Web Desc
Mass Spectrometry in Systems Biology
Organizer(s): John R. Yates and Vicki H. Wysocki
Date: February 14 - 19, 2004
Location: Hilton Santa Fe Historic Plaza Hotel, Santa Fe, NM, USA
Supported by Keystone Symposia
Summary of Meeting:
Systems biology represents integration of measurements of genomics, gene transcription, proteomics and metabonomics. The completion of a genome sequence for an organism provides the basic set of proteins and enzymes that are present in the organism. In multi-cellular organisms each cell type uses a portion of the set genes to perform specialized functions. Cells must respond to changes in the environment, the molecules of the cell must do so as part of a system, and the cell must respond as part of the organism or physiology. Integral to understanding biological systems is the ability to discover and measure changes in the system. Mass spectrometry is a key technology for the measurement of molecular structure and molecular abundance. Mass spectrometry is being applied to the measurement of DNA, RNA, protein and small molecule metabolites. This meeting will present the latest developments in the methods and applications of mass spectrometry for the analysis of DNA, RNA, proteins and naturally occurring metabolites. Topics emphasizing global measurements as well as highly specific and accurate molecular measurements will be presented.
Discounted Abstract Deadline: October 15 2003
Discounted Registration Deadline: December 15 2003
We gratefully acknowledge additional support for this conference from:
Advion BioSciences, Inc.
Cell Signaling Technology, Inc.
We gratefully acknowledge the generous grant for this conference provided by:

National Institute of General Medical Sciences (NIGMS)
Grant No. 1R13GM070004-01
We appreciate the organizations that provide Keystone Symposia with additional support, such as marketing and advertising:

Click here to view more of these organizations
Special thanks to the following for their support of Keystone Symposia initiatives to increase participation at this meeting by scientists from underrepresented backgrounds:

Click here to view more of these organizations

Program

Saturday, February 14 | 3:00PM - 7:00PM
Registration
Room: Promenade


Saturday, February 14 | 6:15PM - 7:15PM
Refreshments
Room: Promenade


Saturday, February 14 | 7:15PM - 7:30PM
Orientation
Room: Mesa A-B


Saturday, February 14 | 7:30PM - 8:30PM
Keynote Address
Room: Mesa A-B

Speaker 1 of 2
* John R. Yates III, The Scripps Research Institute, USA

Saturday, February 14 | 7:30PM - 8:30PM
Keynote Address
Room: Mesa A-B

Speaker 2 of 2
R. Graham Cooks, Purdue University, USA
Advances in Mass Spectrometry Instrumentation

Sunday, February 15 | 7:00AM - 8:00AM
Breakfast
Room: Chamisa


Sunday, February 15 | 8:00AM - 11:00AM
Technology I
Room: Mesa A-B

Speaker 1 of 5
* R. Graham Cooks, Purdue University, USA

Sunday, February 15 | 8:00AM - 11:00AM
Technology I
Room: Mesa A-B

Speaker 2 of 5
Stephen Naylor, Beyond Genomics, USA
Case Studies in System Biology: Role of Technologies

Sunday, February 15 | 8:00AM - 11:00AM
Technology I
Room: Mesa A-B

Speaker 3 of 5
Marvin Vestal, Applied Biosystems, USA
TOF/TOF Mass Spectrometer

Sunday, February 15 | 8:00AM - 11:00AM
Technology I
Room: Mesa A-B

Speaker 4 of 5
Alan G. Marshall, Florida State University, USA
Advances in FT-ICR MS Technology for Biological Molecules

Sunday, February 15 | 8:00AM - 11:00AM
Technology I
Room: Mesa A-B

Speaker 5 of 5
Vicki H. Wysocki, Ohio State University, USA
Two Approaches to Improving Protein Identification by MS/MS

