Exploring the Human Plasma Proteome

Exploring the Human Plasma Proteome

Editor(s): Gilbert S. Omenn

Published Online: 2 NOV 2006

Print ISBN: 9783527317578

Online ISBN: 9783527609482

DOI: 10.1002/9783527609482

About this Book

On the cutting edge of medical diagnostics, plasma proteomics promises to generate a new wave of technologies to help identify many different diseases and disease risks.
Plasma and serum are the preferred non-invasive specimens to test normal individuals, at-risk groups, and patients for protein biomarkers discovered and validated to reflect physiological, pathological, and pharmacological phenotypes. These specimens present enormous challenges due to extreme complexity, huge dynamic range in protein concentrations, non-standardized methods of sample processing, and intra- and inter-individual variation from genetics, diet, smoking, hormones, and other sources. This book presents the major findings from the collaborative Plasma Proteome Project organized by the international Human Proteome Organization (HUPO). The chapters are drawn from a larger set of publications in the journal PROTEOMICS. This book provides a valuable foundation for development and applications of proteomics.

Table of contents

    1. You have free access to this content
    2. Chapter 1

      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 1–35)

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

    3. Chapter 2

      Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project (pages 37–61)

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

    4. Chapter 3

      HUPO Plasma Proteome Project specimen collection and handling: Towards the standardization of parameters for plasma proteome samples (pages 63–89)

      Dr. 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, Dr. David W. Speicher, Frank Vitzthum, Brian B. Haab, Gerard Siest and Daniel W. Chan

    5. Chapter 4

      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 91–113)

      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

    6. Chapter 9

      Efficient prefractionation of low-abundance proteins in human plasma and construction of a two-dimensional map (pages 201–219)

      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 Professor Young-Ki Paik

    7. Chapter 10

      Comparison of alternative analytical techniques for the characterisation of the human serum proteome in HUPO Plasma Proteome Project (pages 221–247)

      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 Dr. Xiaohong Qian

    8. Chapter 11

      A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy (pages 249–271)

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

    9. Chapter 12

      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 273–287)

      Dr. 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

    10. Chapter 13

      An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis (pages 289–315)

      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, Dr. Gilbert S. Omenn and Professor Richard J. Simpson

    11. Chapter 14

      Human Plasma PeptideAtlas (pages 317–322)

      Dr. 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

    12. Chapter 15

      Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories (pages 323–328)

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

    13. Chapter 16

      A functional annotation of subproteomes in human plasma (pages 329–351)

      Peipei Ping, Thomas M. Vondriska, Chad J. Creighton, T. K. B. 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, Professor Young-Ki Paik, Professor William S. Hancock, Dr. David J. States, Dr. Gilbert S. Omenn and Dr. Akhilesh Pandey

    14. Chapter 17

      Cardiovascular-related proteins identified in human plasma by the HUPO Plasma Proteome Project Pilot Phase (pages 353–370)

      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

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