血漿プロテオーム探索に関する会議 - 1日目

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アジェンダ (英語PDF)

Monday, January 7

7:30am - 6:00 pm Registration Open

7:30am Morning Coffee

8:45 Chairperson’s Opening Remarks

KEYNOTE PRESENTATION

9:00 Driving Biological Discovery Using Mass Spectrometry John R. Yates, III, Ph.D., Professor of Cell Biology, Scripps Research Institute Advances in mass spectrometry-based approaches for biological discovery have led to new advances in biology. This lecture will describe approaches to study different types of biological systems to discover functional elements for the system

9:50 Finding the Mother Lode: Challenges in Mass Spectrometry-Based Biomarker Discovery
Karin Rodland, Ph.D., Science Lead - NIH Programs, Biological Sciences Division, Pacific Northwest National Laboratory
Much of today’s proteomics research is dedicated to discovering new protein-based biomarkers for early diagnosis, therapeutic response, and prognosis that promise to revolutionize management of chronic human disease. This biomarker discovery is constrained by analytical limitations in the sensitivity and throughput of mass spectrometry-based methods used to define the complexity of the human plasma or tissue proteome. This session will discuss current issues involved in the application of mass spectrometry to biomarker discovery and other biomedical research problems, as well as strategies for interpreting and validating mass spectrometric data in a biological context. Examples will be given involving the integration of high-performance mass spectrometers, standardized protocols for sample preparation and processing, data management and analysis, and high-throughput validation assays for the identification and characterization of potential biomarkers in applications ranging from cancer to microbial infection to pulmonary disease.

10:20 Coffee Break

10:45 Speaker to Be Announced

11:15 Enabling Discovery by Combining Tandem Mass Spectra from Overlapping Peptides 
Nuno Bandeira, Ph.D., Postdoctoral Scholar, Department of Computer Science and Engineering, University of California, San Diego
The common limiting procedure in current approaches to the identification of tandem mass (MS/MS) spectra is to analyze each spectrum in isolation, even though high-throughput experiments regularly generates many spectra from related peptides. By capitalizing on this redundancy we show that, similarly to the alignment of protein sequences, unidentified MS/MS spectra can also be aligned for the identification of overlapping peptides or modified and unmodified variants of the same peptide. Beyond peptide identification, this approach allows for database-free discovery of post-translational modifications and enables unprecedented de novo sequencing accuracy.

11:45 New Software and Algorithms for Protein, Glycan, and Glycopeptide Identification
Marshall Bern, Ph.D., Principal Scientist, Computing Sciences, Palo Alto Research Center
This presentation will cover ways to improve the sensitivity and accuracy of identification tools, using both single- and tandem-MS. I will talk about how to optimize the database, the allowed modifications, and the types of searches in order to get the most out of a set of spectra.

12:15pm Close of Morning Session

12:30 Luncheon Technology Workshop Antibody Capture and Reverse Antigen Arrays for the Determination of Protein Expression Patterns in Cell Lysates Using Whatman FAST® Slides

Sponsored by

Michael Harvey, Ph.D., Director of Development, Microarrays, Molecular Biology, Research and Development, Whatman Inc.  Microarrays can support different approaches to understanding protein expression in multiple cells or tumor types. Single antibody capture arrays, in combination with a general protein labeling system, permit the interrogation of a protein population with a large number of different antibody specificities. An alternative method is to immobilize cell lysates and probe these lysates with different antibodies. These reverse antigen arrays support a more quantitative approach.

2:30 Chairperson’s Remarks

2:35 A Native Antigen “Reverse Capture” Microarray Platform for Autoantibody Profiling and Biomarker Discovery
Brian Liu, Ph.D., Director, Translational Research and Assistant Professor, Urology, Brigham and Women’s Hospital
Identification of antigens and the detection of autoantibody reactivity are useful in biomarker discovery and for explaining the role of important biochemical pathways in disease. Despite all of their potential advantages, the main challenge to working with autoantibodies is their sensitivity. Nevertheless, proteomics may hold the key to overcoming this limitation by providing the means to multiplex. To date, studies of antigen-autoantibody reactivity using microarrays have relied on recombinant proteins or synthetic peptides as arrayed features. However, recombinant proteins and/or peptides may fail to accurately detect autoantibody binding due to the lack of proper PTMs. We now describe the use of a native antigen “reverse capture” platform that facilitates the autoantibody reactivities to native antigens, as well as facilitating the protein-protein interaction mapping with native biological samples.

3:05 Speaker to be Announced 

KEYNOTE PRESENTATION

3:35 Analyzing Human Disease Using Protein Microarrays Michael Snyder, Ph.D., Lewis B. Cullman Professor, Molecular Cellular & Developmental Biology, Yale University We have used protein microarrays covering much of the proteomes of humans and other organisms to analyze human disease. Viral proteomes have been built and used to probe coronavirus infections and human proteome chips  have been used to identify candidate cancer biomarkers.

4:05 Refreshment Break

Challenge Team Discussion

4:30 Fly It or Capture It? Deciding between Mass Spectrometry and Protein Arrays Moderator: Karin Rodland, Ph.D., Science Lead - NIH Programs, Biological Sciences Division, Pacific Northwest National Laboratory Proteomic researchers are constantly faced with the challenge of choosing between mass spectrometry-based approaches and affinity reagent-based approaches. What are the strengths and weaknesses of each approach? What applications are best for either approach? Is there an optimal strategy for using mass spec and protein arrays, singly and in combination, for discovery, validation and/or diagnosis? What technical challenges need to be overcome to get the most out of biomarker discovery? Topics for Discussion: Mass spec throughput and coverage Cost and complexity: will mass spec ever work in the clinic? Affinity reagents: specificity, selectivity, and availability The problem of poorly immunogenic antigens Protein arrays: how densely can you tile without cross-reactivity? Protocols and procedures: how to implement mass spec and protein arrays for reproducibility New technologies: Is there a solution on the horizon?

5:30 Welcoming Reception in the Exhibit Hall

7:00 Close of Day