PROTEOMICS

Cover image for Vol. 5 Issue 13

Special Issue: EXPLORING THE HUMAN PLASMA PROTEOME The HUPO Plasma Proteome Project (HPPP)

No. 13 August 2005

Volume 5, Issue 13

Pages 3223–3549

Issue edited by: Gilbert S. Omenn

    1. Cover Picture: Proteomics 13/2005

      Version of Record online: 16 AUG 2005 | DOI: 10.1002/pmic.200590059

    2. Contents: Proteomics 13/2005

      Version of Record online: 16 AUG 2005 | DOI: 10.1002/pmic.200590060

    3. Exploring the Human Plasma Proteome (pages 3223–3225)

      Gilbert S. Omenn

      Version of Record online: 16 AUG 2005 | DOI: 10.1002/pmic.200590056

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      Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database (pages 3226–3245)

      Gilbert S. Omenn, David J. States, Marcin Adamski, Thomas W. Blackwell, Rajasree Menon, Henning Hermjakob, Rolf Apweiler, Brian B. Haab, Richard J. Simpson, James S. Eddes, Eugene A. Kapp, Robert L. Moritz, Daniel W. Chan, Alex J. Rai, Arie Admon, Ruedi Aebersold, Jimmy Eng, William S. Hancock, Stanley A. Hefta, Helmut Meyer, Young-Ki Paik, Jong-Shin Yoo, Peipei Ping, Joel Pounds, Joshua Adkins, Xiaohong Qian, Rong Wang, Valerie Wasinger, Chi Yue Wu, Xiaohang Zhao, Rong Zeng, Alexander Archakov, Akira Tsugita, Ilan Beer, Akhilesh Pandey, Michael Pisano, Philip Andrews, Harald Tammen, David W. Speicher and Samir M. Hanash

      Version of Record online: 16 AUG 2005 | DOI: 10.1002/pmic.200500358

    5. Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project (pages 3246–3261)

      Marcin Adamski, Thomas Blackwell, Rajasree Menon, Lennart Martens, Henning Hermjakob, Chris Taylor, Gilbert S. Omenn and David J. States

      Version of Record online: 16 AUG 2005 | DOI: 10.1002/pmic.200500186

    6. HUPO Plasma Proteome Project specimen collection and handling: Towards the standardization of parameters for plasma proteome samples (pages 3262–3277)

      Alex J. Rai, Craig A. Gelfand, Bruce C. Haywood, David J. Warunek, Jizu Yi, Mark D. Schuchard, Richard J. Mehigh, Steven L. Cockrill, Graham B. I. Scott, Harald Tammen, Peter Schulz-Knappe, David W. Speicher, Frank Vitzthum, Brian B. Haab, Gerard Siest and Daniel W. Chan

      Version of Record online: 29 JUL 2005 | DOI: 10.1002/pmic.200401245

    7. Immunoassay and antibody microarray analysis of the HUPO Plasma Proteome Project reference specimens: Systematic variation between sample types and calibration of mass spectrometry data (pages 3278–3291)

      Brian B. Haab, Bernhard H. Geierstanger, George Michailidis, Frank Vitzthum, Sara Forrester, Ryan Okon, Petri Saviranta, Achim Brinker, Martin Sorette, Lorah Perlee, Shubha Suresh, Garry Drwal, Joshua N. Adkins and Gilbert S. Omenn

      Version of Record online: 22 JUL 2005 | DOI: 10.1002/pmic.200401276

    8. Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma (pages 3292–3303)

      Lynn A. Echan, Hsin-Yao Tang, Nadeem Ali-Khan, KiBeom Lee and David W. Speicher

      Version of Record online: 29 JUL 2005 | DOI: 10.1002/pmic.200401228

    9. Differences among techniques for high-abundant protein depletion (pages 3304–3313)

      Nina Zolotarjova, James Martosella, Gordon Nicol, Jerome Bailey, Barry E. Boyes and William C. Barrett

      Version of Record online: 29 JUL 2005 | DOI: 10.1002/pmic.200402021

    10. Immunoaffinity separation of plasma proteins by IgY microbeads: Meeting the needs of proteomic sample preparation and analysis (pages 3314–3328)

      Lei Huang, Gulia Harvie, Jerald S. Feitelson, Kosi Gramatikoff, David A. Herold, David L. Allen, Ravi Amunngama, Rachel A. Hagler, Michael R. Pisano, Wei-Wei Zhang and Xiangming Fang

      Version of Record online: 22 JUL 2005 | DOI: 10.1002/pmic.200401277

    11. A novel four-dimensional strategy combining protein and peptide separation methods enables detection of low-abundance proteins in human plasma and serum proteomes (pages 3329–3342)

