsored By: Bruker Daltonics

Time: 17:15 – 18:15 UTC
Industry Hub Auditorium 2

ISS6 – Exploring Molecular Phenotypes of Incident Breast Cancer through Population-based Proteogenomics

Description

Speaker:  Anders Malarstig, Director Target Sciences, Pfizer Worldwide Research, Development & Medical, Stockholm & Senior Researcher, Department of Medical Epdiemiology and Biostatistics, Karolinska Institute, Sweden 

Proteins play key roles in malignant transformation and represent an important hub for oncogenic signaling. Elevated levels of circulating proteins can be identified years before onset of cancer diagnoses. This session will focus on exploring the power of proteomic discoveries at the population scale in breast cancer cohort, and integration of proteogenomics to generate key biological insights into risk prediction of breast cancer that may lead to translational applications for breast cancer prevention.

Sponsored By:

Time: 17:15 – 18:15 UTC
Industry Hub Auditorium 1

ISS7 – New Insights and Discoveries from Massive Scale Proteomics

Description

Speaker: Dr. Kári Stefánsson, CEO deCode Genetics 

In this 45-minute talk, Dr. Stefánsson will discuss the largest population proteomics study ever performed to help provide more insight on disease and health outcomes. This collaborative research assembled expertise from deCode Genetics and SomaLogic to combine the study of genetic and protein diversity to characterize disease biomarkers in the human population. The data from this type of proteomic study will inform drug discovery and development as well as improvements in health management. 

You will learn about:  

  • The high-throughput technologies (e.g., mass spectrometry) that made this study possible  
  • The application of population proteomics in diagnosis and management of common and rare diseases

Sponsored By:

Time: 21:15 – 22:15 UTC
Industry Hub Auditorium 2

ISS8 – Post-translational Modifications – The Third Disruptive Wave in Proteomics 

Description

We have lived through two waves of disruptions in proteomics, the “identification ID” disruption where the large number of identified proteins enabled by LC/MS and bioinformatics. The second wave became “quantitative” enabling 1000’s of proteomes to be quantitatively compared among each other. 

Now, we are about to enter the third disruptive wave, where deciphering protein function is key to push the understanding of biology further. To that end, the study of “post-translational modifications PTMs” is becoming more important due to their contribution to the regulation of protein function and exponentially growing the functional diversity of the proteome and even efforts to generate PTM atlases. 

This session will focus on several approaches to PTM analysis from leaders in the community, on the path for the elucidation of the biological function of proteins or protein groups and classes on a proteome-wide level. to understand the physiological processes by pushing MS approaches and seeing the complete picture of the modified proteome.

Sponsored By: Thermo Fisher Scientific

Time: 21:15 – 22:15 UTC
Industry Hub Auditorium 1

ISS9 – Advances in Untargeted Plasma Proteomics Analysis with the ProteographTM Product Suite

Description

Chair: Khatereh Motamedchaboki, Seer Inc.

  • Enhanced Protein Coverage and Analysis Scale with New Nanoparticle-based Technology for Plasma Proteomics
    Speaker: Daniel Hornburg, Ph.D. Sr. Director of Research and Tech Development, Seer Inc.
    • Current challenges in scaling plasma proteomics
    • Enhanced depth of coverage and throughput with Seer’s Proteograph platform
    • Exploration of physicochemical properties of engineered nanoparticles with protein selectivity enabling deeper proteome coverage
  • Large-Scale, Deep and Untargeted Plasma Proteomics for a Multi-Cancer Biomarker Discovery Study
    Speaker: Bruce E.Wilcox, Ph.D. VP of Proteomics, PrognomiQ
    • The importance of plasma proteomics in multi-omics research and biomarker discovery
    • Advantages of Seer’s Proteograph Product Suite to analyze the plasma proteome at scale
    • Experience with the Proteograph platform for a large-scale plasma proteomics project in multi-cancer clinical research

Visit our content library for more information about Seer and the Proteograph Product Suite: https://seer.bio/library.

Sponsored By:

 

Time: 05:45 -06:45 UTC
Industry Hub Auditorium 1

ISS10 – Advances in 4D-Proteomics™: Single Cell Proteomics and PaSER Real-Time Search 

Description

Chair:  Gary Kruppa, Bruker Daltonics 

  • Single Cell Proteome (SCP) using Glass-Oil-Air-Droplet (GOAD) nano chip device and its application on embryo development 

Speaker: Prof. Catherine C.L. Wong, School of Basic Medical Sciences, Peking University Health Science Center, Center for Precision Medicine Multi-Omics Research

Deep single-cell proteome has great biological significance for understanding cellular heterogeneity. To overcome the barriers along the processes of shotgun SCP, we firstly developed a nanoliterscaled glass-oil-air-droplet (GOAD) chip using miniaturized stationary droplet microreaction and manipulation techniques for multi-step sample pretreatment. We identified more than 1300 protein groups from a 200pg standard cell digest using timsTOF mass spectrometer in parallel-accumulation-serial-fragmentation (PASEF) scanning mode. We further demonstrate the application of GOAD chip device for the first time SCP analysis on embryo development. This method has great potential for achieving ultrasensitive proteomic analysis on single-cell level.

  • PaSER and CCS-aware 4D Informatics 

Speaker: Robin Park, Director of Bioinformatics, Bruker Daltonics

PaSER is a real time GPU-based search engine designed to take advantage of the massive parallelization possible on GPUs to enable real time search.  Real-time database search means that bottom-up shotgun proteomics data can be processed as quickly as it is acquired by the mass spectrometer.  This results in “Run and Done”, meaning that when your sample run is done the database search results are ready and can be used for making real time decisions about the next steps in your sample queue.  PaSER will also implement the use of CCS values obtained with 4D-Proteomics methods for improving the FDR in database searches and in particular to improving de novo peptide identification.  Additional late breaking developments in PaSER portfolio will be discussed.

Sponsored By: Bruker Daltonics

Sponsored Content