Sunday, February 15 | 9:20AM - 9:40AM
Coffee Break
Room: Promenade


Sunday, February 15 | 11:00AM - 1:00PM
Poster Setup
Room: Mesa C


Sunday, February 15 | 1:00PM - 10:00PM
Poster Viewing
Room: Mesa C


Sunday, February 15 | 2:00PM - 4:00PM
Workshop 1
Room: Mesa A-B

Speaker 1 of 6
John R. Engen, Northeastern University, USA
Probing Protein Dynamics with Hydrogen Exchange and Mass Spectrometry

Sunday, February 15 | 2:00PM - 4:00PM
Workshop 1
Room: Mesa A-B

Speaker 6 of 6
* Ansgar Brock, Genomics Institute, Novartis Research Foundation, USA
An Intelligent Approach for the Bootstrapping of Proteomes by Multidimensional LC MALDI QFT-ICR MS

Sunday, February 15 | 2:00PM - 4:00PM
Workshop 1
Room: Mesa A-B

Speaker 5 of 6
Brandon T. Ruotolo, University of Michigan, USA
Biomolecule Imaging Mass Spectrometry Based on MALDI-Ion Mobility-TOFMS

Sunday, February 15 | 2:00PM - 4:00PM
Workshop 1
Room: Mesa A-B

Speaker 4 of 6
Michail A. Alterman, Food and Drug Administration, USA
Qualitative and Quantitative Maldi Tof-Based Proteomic Approach to the Profiling of Cytochrome P450 Isozymes

Sunday, February 15 | 2:00PM - 4:00PM
Workshop 1
Room: Mesa A-B

Speaker 3 of 6
Yingming Zhao, University of Texas Southwestern Medical Center, USA
Proteomic Analysis of O-GIcNAc Modified Proteins

Sunday, February 15 | 2:00PM - 4:00PM
Workshop 1
Room: Mesa A-B

Speaker 2 of 6
Feng Zhong, MDS Sciex, Canada
A Novel PTM Discovery Method Using a Hybrid Linear Quadruple Ion Trap Mass Spectrometer

Sunday, February 15 | 4:30PM - 5:00PM
Coffee & Snacks Available
Room: Promenade


Sunday, February 15 | 5:00PM - 7:00PM
Technology II
Room: Mesa A-B

Speaker 4 of 4
Michael Senko, Thermo Electron Corporation, USA
Acquisition Strategies for Proteomic Analysis with a Hybrid Linear Ion Trap/Fourier Transform Mass Spectrometer

Sunday, February 15 | 5:00PM - 7:00PM
Technology II
Room: Mesa A-B

Speaker 3 of 4
Luke V. Schneider, Target Discovery, Inc., USA
Differential Display on System Biological Research

Sunday, February 15 | 5:00PM - 7:00PM
Technology II
Room: Mesa A-B

Speaker 2 of 4
Donald Douglas, University of British Colmbia, Canada
Linear Ion Traps in Mass Spectrometry

Sunday, February 15 | 5:00PM - 7:00PM
Technology II
Room: Mesa A-B

Speaker 1 of 4
* Richard D. Smith, Pacific Northwest National Laboratory, USA

Sunday, February 15 | 7:00PM - 8:00PM
Social Hour
Room: Mesa C


Sunday, February 15 | 7:30PM - 10:00PM
Poster Session 1
Room: Mesa C


Monday, February 16 | 7:00AM - 8:00AM
Breakfast
Room: Chamisa


Monday, February 16 | 8:00AM - 9:25AM
Applications of Mass Spectrometry: DNA
Room: Mesa A-B

Speaker 4 of 4
Kevin R. Ramkissoon, University of North Carolina at Chapel Hill, USA
Short Talk: Comparative Proteomic Analysis of Adaptive Evolution in Bacteria

Monday, February 16 | 8:00AM - 9:25AM
Applications of Mass Spectrometry: DNA
Room: Mesa A-B

Speaker 3 of 4
David C. Muddiman, North Carolina State University, USA
Nucleic Acid Analysis Using High Field FT-ICR Mass Spectrometry