      Hsin-Yao Tang, Nadeem Ali-Khan, Lynn A. Echan, Natasha Levenkova, John J. Rux and David W. Speicher

      Version of Record online: 29 JUL 2005 | DOI: 10.1002/pmic.200401275

    12. A wide range of protein isoforms in serum and plasma uncovered by a quantitative intact protein analysis system (pages 3343–3352)

      David E. Misek, Rork Kuick, Hong Wang, Vladimir Galchev, Bin Deng, Rong Zhao, John Tra, Michael R. Pisano, Ravi Amunugama, David Allen, Angela K. Walker, John R. Strahler, Philip Andrews, Gilbert S. Omenn and Samir M. Hanash

      Version of Record online: 26 JUL 2005 | DOI: 10.1002/pmic.200500103

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    14. Utility of electrophoretically derived protein mass estimates as additional constraints in proteome analysis of human serum based on MS/MS analysis (pages 3376–3385)

      Jin Young Kim, Jeong Hwa Lee, Gun Wook Park, Kun Cho, Kyung-Hoon Kwon, Young Mok Park, Sang Yun Cho, Young-Ki Paik and Jong Shin Yoo

      Version of Record online: 29 JUL 2005 | DOI: 10.1002/pmic.200401220

    15. Efficient prefractionation of low-abundance proteins in human plasma and construction of a two-dimensional map (pages 3386–3396)

      Sang Yun Cho, Eun-Young Lee, Joon Seok Lee, Hye-Young Kim, Jae Myun Park, Min-Seok Kwon, Young-Kew Park, Hyoung-Joo Lee, Min-Jung Kang, Jin Young Kim, Jong Shin Yoo, Sung Jin Park, Jin Won Cho, Hyon-Suk Kim and Young-Ki Paik

      Version of Record online: 26 JUL 2005 | DOI: 10.1002/pmic.200401310

    16. Two-dimensional liquid chromatography/tandem mass spectrometry analysis of Gradiflow™ fractionated native human plasma (pages 3397–3401)

      Valerie C. Wasinger, Vicki L. Locke, Mark J. Raftery, Mark Larance, Deborah Rothemund, Audrey Liew, Irene Bate and Michael Guilhaus

      Version of Record online: 16 AUG 2005 | DOI: 10.1002/pmic.200401160

    17. Application of 2-D free-flow electrophoresis/RP-HPLC for proteomic analysis of human plasma depleted of multi high-abundance proteins (pages 3402–3413)

      Robert L. Moritz, Andrew B. Clippingdale, Eugene A. Kapp, James S. Eddes, Hong Ji, Sam Gilbert, Lisa M. Connolly and Richard J. Simpson

      Version of Record online: 29 JUL 2005 | DOI: 10.1002/pmic.200500096

    18. Peptidomic analysis of human blood specimens: Comparison between plasma specimens and serum by differential peptide display (pages 3414–3422)

      Harald Tammen, Imke Schulte, Rudiger Hess, Christoph Menzel, Markus Kellmann, Thomas Mohring and Peter Schulz-Knappe

      Version of Record online: 22 JUL 2005 | DOI: 10.1002/pmic.200401219

    19. Comparison of alternative analytical techniques for the characterisation of the human serum proteome in HUPO Plasma Proteome Project (pages 3423–3441)

      Xiaohai Li, Yan Gong, Ying Wang, Songfeng Wu, Yun Cai, Ping He, Zhuang Lu, Wantao Ying, Yangjun Zhang, Liyan Jiao, Hongzhi He, Zisen Zhang, Fuchu He, Xiaohang Zhao and Xiaohong Qian

      Version of Record online: 29 JUL 2005 | DOI: 10.1002/pmic.200401226

    20. The human plasma proteome: Analysis of Chinese serum using shotgun strategy (pages 3442–3453)

      Ping He, Hong-Zhi He, Jie Dai, Ying Wang, Quan-Hu Sheng, Lan-Ping Zhou, Zi-Sen Zhang, Yu-Lin Sun, Fang Liu, Kun Wang, Jin-Sheng Zhang, Hui-Xin Wang, Zhen-Mei Song, Hai-Rong Zhang, Rong Zeng and Xiaohang Zhao

      Version of Record online: 26 JUL 2005 | DOI: 10.1002/pmic.200401301

    21. A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy (pages 3454–3466)

      Joshua N. Adkins, Matthew E. Monroe, Kenneth J. Auberry, Yufeng Shen, Jon M. Jacobs, David G. Camp II, Frank Vitzthum, Karin D. Rodland, Richard C. Zangar, Richard D. Smith and Joel G. Pounds

