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Molecular & Cellular Proteomics 2:S1-S15, 2003.
© 2003 by The American Society for Biochemistry and Molecular Biology, Inc.

Program

Sunday, August 24

1:00 p.m.

Pre-Conference Forum: New Solutions for Integrating Genomics and Advanced MS-based Proteomic Data

Hosted by Applied Biosystems

Room TBA

3:00 p.m.

Registration

Mezzanine

3:00 p.m.

Poster Set-up

Gold & Venetian Rooms

6:00 p.m.

Opening Reception

Pavilion Room

Monday, August 25

7:30 a.m.

Registration

Grand Ballroom Vestibule

Session 1

Monday, August 25, Grand Ballroom

8:15 a.m.

Introduction

A. L. Burlingame, University of California, San Francisco, CA

John T. Stults, Biospect, Inc., S. San Francisco, CA

Plenary Lecture

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

8:30 a.m.

1.1¹ Has the Time Finally Come to Replace Gel Electrophoresis of DNA with Mass Spectrometry?

Charles R. Cantor, SEQUENOM, Inc., San Diego, CA

Session

Chair: Kenneth G. Standing, University of Manitoba, Canada

9:30 a.m.

1.2 Nano-electrospray Mass Spectrometry of Dynamic Multi Protein Complexes

Carol V. Robinson, Cambridge University, Cambridge, UK

10:10 a.m.

Coffee Break

Chair: Michael A. Baldwin, University of California, San Francisco, CA

10:30 a.m.

1.3 Identification of Posttranslational Modifications of Peptides Using a Hybrid Triple Quadrupole Linear Ion Trap Mass Spectrometer

David A. Maltby, University of California, San Francisco, CA

11:10 a.m.

1.4 High Resolution/High Accuracy Mass Spectrometry of Biopolymers Using a New Hybrid Linear Trap-FT ICR Mass Spectrometer

Michael W. Linscheid, Humboldt Universitaet zu Berlin, Berlin, Germany

11:50 a.m.

1.5 Towards Proteomics-type Analysis of Post-translational Modifications in Proteins by Tandem Mass Spectrometry Using Electron Capture Dissociation

Roman A. Zubarev, University of Southern Denmark, Odense, Denmark

12:30 p.m.

Lunch Break

Session 2

Chair: Emilio Gelpi, IIBB-CSIC, Spain

Monday, August 25, Grand Ballroom

2:00 p.m.

2.1 Measurement of Enzyme Activation in Single Cells

Nancy L. Allbritton, University of California, Irvine

2:40 p.m.

2.2 Free-Flow-Electrophoresis: A Highly Versatile Fractionation Method for Protein Analysis and Proteomics

Christoph Eckerskorn, Tecan Munich GmbH, Kirchheim, Germany

3:20 p.m.

2.3 Quantitating Molecular Interactions

David Myszka, University of Utah, Salt Lake City, UT

Poster Session A

Co-Chairs: Katalin F. Medzihradszky, University of California, San Francisco, CA, and James Webb, Illinois State University, Normal, IL

Monday, August 25, 4:00 p.m., Gold & Venetian Rooms

A.1² (1100)

Peroxisomal Proteomics, a New Tool to Study Peroxisomal Disorders

J. Mi and S. Cristobal

A.2 (1103)

Combining Metabolomics and Proteomics in Plant Systems Using GC/TOF and Multidimensional LC/MS

W. Weckwerth

A.3 (1106)

Probing Ffh-FtsY Complex Interface Using Chemical Cross-linking and Mass Spectrometry

F. Chu and A. L. Burlingame

A.4 (1109)

Enrichment and Identification of WEHI 231 Phosphoproteins Using IMAC and LC-MS/MS

H. Shu, S. Chen, R. Hsueh, and D. Brekken

A.5 (1116)

Quantifying Multidimensional Liquid Chromatographic Proteomics Without Isotopes

H. Lin, W. Wang, S. Roy, T. A. Shaler, H. Zhou, L. R. Hill, M. Anderle, P. Kumar, and C. H. Becker

A.6 (1119)

Strategies to monitor structurally altered estrogen receptor as found in breast cancers

C. Atsriku, J. E. Meza, G. K. Scott, C. C. Benz, and M. A. Baldwin

A.7 (1122)

Development of a Fully Automated Two-dimensional Nano-electrospray LC/MS System for Sub-fmol Proteomics Analysis

T. Zhang, K. Miller, and D. Chelius

A.8 (1125)

Mass Spectrometry Based Scanning for Post-translational Modifications of Histones

P. Schindler, H. Towbin, M. Coulot, O. Zingel, and J. van Oostrum

A.9 (1128)

Effects of Different Ventilation Strategies on the Proteome of Rat Alveolar Type II Cells

