Molecular &

CellularProteomics

Volume 5, Number 4, April 2006 www.mcponline.org

In this issue

ISSN: 1535-9476

Elucidation of the neutrophil phagosome proteome

MRM Assays for Plasma Proteins

Analyzing the E. coli Proteome

Skeletal Muscle Mitochondria

Neutrophil Phagosomes Exposed

Proteomics of RNA Granules

MS/MS Spectrum Quality Scoring

G Protein γ Heterogeneity

Man-6-P Glycopeptide Analysis

H. pylori-Host Interaction

Label-free Quantitation

Antioxidant Proteins

His-Bio Tandem Affinity Tag

Phosphate-binding Tag

Phosphoproteomic Analysis

Protein Enzymatic Digestion

Published by the AmericanSociety for Biochemistryand Molecular Biology

©Agilent Technologies, Inc. 2006 MC 15774

New• Agilent 1200 Series LC Systems and Modules

• Agilent 1200 Series Rapid Resolution LC System

• Agilent 1200 Series HPLC-Chip/MS System

• Agilent Rapid Resolution High Throughput LC Columns

• Agilent 1200 Series Quadrupole LC/MS

• Agilent 6210 Time-of-Flight LC/MS

• Agilent 6300 Series Ion Trap LC/MS Systems

• Agilent 6410 Triple Quadrupole LC/MS

• Agilent 6510 Quadrupole Time-of-Flight LC/MS

• Agilent Mass Profiler Software

• Agilent ChemStation and EZChrom Elite Software

• Agilent Intelligent Services

www.agilent.com/chem/performanceA6

All the performance.All the time.

Now, get all the sensitivity, all the speed, and all the resolution

your application demands. All on one platform. All without

compromise. From rapid resolution LC to HPLC-Chip sensitivity,

our 1200 Series LC systems and ZORBAX columns offer a

complete choice of scalable LC solutions. Our 6000 Series

is a whole new portfolio of LC/MS systems. A new triple

quadrupole and Q-TOF, new model ion trap and TOF, all with the

high performance and reliability you expect from Agilent.

Together with new workflow-specific software, Agilent LC and

LC/MS systems enable you to do more, with less. And they are

all backed up with comprehensive services to help keep your

operations running at peak performance, all the time.

All the performance.All the time.

Introducing Agilent’s ground-breaking 1200 Series LC and 6000 Series LC/MS systems

Agilent 6510 Q-TOF LC/MS

Attomole sensitivityFTMS mass accuracyAgilent reliabilityIntroducing the new Agilent 6510 Q-TOF LC/MS

www.agilent.com/chem/QTOFA6

All the Performance. All the Time.

© Agilent Technologies, Inc. 2006 MC15458

Meet the first Q-TOF LC/MS that combines the highest

level of analytical performance with Agilent’s legendary

reliability. With a ten-fold sensitivity increase over avail-

able Q-TOF systems, routine 1–2 ppm mass accuracy,

unmatched dynamic range, and the fastest data-dependent

acquisition speeds, the 6510 Q-TOF quickly turns complex

biological or chemical analyses into meaningful results.

Put it together with the new Agilent 1200 Series HPLC,

and you’ve got an integrated, easy-to-use LC/MS solution

that delivers all the performance your critical work

demands — run after run, day after day, year after year.

����� ��� �� ��� �� ������������ ��� ��������� ��������� ������

���������� ��

���� ��� ����

online offlineHigh flow or low flow, you’re good to go.

SilicaTips™

TaperTips™

Metal TaperTips™

OPTIMAL ONLINE NANOSPRAY

Your supervisor put his neck on the line to get you hundreds of thousand of dollars ofinstrumentation. Hours were spent in the labto produce that precious sample. And nowyou want to push it through your home-pulledtip? Can you really trust its performance?Online fused-silica PicoTips® are manufacturedto stringent specifications ensuring that eachemitter is consistent and reliable every time to maximize your performance, every time.

GlassTips™

EconoTips™

QuartzTips™

OPTIMAL OFFLINE NANOSPRAY

Are you still using break-to-open glass tips?Broken tips are inconsistent, unreliable andinefficient, all barriers to top performance.Our offline glass and quartz PicoTips® are readyto use right out of the package – no breakingrequired. Their self-filling design makes themeasy-to-use and each PicoTip is video inspectedto meet strict standards for shape and tipopening to ensure quality and performance.Break your performance barrier, not your tips.

Innovations for High-Sensitivity LC-MS Research

www.newobjective.comsales@newobjective.com

888 220 2998 Orders781 933 9560 Phone781 933 9564 Fax

New Objective, Inc.Two Constitution WayWoburn, MA 01801-1023

When Performance MattersP I C O T I P ® E M I T T E R S

AUTHOR INDEXAdkins, Joshua N., 714Aebersold, Ruedi, 652Anderson, Leigh, 573Auer, Bernhard, 737

Baginsky, Sacha, 652Baldi, Pierre, 737Bell, Alexander W., 635Blandford, Vanessa, 635Boismenu, Daniel, 635Burlak, Christopher, 620

Callister, Stephen J., 714Campanaro, Stefano, 608Chan, Chia-Hsin, 702Chang, Jan-Gowth, 702Chen, Sung-Fang, 702Chen, Yong, 769Chow, Lu-Ping, 702Cook, Lana A., 671Cui, Meng, 737

DeLeo, Frank R., 620Denny, Richard, 589DesGroseillers, Luc, 635Diemer, Helene, 726Dingus, Jane, 671Dorschel, Craig, 589Dou, Yimeng, 737