      Version of Record online: 29 JUL 2005 | DOI: 10.1002/pmic.200401333

    22. Analysis of Human Proteome Organization Plasma Proteome Project (HUPO PPP) reference specimens using surface enhanced laser desorption/ionization-time of flight (SELDI-TOF) mass spectrometry: Multi-institution correlation of spectra and identification of biomarkers (pages 3467–3474)

      Alex J. Rai, Paul M. Stemmer, Zhen Zhang, Bao-ling Adam, William T. Morgan, Rebecca E. Caffrey, Vladimir N. Podust, Manisha Patel, Lih-yin Lim, Natalia V. Shipulina, Daniel W. Chan, O. John Semmes and Hon-chiu Eastwood Leung

      Version of Record online: 29 JUL 2005 | DOI: 10.1002/pmic.200401320

    23. An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis (pages 3475–3490)

      Eugene A. Kapp, Frédéric Schütz, Lisa M. Connolly, John A. Chakel, Jose E. Meza, Christine A. Miller, David Fenyo, Jimmy K. Eng, Joshua N. Adkins, Gilbert S. Omenn and Richard J. Simpson

      Version of Record online: 27 JUL 2005 | DOI: 10.1002/pmic.200500126

    24. Human Plasma PeptideAtlas (pages 3497–3500)

      Eric W. Deutsch, Jimmy K. Eng, Hui Zhang, Nichole L. King, Alexey I. Nesvizhskii, Biaoyang Lin, Hookeun Lee, Eugene C. Yi, Reto Ossola and Ruedi Aebersold

      Version of Record online: 29 JUL 2005 | DOI: 10.1002/pmic.200500160

    25. Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories (pages 3501–3505)

      Lennart Martens, Alexey I. Nesvizhskii, Henning Hermjakob, Marcin Adamski, Gilbert S. Omenn, Joël Vandekerckhove and Kris Gevaert

      Version of Record online: 22 JUL 2005 | DOI: 10.1002/pmic.200401302

    26. A functional annotation of subproteomes in human plasma (pages 3506–3519)

      Peipei Ping, Thomas M. Vondriska, Chad J. Creighton, TKB Gandhi, Ziping Yang, Rajasree Menon, Min-Seok Kwon, Sang Yun Cho, Garry Drwal, Markus Kellmann, Suraj Peri, Shubha Suresh, Mads Gronborg, Henrik Molina, Raghothama Chaerkady, B. Rekha, Arun S. Shet, Robert E. Gerszten, Haifeng Wu, Mark Raftery, Valerie Wasinger, Peter Schulz-Knappe, Samir M. Hanash, Young-ki Paik, William S. Hancock, David J. States, Gilbert S. Omenn and Akhilesh Pandey

      Version of Record online: 16 AUG 2005 | DOI: 10.1002/pmic.200500140

    27. Cardiovascular-related proteins identified in human plasma by the HUPO Plasma Proteome Project Pilot Phase (pages 3520–3530)

      Beniam T. Berhane, Chenggong Zong, David A. Liem, Aaron Huang, Steven Le, Ricky D. Edmondson, Richard C. Jones, Xin Qiao, Julian P. Whitelegge, Peipei Ping and Thomas M. Vondriska

      Version of Record online: 29 JUL 2005 | DOI: 10.1002/pmic.200401308

    28. Plasma Proteome Database as a resource for proteomics research (pages 3531–3536)

      Babylakshmi Muthusamy, G. Hanumanthu, Shubha Suresh, B. Rekha, D. Srinivas, L. Karthick, B. M. Vrushabendra, Salil Sharma, Goparani Mishra, Pritam Chatterjee, K. S. Mangala, H. N. Shivashankar, K. N. Chandrika, Nandan Deshpande, M. Suresh, N. Kannabiran, Vidya Niranjan, Anuradha Nalli, T. S. Keshava Prasad, K. S. Arun, Raghunath Reddy, Sreenath Chandran, Trafina Jadhav, D. Julie, M. Mahesh, S. Lynate John, Kshitish Palvankar, D. Sudhir, P. Bala, N. S. Rashmi, G. Vishnupriya, Kaushik Dhar, S. Reshma, Raghothama Chaerkady, T. K. B. Gandhi, H. C. Harsha, S. Sujatha Mohan, Krishna S. Deshpande, Malabika Sarker and Akhilesh Pandey

      Version of Record online: 22 JUL 2005 | DOI: 10.1002/pmic.200401335

    29. You have free access to this content
      PRIDE: The proteomics identifications database (pages 3537–3545)

      Lennart Martens, Henning Hermjakob, Philip Jones, Marcin Adamski, Chris Taylor, David States, Kris Gevaert, Joël Vandekerckhove and Rolf Apweiler

      Version of Record online: 22 JUL 2005 | DOI: 10.1002/pmic.200401303

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