J. Hirsch, K. C. Hansen, J. A. Frank, R. J. Chalkley, X. Fang, A. L. Burlingame, and M. A. Matthay

A.10 (1131)

Enhanced Throughput and Sensitivity in MALDI Mass Spectrometry

X. Chen, N. Illingworth, M. Shanler, and K. M. Hughes

A.11 (1134)

Taggor-PepMap, a New Software Pipeline Using LC-MS/MS Data for Genome Annotation

E. Reguer, M. Ferro, E. Nugues, T. Vermat, R. Cahuzac, M. Vigouroux, E. Mouton, Y. Vandenbrouck, J. Garin, and A. Viari

A.12 (1138)

Proteomic Analysis of Human Serum by 2D DIGE and SELDI-MS

A. D. Gonzales, B. A. Chromy, G. A. Murphy, M. W. Choi, and S. L. McCutchen-Maloney

A.13 (1141)

Subcellular Proteomic Characterization of Host Response to Yersinia pestis and Near Neighbors

C. G. Zhang, A. D. Gonzales, M. W. Choi, and S. L. McCutchen-Maloney

A.14 (1143)

Modification of Bovine Cytochrome c Oxidase by Peroxide and 4-Hydroxy-2-Nonenal: Changes in Protein and Cardiolipin Structure

S. T. Weintraub, A. Musatov, C. A. Carroll, and N. C. Robinson

A.15 (1146)

Proteomic Analysis of the Complete Ribosome from Rhodopseudomonas palustris Using Integrated "Top-down" and "Bottom-up" Mass Spectrometric Approaches

M. B. Strader, N. C. VerBerkmoes, R. L. Hettich, J. W. Barton, B. D. Bruce, L. J. Hauser, F. W. Larimer, B. H. Davison, D. A. Pelletier, and G. B. Hurst

A.16 (1149)

Enzymatic and Non-enzymatic Acetylation of the HIV-1 Tat Protein: An In Vitro Study

W. Dormeyer, A. Dorr, M. Ott, and M. Schnoelzer

A.17 (1152)

Mapping O-GlcNAc Modification Sites with ß-elimination/Michael Addition Using DTT as an Affinity Tag

K. Vosseller, L. Wells, B. Cole, K. Hansen, R. Chalkely, J. Cronshaw, M. J. Matunis, A. L. Burlingame, and G. Hart

A.18 (1155)

Mass Spectrometry Characterization of Human Erythrocyte Spectrin Phosphorylation Sites and Side-reactions of NTCB Cleavage

H.-Y. Tang and D. W. Speicher

A.19 (1158)

Whole Blood as a Human Model for Proteomic Host Response to Pathogens

S. L. McCutchen-Maloney, G. A. Murphy, A. D. Gonzales, J. L. Heidbrink, M. W. Choi, and B. A. Chromy

A.20 (1162)

Pneumatic Assistance in MALDI—The Properties of Commonly-used Carboxylic Acid Matrices

V. L. Talroze, A. L. Burlingame, I. Leipunsky, and M. A. Baldwin

A.21 (1165)

Affinity Capture of Ligands from Brain-conditioned Medium by Nuclear Receptors: Polyunsaturated Fatty Acids Bind to RXR Alpha

J. Lenqvist, J. Sjovall, T. Perlmann, and W. J. Griffiths

A.22 (1168)

Analysis of Multi-protein Complexes and Whole Cell Organelles

J. Reinders, Y. Wagner, R. Zahedi, C. Joppich, H. E. Meyer, P. Rehling, N. Pfanner, C. Meisinger, and A. Sickmann

A.23 (1172)

MALDI-TOF-MS Differentiation of Yeasts

R. O. Jenkins and R. E. Sherburn

A.24 (1175)

Oxidative Protein Modifications and Age-related Vision Loss

J. W. Crabb, X. Gu, K. Renganathan, M. Miyagi, Q. Ebrahem, B. Anand-Apte, S. L. Hazen, D. T. Organisciak, R. G. Salomon, and J. G. Hollyfield

A.25 (1178)

A New Approach to Profile Ovarian Cancer Serum Using Functionalized Magnetic Beads, AnchorChip\T Technology, MALDI-TOF MS, MALDI-TOF/TOF MS and Bioinformatics

S.-M. Leung and S. C. Mok

A.26 (1182)

Mass Spectrometric Analysis of Intact Shewanella oneidenis Proteins Using Capillary RPLC/FTICR and CIEF/FTICR

S. Ahn, B. Bogdanov, A. N. Vilkov, D.-H. Shin, D. Simpson, R. Zhao, L. Pasa-Tolic, M. Lipton, and R. D. Smith

A.27 (1185)

Pathogenic Bacterial Profiling and Cataloguing by LC MALDI Tandem MS Analysis

S. Bhardwaj and M. Lin

A.28 (1188)