Monday, February 16 | 8:00AM - 9:25AM
Applications of Mass Spectrometry: DNA
Room: Mesa A-B

Speaker 2 of 4
Charles R. Cantor, Sequenom Inc., USA
Nucleic Acid Analysis by High Throughput Automated Mass Spectrometry

Monday, February 16 | 8:00AM - 9:25AM
Applications of Mass Spectrometry: DNA
Room: Mesa A-B

Speaker 1 of 4
* Stephen Naylor, Beyond Genomics, USA

Monday, February 16 | 9:25AM - 9:45AM
Coffee Break
Room: Promenade


Monday, February 16 | 9:45AM - 11:00AM
Application of Mass Spectrometry Technology: Protein Express
ion

Room: Mesa A-B

Speaker 2 of 2
Rudolf H. Aebersold, Institute of Molecular Systems Biology, ETH Zürich, Switzerland
Quantitative Proteomics: Current Status, Challenges and New Directions

Monday, February 16 | 9:45AM - 11:00AM
Application of Mass Spectrometry Technology: Protein Express
ion

Room: Mesa A-B

Speaker 1 of 2
Richard D. Smith, Pacific Northwest National Laboratory, USA
Comprehensive Proteomices Using Nano-Scale Separations and FTICR Mass Spectrometry

Monday, February 16 | 11:00AM - 1:00PM
Poster Setup
Room: Mesa C


Monday, February 16 | 1:00PM - 10:00PM
Poster Viewing
Room: Mesa C


Monday, February 16 | 2:00PM - 4:00PM
Workshop 2
Room: Mesa A-B

Speaker 2 of 6
Megan R. Jones, University of Washington, USA
Protein Identification in Barrett’s Esophagus through LCQ/Mass Spectrometry

Monday, February 16 | 2:00PM - 4:00PM
Workshop 2
Room: Mesa A-B

Speaker 1 of 6
Jason D. Hoffert, NIDDK, National Institutes of Health, USA
Analysis of Inner Modullary Collecting Duct Protein

Monday, February 16 | 2:00PM - 4:00PM
Workshop 2
Room: Mesa A-B

Speaker 3 of 6
Jeffrey R. Johnson, University of California, San Francisco, USA
Targeted Proteomic Analysis of P. falciparum Asexual-Stage Antigens Reveals a Novel Multigene Family of Maurer’s Cleft Membrane Proteins

Monday, February 16 | 2:00PM - 4:00PM
Workshop 2
Room: Mesa A-B

Speaker 4 of 6
* Anna T. Neill, University of California, San Diego, USA
Tandem MS Analysis and an Emerging Genome: The Sea Urchin Sperm Plasma Membrane Proteome

Monday, February 16 | 2:00PM - 4:00PM
Workshop 2
Room: Mesa A-B

Speaker 5 of 6
Patrick A. Everley, Harvard Medical School, USA
Quantitative Proteomics: Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) as a Tool for Prostate Cancer Research

Monday, February 16 | 2:00PM - 4:00PM
Workshop 2
Room: Mesa A-B

Speaker 6 of 6
Brian D. Halligan, University of Michigan, USA
Alternative Approaches to Peptide Identification from MS Data

Monday, February 16 | 4:30PM - 5:00PM
Coffee & Snacks Available
Room: Promenade


Monday, February 16 | 5:00PM - 7:00PM
Application of Mass SpectrometryTechnology: Protein Expressi
on

Room: Mesa A-B

Speaker 1 of 5
* Rudolf H. Aebersold, Institute of Molecular Systems Biology, ETH Zürich, Switzerland

Monday, February 16 | 5:00PM - 7:00PM
Application of Mass SpectrometryTechnology: Protein Expressi
on

Room: Mesa A-B

Speaker 2 of 5
Catherine Fenselau, USA
Isotope Labeling Studies of Acquired Drug Resistance

Monday, February 16 | 5:00PM - 7:00PM
Application of Mass SpectrometryTechnology: Protein Expressi
on