Eddes, James S., 652Eisinger, Dominic, 758Elias, Dwayne A., 714Elvira, George, 635Ettling, Rebecca, 671

Fan, Xiaotang, 635Fang, Ruihua, 714Flick, Karin, 737Forner, Francesca, 608Foster, Leonard J., 608Fredrickson, Jim K., 714

Gao, Shijuan, 769Gao, Youhe, 769Geromanos, Scott J., 589Goddard, Carrie D., 714Gorby, Yuri A., 714Gorenstein, Marc V., 589Grossmann, Jonas, 652Gruissem, Wilhelm, 652Guerrero, Cortnie, 737

Hackstadt, Ted, 620Hanau, Daniel, 726

Hildebrandt, John D., 671Huang, Lan, 737Hunter, Christie L., 573

Kaiser, Peter, 737Khan, Imran H., 758Kinoshita, Eiji, 749Kinoshita-Kikuta, Emiko, 749Knapp, Daniel R., 671Ko, Chia-Cheng, 702Koike, Tohru, 749Kung, Hsing-Jien, 758

Lacaille, Jean-Claude, 635Li, Guo-Zhong, 589Lin, Jaw-Town, 702Lipton, Mary S., 714Lobel, Peter, 686Lotteau, Vincent, 726Luche, Sylvie, 726Luciw, Paul A., 758

Mann, Matthias, 608Mcintosh, Martin, 714McPherson, Peter S., 635Mead, David J., 620Mendoza, Sara, 758Monroe, Matthew E., 714Moore, Ronald J., 714

Nelson, Troy, 671Nesvizhskii, Alexey I., 652

Perrin-Cocon, Laure, 726

Qian, Meiqian, 686

Rabilloud, Thierry, 726Rabourdin-Combe, Chantal, 726Rhyne, Paul, 758Richardson, Keith, 589Rivollier, Aymeric, 726Roos, Franz F., 652

Sanchez-Carbente, Maria del Rayo, 635Schey, Kevin L., 671Serrano, Alexandre, 635Servant, Florence, 635Servet-Delprat, Christine, 726Shen, Yufeng, 714Silva, Jeffrey C., 589Sleat, David E., 686Smith, Richard D., 714Sossin, Wayne S., 635Strub, Jean-Marc, 726Sun, Wei, 769

ix

Tagwerker, Christian, 737Takiyama, Kei, 749Tong, Xin-Kang, 635Tuscano, Joseph, 758

Valle, Giorgio, 608van Dorsselaer, Alain, 726Vogelzang, Mathijs, 652

Wall, Daniel, 589Wang, Linjie, 769

Wang, Pei, 714Wang, Xiaorong, 769Wasiak, Sylwia, 635Whitney, Adeline R., 620Wilcox, Michael D., 671Wu, Ming-Shiang, 702Wu, Shuzhen, 769

Zheng, Dexian, 769Zheng, Haiyan, 686Ziman, Melanie, 758

x

In our Classic Articles you can explore original reprinted articles

dating back to 1905. When completed, this series will contain

over 300 original papers by the legends in biochemistry: including

Folin, Van Slyke, the Coris, Doisy, McCollum, Hastings, Lowry,

Kornberg, Kennedy, Brown, Goldstein, and many more!

JBC Reflections were created as a celebration of JBC’s 100th

Birthday! We have invited premier biochemists to write about

their contributions that have helped mark the many advances in

biochemistry and molecular biology since 1905.

Visit us at: www.jbc.org

Take a journeywith The Journal of Biological Chemistry (JBC) and explore all the exciting and

important discoveries that biochemists have made in the world of science!

Above photograph (by Sam Vandivert, ©The Rockefeller University) shows Stanford Moore (left) and William H. Stein (right) in front of the original amino acid analyzer in 1965.

It is our hope that Classic Articles & Reflections will, in small part, share some of the personal experiences and history of biochemistry.

ReflectionsClassic Articles

We’re experts in our industries and professions. We work in the areas of biochemistry, molecular biology, pharmacology, physiology, nutrition, anatomy and proteomics. We come from diverse backgrounds and have dedicated our professional lives to working in the biological and molecular biology fields.

Publications• Receive FREE individual subscriptions to JBC & MCP (online only)• FREE print subscription to ASBMB Today (our monthly member magazine) • Discounted rates on many scientific journals such as: Journal of Lipid

Research (print only), Trends in Biochemical Sciences, Biotechnology & Applied Biochemistry

Meetings• Discounted ASBMB Annual Meeting registration fees• Discounted ASBMB sponsored symposia registration fees• Access to Fellowship Travel Awards, Career Networking and

Employment Assistance.

Advocacy• Become involved in all levels of governmental activities• Attend special symposia on exciting topics like Evolution• Stay connected with areas of legislation that relate to research with our

online resources.

Education• Annual meeting symposia sponsored by the Education & Professional

Development Committee • Free access to all the resources the ASBMB Undergraduate Affiliate

Network offers• Access to the ASBMB Annual Undergraduate Poster Competition• Links to more educational resources available at www.asbmb.org• Undergrads…join now and become an ASBMB member for only

$20.00 USD!

Diversity• Special Annual meeting symposia sponsored by the

Minority Affairs Committee• FASEB/MARC Visiting Scientists Referral Network• Access to Minority Travel Awards.

Want more information? Visit our Web site at

www.asbmb.org or call us at 301-634-7145 for further membership information.

Why join ASBMB?

just like you.12,000 People

We are your peers.