LC/MS/MS Analysis of Post-translational Modifications in Chicken Myelin Basic Proteins with Trypsin and Endoproteinase Glu-C Digestions

J. Kim, D. G. Camp II, H. Udseth, R. D. Smith, and R. Zand

A.29 (1191)

Atmospheric Pressure IR Ionization From Solutions (AP IRIS)for Analysis of Complex Carbohydrates

N. I. Taranenko, P. Tan, V. Doroshenko, and B. Musselman

A.30 (1194)

Toward the Automated Identification of Phosphorylation Sites in Proteomics by LC-MS/MS

P. Juhasz, B. Williamson, J. Marchese, and S. Martin

A.31 (1197)

Use of Automated MDLC with Time Filtered Exclusion for the Identification of DNA Binding Proteins in E. coli

C. L. Hunter and L. Nuwaysir

A.32 (1200)

Singlet Oxygen-induced Oxidation of Proteins: Evidence for Non-catalytic Production of Hydrogen Peroxide

J. Shao, J. Lancaster, M. Kirk, and S. Barnes

A.33 (1203)

Chemical Adduction Sites in Cytochrome c Characterized by Mass Spectrometry

M. D. Person, S. L. Habib, T. J. Monks, and S. S. Lau

A.34 (1206)

Automated Chip-based Nanoelectrospray Mass Spectrometry for the Quantitative Determination of Noncovalent Protein-ligand Binding Interactions

S. Zhang, C. K. Van Pelt, and W. C. Muster

A.35 (1209)

Strategies for MS Westerns Using a Quadrupole Time-of-Flight MS

D. M. Schlatzer, J. Krise, K. Blackburn, and A. Moseley

A.36 (1212)

Using Comparative Proteomics and Functional Genomics to Understand Cytokinesis

A. R. Skop, H. Liu, J. Yates, B. J. Meyer, and R. Heald

A.37(1215)

Multidimensional Liquid Phase Separations of Intact Proteins as an Alternative to 2D Gel Electrophoresis for Proteomics

A. Apffel, H. Yin, T. Vandegoor, and K. Killeen

A.38 (1219)

PrepTips: A New Method for Cleaning and Concentrating Biological Samples Prior to Mass Spectrometric Analysis

J. R. Krone, D. Miller, I. Isaac, C. Periana, M. Pisano, and R. Sostek

A.39 (1220)

The Role of TMT1 in a Common Repair System for Methylene Addition Pathway Byproducts: The EI GC/MS Identification of 3-Isopropylmalate as a Novel Tmt1p Substrate

D. S. Dumlao, J. E. Katz, J. I. Wasserman, M. E. Jung, K. F. Faull, and S. G. Clarke

A.40 (1221)

Intact Mass Proteomics of Biological Membranes

J. P. Whitelegge, R. Aguilera, A. Dooley, S. Gómez, J. Nally, M. Lovett, W. Vermaas, and K. F. Faull

Session 3

Tuesday, August 26, Grand Ballroom

Plenary Lecture

Chair: Ralph A. Bradshaw, University of California, Irvine, CA

8:30 a.m.

3.1 Discovery of Signal Transduction Pathways: Current Tools of Chemical Biology and Other New Technologies

Kevan M. Shokat, University of California, San Francisco, CA

Session

Chair: Scott D. Patterson, Farmal Biomedicines, CA

9:30 a.m.

3.2 A Quantitative View of Protein Phosphorylation

Roland Annan, GlaxoSmithKline, King of Prussia, PA

10:10 a.m.

Coffee Break

10:30 a.m.

3.3 Gentle Methods for Probing Protein Post-translational Modifications with Mass Spectrometry

Catherine E. Costello, Boston University School of Medicine, Boston, MA

11:10 a.m.

3.4 Time-controlled Transcardiac Perfusion Crosslinking (tcTPC): A Novel Tool for the In Vivo Study of Protein Interactions in Complex Tissues

Gerold Schmitt-Ulms, University of Toronto, Toronto, Canada

11:50 a.m.

3.5 Activity-based Protein Profiling: Chemical Approaches for Functional Proteomics

Benjamin F. Cravatt, The Scripps Research Institute, LaJolla, CA

12:30 p.m.

Lunch Break

Session 4

Chair: Steven A. Carr, Millennium Pharmaceuticals, Cambridge, MA

Tuesday, August 26, Grand Ballroom

2:00 p.m.

4.1 Quantitative Proteomics: Current Status, Challenges and New Directions

Ruedi H. Aebersold, Institute for Systems Biology, Seattle, WA

2:40 p.m.

4.2 Mass Spectrometry-based Functional Proteomics: A Maturing Tool in Drug Target Identification and Validation

Yongchang Qiu, Wyeth Research, Cambridge, MA

3:20 p.m.