Room: Mesa A-B

Speaker 3 of 5
David M. Lubman, University of Michigan, USA
2-D Liquid Mapping of a Cancer Cell Lysates

Monday, February 16 | 5:00PM - 7:00PM
Application of Mass SpectrometryTechnology: Protein Expressi
on

Room: Mesa A-B

Speaker 4 of 5
Robert T. Kennedey, University of Michigan, USA
In vivo Monitoring and Discovery of Neurotransmitters

Monday, February 16 | 5:00PM - 7:00PM
Application of Mass SpectrometryTechnology: Protein Expressi
on

Room: Mesa A-B

Speaker 5 of 5
Kimberly A. Lee, Cell Signaling Technology, USA
Short Talk: Immunoaffinity Profiling of Tyrosine Phosphorylation

Monday, February 16 | 7:00PM - 8:00PM
Social Hour
Room: Mesa C


Monday, February 16 | 7:30PM - 10:00PM
Poster Session 2
Room: Mesa C


Tuesday, February 17 | 7:00AM - 8:00AM
Breakfast
Room: Chamisa


Tuesday, February 17 | 8:00AM - 9:20AM
Application of Mass Spectrometry
Room: Mesa A-B

Speaker 1 of 4
* † Catherine E. Costello, Boston University School of Medicine, USA

Tuesday, February 17 | 8:00AM - 9:20AM
Application of Mass Spectrometry
Room: Mesa A-B

Speaker 2 of 4
Richard M. Caprioli, Vanderbilt University Medical Center, USA
Tissue Imaging and Profiling of Proteins by Mass Spectrometry for Discovery in Clinical and Biological Research

Tuesday, February 17 | 8:00AM - 9:20AM
Application of Mass Spectrometry
Room: Mesa A-B

Speaker 3 of 4
Nikolina Babic, University of Chicago, USA
Short Talk: The Effect of High Density Lipoproteins on Protein Expression in Rat Myoblast Cell Lines

Tuesday, February 17 | 8:00AM - 9:20AM
Application of Mass Spectrometry
Room: Mesa A-B

Speaker 4 of 4
Silvia Cermelli, Fred Hutchinson Cancer research Center, USA
Short Talk: Molecular Motor-Based Cargo Transport: A Proteomic Study

Tuesday, February 17 | 9:20AM - 9:40AM
Coffee Break
Room: Promenade


Tuesday, February 17 | 9:40AM - 11:00AM
Protein Structure and Modifications
Room: Mesa A-B

Speaker 1 of 3
Carol V. Robinson, University of Oxford, UK
Studying Protein Complexes Using Mass Spectrometry

Tuesday, February 17 | 9:40AM - 11:00AM
Protein Structure and Modifications
Room: Mesa A-B

Speaker 2 of 3
Natalie G. Ahn, University of Colorado, USA
Studying Protein Phosphorylation in Signal Transduction Pathways

Tuesday, February 17 | 9:40AM - 11:00AM
Protein Structure and Modifications
Room: Mesa A-B

Speaker 3 of 3
Robert L. Hettich, Oak Ridge National Laboratory, USA
Short Talk: Mass Spectrometric Characterization of Protein
Complexes from Rhodopseudomonas palustris


Tuesday, February 17 | 11:00AM - 1:00PM
Poster Setup
Room: Mesa C


Tuesday, February 17 | 1:00PM - 10:00PM
Poster Viewing
Room: Mesa C


Tuesday, February 17 | 2:00PM - 4:00PM
Workshop 3
Room: Mesa A-B

Speaker 1 of 6
Michael A. Freitas, Ohio State University, USA
Cracking the Histone Code: A Mass Spectrometry Based Approach for the Determination of Histone Modifications

Tuesday, February 17 | 2:00PM - 4:00PM
Workshop 3
Room: Mesa A-B

Speaker 2 of 6
* David L. Tabb, Oak Ridge National Laboratory, USA
Sequence Tagging Algorithms Enable Comprehensive Post-Translational Modification Analysis of Proteomic Tandem Mass Spectra

