Program

Symposium and Mini-Symposium Registration
Olympic Room, 25th floor, Hotel Nikko, 222 Mason Street, San Francisco

3:00pm

Registration

Symposium and Mini-Symposium Registration
Nikko Ballroom Foyer

7:30am

Registration

Mini-Symposium on The Relative Merits of Orthogonal Energy Deposition Modes for the Promotion of Fragmentation
Nikko Ballroom

Chair: A. L. Burlingame, University of California, San Francisco, California, USA

8:30am	MS.1	New Technology for the Large-scale Proteomic Comparison of Human Embryonic Stem Cells, Induced Pluripotent Stem Cells, and Somatic Cells Joshua J. Coon, University of Wisconsin, Madison, Wisconsin, USA
9:30	MS.2	Electron Capture Dissociation in Radio-Frequency-Free Cell Douglas F. Barofsky, Oregon State University, Corvallis, Oregon, USA
10:10		Coffee break
10:50	MS.3	Decoding the Histone Code by Quantitative Proteomics Benjamin A. Garcia, Princeton University, Princeton, New Jersey, USA
11:30	MS.4	Fragment Assignment by Visual Assistance (FAVA) Program for Analysis of Complex High Resolution MSMS Spectra Shenheng Guan, University of California, San Francisco, California, USA
12:10pm		Lunch

Chair: Shenheng Guan, University of California, San Francisco, California, USA

1:40pm	MS.5	Use of Electron Transfer Dissociation to Analyze Combinations of Histone Post-Translational Modifications on an LTQ-Orbitrap Shannon Eliuk, University of California, San Francisco, California, USA
2:20	MS.6	Electron Capture Dissociation for Structural Studies of Integral Membrane Proteins and Their Modifications Julian P. Whitelegge, University of California, Los Angeles, California, USA
3:00	MS.7	O-GlcNAcylation: The Post-translational Modification that Best Highlights the Value of ETD Robert Chalkley, University of California, San Francisco, California, USA
3:40	MS.8	The Use of ECD for Proteomics-wide Identification and Quantification of iso-Asp Residues Roman Zubarev, Karolinska Institute, Stockholm, Sweden

Nikko Ballroom Vestibule

4:00pm

Symposium Registration

Monterey & Carmel Rooms

4:00pm

Symposium Poster Set-up

Golden Gate Room, 25th floor

6:00pm

Opening Reception

Nikko Ballroom Vestibule

7:30am

Registration

Symposium
Nikko Ballroom

8:15am

Introduction

Chair: John Stults, Genentech, Inc., South San Francisco, California, USA

8:30am

1.1

Plenary Lecture
Global Analysis of Small Molecule Interactions with Proteins
Michael Snyder, Stanford University, Stanford, California, USA

Chair: Connie R. Jimenez, VU University Medical Center, Amsterdam, The Netherlands

9:30am	1.2	Statistical Analysis of Quantitative Proteomics Datasets via Normalized Spectral Abundance Factors Juan Astorga-Wells, Karolinska Institute, Stockholm, Sweden
10:10		Coffee break
10:30	1.3	Two-Dimensional Liquid Chromatography Coupled with ESI-MS for Protein Identification and Quantification James Langridge, Waters Corporation, Manchester, UK
11:10	1.4	Targeted Proteomic Approaches Provide Insights into Virion Assembly and Chromatin Remodeling During Viral Infection Ileana M. Cristea, Princeton University, Princeton, New Jersey, USA
11:50	1.5	Confident Assignment of Post-Translational Modifications Using Top-down Mass Spectrometry Julian P. Whitelegge, University of California, Los Angeles, California, USA
12:30pm		Lunch

Chair: Ralph Bradshaw, University of California, San Francisco, California, USA

2:00pm	2.1	Protein Quantification Through Targeted Mass Spectrometry: The Way Out of Biomarker Purgatory? Steven A. Carr, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
2:40	2.2	Proteomics Targeted to Sub-Cellular Compartments and Integration with Genomics for Candidate Biomarker Discovery in Colorectal Cancer Connie R. Jimenez, VU University Medical Center, Amsterdam, The Netherlands
3:20	2.3	Towards the Discovery of Biomarkers in Cerebrospinal Fluid by Combining Peptide Ligand Library Treatment and Label Free Protein Quantification on a LTQ-Orbitrap Florence Roux-Dalvai, CNRS - National Center for Scientific Research, Toulouse, France

Symposium Poster Session A
Monterey & Carmel Rooms

Co-Chairs: David Maltby and Shannon Eliuk, University of California, San Francisco, California, USA

4:00pm

Poster Session A

Symposium
Nikko Ballroom

Chair: James A. Wells, University of California, San Francisco, California, USA

8:30am

3.1

Plenary Lecture
Quantitative Analysis of Proteome Localisation and Dynamics
Angus I. Lamond, Wellcome Trust Biocentre, University of Dundee, Scotland, United Kingdom

Chair: Nevan Krogan, University of California, San Francisco, California, USA

9:30am	3.2	Post-Translational Adenosine Monophosphate (AMP) Modification of Proteins Antonius Koller, Stony Brook University, Stony Brook, New York, USA
10:10		Coffee break
10:30	3.3	Dissecting the Structure of the Human Spliceosome by Looking at its Pieces Melissa Jurica, University of California, Santa Cruz, California, USA
11:10	3.4	Protein complexes and functional pathways in S. cerevisiae and E. coli Jack Greenblatt, University of Toronto, Ontario, Canada
11:50	3.5	N-Terminomics: High Confidence, Broad Dynamic Range Coverage Utilizing Novel Polymers for Proteomics Reveals the Functional State of the Proteome Christopher M. Overall, University of British Columbia, Vancouver, British Columbia, Canada
12:30pm		Lunch