4.3 A Human Proteome Resource Initiative

Mathias Uhlen, Royal Institute of Technology (KTH), Stockholm, Sweden

Poster Session B

Co-Chairs: David A. Maltby, University of California, San Francisco, CA, and Lan Huang, University of California, Irvine, CA

Tuesday, August 26, 4:00 p.m., Gold & Venetian Rooms

B.1 (1101)

Subproteomics at a Single Cell Level: Active Pathways in Arabidopsis thaliana Trichomes

S. Wienkoop, M. Glinski, and W. Weckwert

B.2 (1104)

Dual-gradient Capillary LC/MS/MS for Complex Proteomics Analysis

R. van Soest, G. Mitulovic, R. Swart, D. Irina, J.-P. Chervet, and H. Schwartz

B.3 (1107)

Selective-enrichment of Thiophosphorylated Polypeptides as a Tool for the Analysis of Protein Phosphorylation

S. W. Kwon, S. C. Kim, J. R. Falck, and Y. Zhao

B.4 (1110)

Mass Spectrometric Characterization of a Nuclear Protein Complex Isolated from Arabidopsis thaliana

E. Klement, K. Panigrahi, E. Schafer, F. Nagy, and K. F. Medzihradszky

B.5 (1113)

Dramatic Productivity Improvement for Protein Identification Using a New Two-dimensional Ion Trap Mass Spectrometer

D. Chelius, T. Zhang, and K. Miller

B.6 (1117)

Determination of Protein Markers in Human Serum. Analysis of Protein Expression on Toxic Oil Syndrome Studies

C. Quero, N. Colome, M. R. Prieto, M. Carrascal, M. Posada, E. Gelpi, and J. Abian

B.7 (1120)

Analysis of Post-synaptic Receptor Complexes in the Mammalian Central Nervous System

J. C. Trinidad, A. Thalhammer, C. Specht, K. C. Hansen, J. Allen, R. Schoepfer, and A. L. Burlingame

B.8 (1123)

Identification of Tyrosine Phosphorylated Proteins in Chemokine Stimulated Primary Human T-cells

P. J. Hensbergen, C. I. A. Balog, R. C. van der Schors, E. M. van der Raaij-Helmer, A. M. Deelder, and C. P. Tensen

B.9 (1126)

Mass Spectrometric Studies of Benzimidazole Inhibitors in the Secretory Cell System

C. L. Watson and J. G. Forte

B.10 (1129)

The Study of Intracellular Membrane Compartments

C. Ramus, A. Gonzalez, S. Miras, S. Daniel, C. Dahout, S. Brugiere, M. Ferro, J. Joyard, N. Rolland, and J. Garin

B.11 (1132)

Proteome Analysis of the Anoxygenic Photobacterium Rhodopseudomonas palustris

N. C. VerBerkmoes, M. B. Strader, P. Lankford, D. Pelletier, L. Hauser, G. B. Hurst, S. J. Kennel, C. S. Harwood, R. L. Hettich, and F. W. Larimer

B.12 (1135)

An Improved Accelerated In-gel Tryptic Digestion Method for Protein Identification by Mass Spectrometry

X. Zhang, K. C. Hansen, R. J. Chalkley, and A. L. Burlingame

B.13 (1137)

Statistical Analysis of SELDI Mass Spectral Profiles from Whole Nipple Fluid as a Diagnostic Marker for Breast Cancer.

H. Shau, D. Shen, J. P. Whitelegge, J. Gornbein, J. He, K. F. Faull, and H. R. Chang

B.14 (1139)

Relative Quantitation of Polypeptides in the Urine of Dents Disease Patients by Multidimensional Liquid Chromatography and Complementary Quantitative Mass Spectrometric Approaches

P. R. Cutillas, K. C. Hansen, R. J. Chalkley, R. J. Unwin, and A. L. Burlingame

B.15 (1142)

Structural Characterization of Native Mouse ZP3

E. S. Boja, T. Hoodbhoy, J. Dean, and H. M. Fales

B.16 (1147)

A Focused Proteometric Approach for the Mass Spectrometric Identification of Relevant Tumor-specific Cell Surface Antigens

T. E. Hotaling, T. W. Liang, J. D. Leszyk, and G. A. Vehar

B.17 (1150)

Proteomic Analysis of Shewanella oneidensis Using Three-dimensional LC and Tandem MS

H. M. Mottaz, R. J. Moore, K. Petritis, K. J. Auberry, D. J. Anderson, R. D. Smith, and M. S. Lipton

B.18 (1153)

Polyprotein Processing: Cis and Trans Proteolytic Activities of Sesbania Mosaic Virus Serine Protease