Tuesday, February 17 | 2:00PM - 4:00PM
Workshop 3
Room: Mesa A-B

Speaker 3 of 6
Sean A. Beausoleil, Harvard Medical School, USA
Phosphopeptide Detection by a Data-Dependent, Neutral-Loss Driven MS3 Scan Using Ion Trap Mass Spectrometry

Tuesday, February 17 | 2:00PM - 4:00PM
Workshop 3
Room: Mesa A-B

Speaker 4 of 6
Yun Han, University of California, Los Angeles, USA
Phosphorylation Profiling of Cancer Using Mass Spectrometry

Tuesday, February 17 | 2:00PM - 4:00PM
Workshop 3
Room: Mesa A-B

Speaker 5 of 6
Huang-Chun Tseng, Harvard Medical School, USA
Phosphoproteomic Analysis of Cellular Microtubule-Associated Proteins Using a Novel Solid-Phase Capture-Release-Tag Chemistry

Tuesday, February 17 | 2:00PM - 4:00PM
Workshop 3
Room: Mesa A-B

Speaker 6 of 6
Majbrit Hjerrild, Glostrup Hospital, Denmark
Neural Network and Mass Spectrometry Analysis for Identification of Protein Kinase A Phosphorylation Sites

Tuesday, February 17 | 4:30PM - 5:00PM
Coffee & Snacks Available
Room: Promenade


Tuesday, February 17 | 5:00PM - 7:00PM
Applications of Mass Spectrometry Technology: Protein Modifi
cations

Room: Mesa A-B

Speaker 1 of 5
* Carol V. Robinson, University of Oxford, UK

Tuesday, February 17 | 5:00PM - 7:00PM
Applications of Mass Spectrometry Technology: Protein Modifi
cations

Room: Mesa A-B

Speaker 2 of 5
Steven P. Gygi, Harvard Medical School, USA
New Age Proteomics for the Study of Protein Ubiquitination

Tuesday, February 17 | 5:00PM - 7:00PM
Applications of Mass Spectrometry Technology: Protein Modifi
cations

Room: Mesa A-B

Speaker 3 of 5
Neil L. Kelleher, Northwestern University, USA
Realizing the Potential of Q-FTMS for Top Down Proteomics of Yeast in Controlled Oxygen Environments

Tuesday, February 17 | 5:00PM - 7:00PM
Applications of Mass Spectrometry Technology: Protein Modifi
cations

Room: Mesa A-B

Speaker 4 of 5
Michael MacCoss, University of Washington, USA
Measurement of Stable Isotope Labeled Peptides by Mass Spectormetry: Limitations, Solutions and Applications

Tuesday, February 17 | 5:00PM - 7:00PM
Applications of Mass Spectrometry Technology: Protein Modifi
cations

Room: Mesa A-B

Speaker 5 of 5
Irwin Jack Kurland, Albert Einstein College of Medicine, USA
Short Talk: Metabolomic Determination of the Optimally Adapted versus Maladapted Glucose Metabolic Network

Tuesday, February 17 | 7:00PM - 8:00PM
Social Hour
Room: Mesa C


Tuesday, February 17 | 7:30PM - 10:00PM
Poster Session 3
Room: Mesa C


Wednesday, February 18 | 7:00AM - 8:00AM
Breakfast
Room: Chamisa


Wednesday, February 18 | 8:00AM - 11:30AM
Application of Mass Spectrometry Technology: Metabolomics I
Room: Mesa A-B

Speaker 1 of 7
* Neil L. Kelleher, Northwestern University, USA

Wednesday, February 18 | 8:00AM - 11:30AM
Application of Mass Spectrometry Technology: Metabolomics I
Room: Mesa A-B

Speaker 2 of 7
Bernhard O. Palsson, University of California, San Diego, USA
Keynote: Metabolomics

Wednesday, February 18 | 8:00AM - 11:30AM
Application of Mass Spectrometry Technology: Metabolomics I
Room: Mesa A-B