Chair: Charles Craik, University of California, San Francisco, California, USA

2:00pm	4.1	Activity-based proteomics: applications for enzyme and inhibitor discovery Benjamin F. Cravatt III, The Scripps Research Institute, La Jolla, California, USA
2:40	4.2	Global Profiling of Proteolytic Cleavage Sites in Apoptosis Sami Mahrus, University of California, San Francisco, California, USA
3:20	4.3	N-terminal & ‘Genome Free’ Proteomics; de novo Sequence Analysis by a Combination of LysN Protein Digestion and Electron Transfer Dissociation Albert Heck, Netherlands Proteomics Center and Utrecht University, Utrecht, The Netherlands

Symposium Poster Session B
Monterey & Carmel Rooms

Co-Chairs: Jonathan Trinidad and Katalin Medzihradszky, University of California, San Francisco, California, USA

4:00pm

Poster Session B

Symposium
Nikko Ballroom

Chair: Jonathan Trinidad, University of California, San Francisco, California, USA

8:30am	5.1	Characterization of the Velos, an Enhanced LTQ Orbitrap, for Proteomics Jesper Velgaard Olsen, University of Copenhagen, NNF Center for Protein Research, Copenhagen, Denmark
9:10	5.2	Analysis of the Yeast Kinase-Substrate Networks by Quantitative Phosphoproteomics Bernd Bodenmiller, ETH - Swiss Federal Institute of Technology, Zurich, Switzerland
9:50	5.3	Quantitative Phosphoproteomics to Define Kinase-substrate Relationships in Cell Division Judit Villén, Harvard Medical School, Boston, Massachusetts, USA
10:30		Coffee break

Chair: John Stults, Genentech, South San Francisco, California, USA

10:50am	5.4	Plenary Lecture Global Analysis of Cdk1 Substrate Phosphorylation Sites in vivo David O. Morgan, University of California, San Francisco, California, USA
11:50		Lunch

Chair: Ileana M. Cristea, Princeton University, Princeton, New Jersey, USA

1:20pm	6.1	Characterization and Quantification of Phosphosites in the Proteome of Human Primary T-Lymphocytes Emilio Gelpi, Instituto de Investigaciones Biomedicas, Barcelona, Spain
2:00	6.2	Analysis of Ubiquitin Chain Editing by Quantitative Mass Spectrometry Donald S. Kirkpatrick, Genentech, Inc., South San Francisco, California, USA
2:40	6.3	Age Determination in the Adult Human Brain and Body Using Bomb-Carbon Kirsty L. Spalding, Karolinska Institute, Stockholm, Sweden

Symposium Poster Session C
Monterey & Carmel Rooms

Co-Chairs: Robert Chalkley and Nicholas Hertz, University of California, San Francisco, California, USA

3:20pm

Poster Session C

Conference Dinner
Julia Morgan Ballroom

6:00pm		Conference Dinner Reception Julia Morgan Ballroom
7:00		Conference Dinner Julia Morgan Ballroom

Symposium
Nikko Ballroom

Chair: Emilio Gelpi, Instituto de Investigaciones Biomedicas, Barcelona, Spain

8:30am	7.1	Signaling to Transcription Networks in Nerve Injury Response Michael Fainzilber, Weizmann Institute of Science, Rehovot, Israel
9:10	7.2	Regulation of Neuronal Protein Levels at Subcellular Sites Distant from the Cell Body Jeffery L. Twiss, A.I. duPont Hospital for Children, Wilmington, Delaware, USA
9:50	7.3	Organelle Proteomics: Linking Axonal Transport to Nerve Regeneration Valeria Cavalli, Hope Center for Neurological Disorders, Washington University in St. Louis, Missouri, USA
10:30		Coffee break
11:00	7.4	Quantitative Phosphoproteomics Identifies Sites in K-Cl Co-Transporters that Regulate Cell Volume and Neuronal Excitation Jesse J. Rinehart, Yale University, New Haven, Connecticut, USA
11:40		Lunch

Chair: Pete Wildes, University of California, San Francisco, California, USA

1:40pm	8.1	Mass Spectrometry as a Detector for Protein Ubquitination Jill Barber, University of Manchester, Manchester, UK
2:20	8.2	Quantitative Proteomics Analysis of C/EBPα Transcription Factor Complexes in Leukemia Jarrod A. Marto, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
3:00	8.3	Rapid, Near Proteome-wide, Quantitative Analysis of Aneuploid Budding Yeast Noah Dephoure, Harvard Medical School, Boston, Massachusetts, USA

Chair: A. L. Burlingame, University of California, San Francisco, California, USA

3:40pm

8.4

Plenary Lecture
Advancing Epigenetics Research by Proteomics: Technologies, Applications and Perspectives
Ole N. Jensen, University of Southern Denmark, Odense, Denmark

4:40pm		Closing remarks
5:00		Adjourn

Program

Saturday, August 22

Sunday, August 23

Monday, August 24

Tuesday, August 25

Wednesday, August 26

Thursday, August 27