P. S. Satheshkumar, G. L. Lokesh, and H. S. Savithri

B.19 (1156)

Precursor Ion Scanning MS Identification of Cysteine-containing Peptides after their Selective Conversion to Phosphopeptides: A Method to Study Sulfhydryl Redox Chemistry in Proteins

F. Hubalek, D. E. Edmondson, and J. Pohl

B.20 (1159)

A Method for High Efficiency Peptide Sequencing Using Combined Enzymatic Digestion and Chemical Derivatization on MALDI MSMS

Y. Huang, P. L. Ross, I. Smirnov, S. Martin, and D. Pappin

B.21 (1163)

Proteomic Measurements by (Off-line HPLC)-MALDI-QqTOF

K. G. Standing, O. Krokhin, W. Ens, and H. Perreault

B.22 (1166)

Discovery of Protein Biomarkers in Dialysis Patients Using SELDI-MS

G. A. Murphy, J. L. Heidbrink, R. G. Langlois, J. E. Trebes, E. Dalmasso, Y. Ying, R. W. Davies, J. P. Fitch, and S. L. McCutchen-Maloney

B.23 (1169)

The pH Dependence of Liposome Protection Studies on the Steroidogenic Acute Regulatory Protein (StAR)

D. C. Yaworsky, H. S. Bose, J. D. Bell, L. B. Jensen, W. L. Miller, and M. A. Baldwin

B.24 (1173)

Determination of Metallothionein Bound Zinc from Pacific Giant Clam Kidney Using Conventional and Isotope Dilution Inductively Coupled Plasma Mass Spectrometry

D. S. Vidler, R. O. Jenkins, B. Fairman, J. F. Hall, and C. F. Harrington

B.25 (1176)

CRALBP and a Visual Cycle Protein Complex

J. W. Crabb, S. K. Bhattacharya, Z. Wu, A. Hasan, K. A. West, K. Nakanishi, M. Nawrot, and J. C. Saari

B.26 (1180)

New Features of Protein Prospector: Improved Database Scoring and Analysis of ICAT Data

K. C. Hansen, R. J. Chalkley, L. Huang, P. R. Baker, and A. L. Burlingame

B.27 (1183)

Primary Sequence Characterization of Catestatin Intermediates and Peptides Defines Proteolytic Cleavage Sites Utilized for Converting Chromogranin A into Active Catestatin Secreted from Neuroendocrine Chromaffin Cells

J. C. Lee, C. V. Taylor, S. P. Gaucher, T. Toneff, L. Taupenot, S. Yasothornsrikul, S. K. Mahata, C. Sei, R. J. Parmer, J. M. Neveu, W. S. Lane, B. W. Gibson, D. T. O’Connor, and V. Y H. Hook

B.28 (1186)

A Systematic Study of Signal Suppression and Protein Identification with MALDI

A. S. Meyers

B.29 (1189)

Cathepsin L in Secretory Vesicles Functions as a Prohormone Processing Enzyme for Production of the Enkephalin Peptide Neurotransmitter

S. Yasothornsrikul, V. Hook, D. Greenbaum, K. F. Medzihradszky, T. Toneff, R. Bundey, R. Miller, B. Schilling, I. Petermann, J. Dehnert, A. Logvinova, P. Goldsmith, J. M. Neveu, W. S. Lane, B. Gibson, T. Reinheckel, C. Peters, and M. Bogyo

B.30 (1192)

Web Based DBParser for Proteome Data Analysis

X. Yang, V. Dondeti, R. Dezube, D. M. Maynard, S. P. Markey, L. Y Geer, J. Epstein, and J. A. Kowalak

B.31 (1195)

Deblocking N-terminal Pyroglutamyl Residues in Peptides and Proteins with Methylamine

M. S. Reed and J. Pohl, WITHDRAWN

B.32 (1198)

Mass Spectrometric Analysis of Altered Processing in Ras and Other CaaX Proteins from Rce1 and ICMT Deficient Mouse Embryo Fibroblasts

D. M. Smith-Beckerman, S. C. Hall, M. Lobo, A. Anton, Q. Bin, S. Sing, F. Raoufi, and Y.-H. Da

B.33 (1201)

Data Management and Analysis of Serum Peptide Profiling Studies

J. Philip, J. Villanueva, and P. Tempst

B.34 (1204)

Proteomics of Common Brain Protein Modulations by Different Dietary Polyphenols

J. Deshane, C. Grubbs, S. Barnes, S. Meleth, and H. Kim

B.35 (1207)

Increased Sensitivity for Protein Digest Analysis with a High Capacity AP-MALDI Trap

J. E. Meza, D. Yi, P. D. Perkins, B. D. Miller, C. A. Miller, and A. Mordehai

B.36 (1210)