Speaker 3 of 7
Dayan B. Goodenowe, Phenomenome Discoveries Inc., Canada
Comprehensive Metabolomics: Analytical and Bioinformatic Challenges

Wednesday, February 18 | 8:00AM - 11:30AM
Application of Mass Spectrometry Technology: Metabolomics I
Room: Mesa A-B

Speaker 4 of 7
Stephen George Oliver, Cambridge University, UK
Capture, Interpretation and Integration of MS Data for Proteomics and Metabolomics

Wednesday, February 18 | 8:00AM - 11:30AM
Application of Mass Spectrometry Technology: Metabolomics I
Room: Mesa A-B

Speaker 5 of 7
Robert C. Murphy, University of Colorado Denver, USA
Mass Spectrometry of Lipids: A Diverse Family Regulating Cellular Function

Wednesday, February 18 | 8:00AM - 11:30AM
Application of Mass Spectrometry Technology: Metabolomics I
Room: Mesa A-B

Speaker 6 of 7
Cecil R. Pace-Asciak, Hospital for Sick Children, Canada
Short Talk: LCMSMS Profiling of Prostaglandins and Related Eicosanoids

Wednesday, February 18 | 8:00AM - 11:30AM
Application of Mass Spectrometry Technology: Metabolomics I
Room: Mesa A-B

Speaker 7 of 7
Peter Sjövall, SP Swedish National Testing and Research Institute, Sweden
Short Talk: High-Resolution Imaging of Membrane Lipids in Single Cells and Tissue by Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS)

Wednesday, February 18 | 9:20AM - 9:40AM
Coffee Break
Room: Promenade


Wednesday, February 18 | 4:30PM - 5:00PM
Coffee & Snacks Available
Room: Promenade


Wednesday, February 18 | 5:00PM - 7:15PM
Application of Mass Spectrometry Technology: Metabolomics II
Room: Mesa A-B

Speaker 1 of 6
* Vicki H. Wysocki, Ohio State University, USA

Wednesday, February 18 | 5:00PM - 7:15PM
Application of Mass Spectrometry Technology: Metabolomics II
Room: Mesa A-B

Speaker 2 of 6
Catherine E. Costello, Boston University School of Medicine, USA
Analysis of Biological Molecules Using Mass Spectrometry

Wednesday, February 18 | 5:00PM - 7:15PM
Application of Mass Spectrometry Technology: Metabolomics II
Room: Mesa A-B

Speaker 3 of 6
Richard N. Trethewey, Metanomics GmbH, Germany
Metabolite Profiling: High Throughput Mass Spectrometry for Discovery and Development

Wednesday, February 18 | 5:00PM - 7:15PM
Application of Mass Spectrometry Technology: Metabolomics II
Room: Mesa A-B

Speaker 4 of 6
Jonathan V. Sweedler, University of Illinois at Urbana-Champaign, USA
How Small Can We Go: Measuring the Neuropeptides in Single Cells to Single Organelles

Wednesday, February 18 | 5:00PM - 7:15PM
Application of Mass Spectrometry Technology: Metabolomics II
Room: Mesa A-B

Speaker 5 of 6
Michael MacCoss, University of Washington, USA
For

Wednesday, February 18 | 5:00PM - 7:15PM
Application of Mass Spectrometry Technology: Metabolomics II
Room: Mesa A-B

Speaker 6 of 6
Christine C. Wu, University of Colorado Health Sciences Center, USA
Shotgun Proteomic Analysis of Membrane Proteins in Mammalian Tissue Samples

Wednesday, February 18 | 7:45PM - 8:45PM
Social Hour
Room: Mesa C


Wednesday, February 18 | 8:00PM - 11:00PM
Entertainment
Room: Mesa C


Wednesday, February 18 | 8:15PM - 11:00PM
Cash Bar
Room: Mesa C


Thursday, February 19 | 10:26AM - 10:26AM
Departure


*Session Chair.