Influence of Quinupristin/Dalfopristin on Growth and Exotoxin Production of Staphylococcus aureus

C. Koszczol, M. Kroenke, and K. Bernardo

B.37 (1213)

An Analysis of Cold Induced Changes in Protein Expression of Tulip Bulbs

T. W. Thannhauser, B. Xiang, Y. Yang, A. P. Ranwala, and W. B. Miller

B.38 (1217)

Automation of Sample Preparation for MALDI-TOF Mass Spectrometry

D. S. Lee, H.-R. Aerni, A. R. Erskine, M. L. Reyzer, D. S. Cornett, M. W. Mutz, R. M. Caprioli, and R. N. Ellson

B.39 (1222)

The Arabidopsis thaliana Cytoplasmic Ribosomal Proteome

I.-F. Chang, K. Szick-Miranda, S. Pan, and J. Bailey-Serres

Session 5

Wednesday, August 27, Grand Ballroom

Session

Chair: Ruedi H. Aebersold, Institute for Systems Biology, Seattle, WA

8:30 a.m.

5.1 Proteomics Reveals New Concepts in the Immune Response to Infectious Agents

Michel Desjardins, Universite de Montreal, Montreal, Canada

9:10 a.m.

5.2 Functional Encoding of Proteomes Through the Use of Stable-isotope Labeling by Amino Acids in Cell Culture (SILAC)

Leonard J. Foster, University of Southern Denmark, Odense, Denmark

9:50 a.m.

5.3 Systematic Identification of Kinetochore Proteins and their Phosphorylation Sites

David G. Drubin, University of California, Berkeley, CA

10:30 a.m.

Coffee Break

Plenary Lecture

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

10:50 a.m.

5.4 Writing and Reading the Histone Code

C. David Allis, The Rockefeller University, New York, NY

11:50 a.m.

Lunch Break

Session 6

Chair: Sandrine Uttenweiler, CNRS, Toulouse, France

Wednesday, August 27, Grand Ballroom

1:30 p.m.

6.1 Proteomics of the Gsp1pGTPase System in S. cerevisiae

Nadia P. C. Allen, Stanford University, Stanford CA

2:10 p.m.

6.2 Functional Proteomic Analysis of Mitotic Substructures Reveals Conserved Cell Division components

Rebecca Heald, University of California, Berkeley, CA

Poster Session C

Co-Chairs: Michael A. Baldwin, University of California, San Francisco, CA, and Keith Vosseller, University of California, San Francisco, CA

Wednesday, August 27, 2:50 p.m., Gold & Venetian Rooms

C.1 (1102)

Quantitative Proteomic Analysis of Interferon Response in Human Liver Cells Using the Isotope Coded Affinity Tag Method and Novel Bioinformatics Tools

Y. Wei, H. Lee, G. Sperrazzo, E. C. Yi, E. Deutsch, A. Keller, X. Li, D. R. Goodlett, M. G. Katze, and R. Aebersold

C.2 (1105)

Stable Isotope Labeling of Phosphopeptides for Multiparallel Kinase Target Analysis and Identification of Phosphorylation Sites

M. Glinski, S. Wienkoop, and W. Weckwerth

C.3 (1108)

Capillary HPLC/Mass Spectrometric Analysis of Proteins from Affinity-purified Plasma Membrane

Y. Zhao, W. Zhao, M. White, and Y. Zhao

C.4 (1111)

A Full Assignment of Yeast Histone H3 Post-transcriptional Modification Sites by Mass Spectrometry

K. Zhang, F. Xu, and M. Grunstein

C.5 (1115)

Deciphering the Protein-interacting Network of dUTPase

E. Hunyadi-Gulyas, A. Bekesi, B. G. Vertessy, and K. F. Medzihradszky

C.6 (1118)

ESI MSⁿ Analyses of Intact Proteins Eluted from SDS PAGE Gels to Characterize Protein Variants and Posttranslational Modifications

S. Claverol, S. Uttenweiler, J.-E. Gairin, O. Burlet-Schiltz, and B. Monsarrat

C.7 (1121)

Identification of Secreted Notch Cleavage Products by Mass Spectrometric Analyses

F. Gharahdaghi, F. Liu, R. C. Spreen, and B. Greenberg

C.8 (1124)

The Role of Prolines in Mass Spectrometry Analysis of Scorpion Toxins

C. V. F. Batista, L. del Pozo, B. Becerril, and L. D. Possani

C.9 (1127)

Chemical Screening by Mass Spectrometry to Identify Inhibitors of Anthrax Lethal Factor

D.-H. Min, W.-J. Tang, and M. Mrksich

C.10 (1130)

Intact Cell MALDI Mass Spectrometry of Bacteria from Double-depleted ¹³C and ¹⁵N Media

C. L. Wilkins, M. J. Stump, J. J. Jones, R. C. Fleming, and J. O. Lay, Jr

C.11 (1133)

Quantitative Proteomic Analysis of Focal Adhesions

C. L. de Hoog, L. J. Foster, M. M. Nielsen, and M. Mann

C.12 (1136)

Approaches to Cross Species Protein Identification from the Polycyclic Aromatic Hydrocarbon-degrading Bacterium Mycobacterium vanbaalenii PYR-1

R. C. Jones, S.-J. Kim, O.-G. Kweon, R. D. Edmondson, and C. E. Cerniglia

C.13 (1140)

Refolding of Aspartate Aminotransferases Analyzed by Hydrogen Exchange and Mass Spectrometry

J. A. Oses-Prieto, A. Artigues, A. J. Iriarte, and M. Martinez-Carrion

C.14 (1144)

Comparison of MALDI-qTOF vs. MALDI-TOFTOF

R. J. Chalkley, D. A. Maltby, K. C. Hansen, and A. L. Burlingame

C.15 (1148)

Serial Quantitation and Identification of Proteins Using Ion Energy Loss and Mass Spectrometry

M. Palmblad, P. G. Grant, S. J. Shields, D. J. Hillegonds, G. Bench, and J. S. Vogel

C.16 (1151)

"Affinity Proteomics": Two Dimensional Chromatographic Approach of Epitope Extraction by Mass Spectrometry

J. Albanese, S. Wong, and S. Deshpande

C.17 (1154)

Proteomic Characterization of the Mechanism of Virulence in Yersinia pestis

B. A. Chromy, A. D. Gonzales, G. A. Murphy, M. W. Choi, J. P. Fitch, and S. L. McCutchen-Maloney

C.18 (1157)

Difference-protein Analysis of Apoptosis in Drosophila melanogaster Using DIGE, Mass Spectrometry, and Time-lapse Fluorescence Microscopy

K. L. Robertson, S. R. Dowd, and J. S. Minden

C.19 (1161)

Improvement of sensitivity in nanoLC-MS/MS analyses of membrane protein extracts using FAIMS

K. Venne, E. Bonneil, K. Eng, D. A. Barnett, and P. Thibault

C.20 (1164)

Multiple Phosphorylation of Nir2, a Human Homolog of Drosophila melanogaster Retinal Degeneration B Protein, a Novel Regulator of Cell Morphogenesis

R. Amariglio, T. Mehlman, A. Shainskaya, and S. Lev

C.21 (1167)

Introduction of Combined Top-down and Bottom-up Proteomics for Shewanella oneidenis by LC-MS/MS and CIEF-FTICR MS

D. H. Shin, S. Ahn, K. Petritis, K. K. Hixon, H. Mottaz, L. Pasa-Tolic, G. A. Anderson, and R. D. Smith

C.22 (1171)

Proteomics of Breast Cancer: From Differential to Functional Analysis

F. Vandermoere, L. Dolle, I. El Yazidi-Belkoura, E. Adriaenssens, C. Cren-Olive, C. Rolando, J. Lemoine, and H. Hondermarck

C.23 (1174)

LC/MS Characterization of Recombinant Monoclonal Antibodies at the Pre-development Stage

P. Mehndiratta, B. C. Grunder, L. A. Marzilli, J. E. McClellan, B. S. Tangarone, T. J. Porter, and J. C. Rouse

C.24 (1177)

Analysis of the Escherichia coli Cytosolic Protein Fraction by 1-D SDS PAGE and LC-MALDI MS/MS of the In-gel Digests

D. B. Wall, J. W. Finch, S. J. Berger, S. A. Cohen, R. Tyldesley, M. Willetts, and J. Brown

C.25 (1181)

Application of Novel Multiplexed Proteomics Technologies in Proteome-wide Analysis of Pregnancy-induced Protection from Mammary Carcinogenesis

Y. Ge, L. Rajkumar, R. C. Guzman, S. Nandi, and B. J. Agnew

C.26 (1184)

Quantification of Site-specific Phosphorylation Using Stable Isotope Tagged Internal Standards: Demonstration of the In Vivo Mechanism of Action for Inhibitors in the MAPK Kinase Pathway

D. L. Friedman, V. Nanayakkara, M. Burgess, D. Raitt, R. Wei, M. Fitzgibbon, L. Licklider, and M. Botfield

C.27 (1187)

Rapid Mass Measurement of Intact Proteins Using LC/ESI-oa-TOF

D. Yi, J. D. Williams, L. L. Lopez, C. A. Miller, and P. D. Perkins

C.28 (1190)

Investigation of a Mammalian Cellular Model for Differential Expression Analysis Using 1D PAGE and Cleavable ICAT\T Reagents

L. R. Zieske, S. Webb, S. W. Yuen, J. Michelotti, L. Evangelista, S. Nimkar, and P.-M. Yuan

C.29 (1193)

Analysis of Complex Biological Mixtures for Disease Detection and Prevention

L. C. Zeller, M. Palmblad, C. G. Bailey, J. L. Heidbrink, S. McCutchen-Maloney, G. A. Murphy, and A. D. Gonzales

C.30 (1196)

Structural Characterization of -lytic Protease Folding Intermediate Ensemble by Cross-linking and Mass Spectrometry

P. Erciyas and D. A. Agard

C.31 (1199)

Analysis of Protein Sequence from Micro-LC Separations Analyses Using Automated Nanoelectrospray Mass Spectrometry

S. Zhang, C. K. Van Pelt, K. Howe, and D. Smith

C.32 (1202)

Strategies for the Automated Identification and Quantitation of Posttranslational Modifications of Proteins Using a Hybrid Quadrupole Linear Ion Trap Mass Spectrometer

T. A. Settineri, B. L. Williamson, and C. L. Hunter

C.33 (1205)

Serum Peptide Profiling by Magnetic Particle-assisted, Automated Sample Processing and MALDI-TOF Mass Spectrometry

J. Villanueva, J. Philip, D. Entenberg, C. A. Chaparro, E. C. Holland, and P. Tempst

C.34 (1208)

Tools to Characterise Asparagine Hydroxylation and Disulfide Bond Arrangements in Proteins

J. J. Gorman, D. J. Peet, D. Lando, D. A. Whelan, P. Young, T. Wallis, and M. L. Whitelaw

C.35 (1211)

Analysis of Synaptic Vesicle Proteins by Mass Spectrometry

H. D. Coughenour, R. S. Spalding, and C. M. Thompson

C.36 (1214)

Proteomic Analysis of Ribosome Biogenesis: Links to the Cell Cycle

K. Breitkreuz, M. Cook, P. Jorgensen, and M. Tyers

C.37 (1218)

Mapping Strategies for Rat Liver Mitochondrial Proteins

R. D. Edmondson, R. C. Jones, and R. J. Feuers

6:00 p.m.

Reception

Fountain/Crystal Rooms

7:00 p.m.

Conference Dinner

Crown Room

Session 7

Chair: Susan Weintraub, University of Texas Health Sciences Center, San Antonio, TX

Thursday, August 28, Grand Ballroom

8:30 a.m.

7.1 Analysis of Protein Interaction Networks by TAP/MS

Bernhard Küster, Cellzome AG, Heidelberg, Germany

9:10 a.m.

7.2 Comprehensive and Quantitative Proteomic Analyses of Plasma Membrane Proteins from Human Cells

Pierre Thibault, Caprion Pharmaceuticals Inc., Montreal, Canada

9:50 a.m.

7.3 Direct Imaging and Profiling of Proteins in Tissues Using Mass Spectrometry to Aid Diagnosis and Treatment of Disease and to Identify Therapeutic Targets

Richard M. Caprioli, Vanderbilt University School of Medicine, Nashville, TN

10:30 a.m.

Coffee Break

10:50 a.m.

7.4 Serum Peptide Signatures of Solid Tumor Cancers

Paul Tempst, Memorial Sloan-Kettering Cancer Center, New York, NY

11:30 a.m.

7.5 Peptide Mass Signature Genotyping

Jonathan W. Jarvik, Carnegie Mellon University, Pittsburgh, PA

12:10 p.m.

Lunch Break

Session 8

Thursday, August 28, Grand Ballroom

Session

Chair: Hubert Hondermarck, University of Lille, France

1:30 p.m.

8.1 Identification of Helicobacter pylori Antigens by Proteomics

Peter R. Jungblut, Max Planck Institute for Infection Biology, Berlin, Germany

2:10 p.m.

8.2 Role of Mass Spectrometry in Systems Biology

Stephen Naylor, Beyond Genomics, Waltham, MA

2:50 p.m.

Coffee Break

3:10 p.m.

8.3 The Application of Proteomics and Genomics in Drug Discovery and Development

Stanley A. Hefta, Bristol-Myers Squibb, Princeton, NJ

Plenary Lecture

Chair: John T. Stults, Biospect, Inc., S. San Francisco, CA

3:50 p.m.

8.4 Biomarker Discovery by Proteomics and its Role in Drug and Diagnostic Development

Steven A. Carr, Millenium Pharmaceuticals, Cambridge, MA

Closing Remarks

A. L. Burlingame, University of California, San Francisco, CA

Thursday, August 28, 4:50 p.m., Grand Ballroom

5:00 p.m.

Adjourn

FOOTNOTES

¹ Numbers prior to titles correspond to abstract numbers (see p. S17).

² Numbers in parentheses are abstract confirmation numbers.

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