Chapter 16. A functional annotation of subproteomes in human plasma

  1. Prof. Dr. Gilbert S. Omenn
  1. Peipei Ping,
  2. Thomas M. Vondriska1,
  3. Chad J. Creighton,
  4. T. K. B. Gandhi,
  5. Ziping Yang,
  6. Rajasree Menon,
  7. Min-Seok Kwon,
  8. Sang Yun Cho,
  9. Garry Drwal,
  10. Markus Kellmann,
  11. Suraj Peri,
  12. Shubha Suresh,
  13. Mads Gronborg,
  14. Henrik Molina,
  15. Raghothama Chaerkady,
  16. B. Rekha,
  17. Arun S. Shet,
  18. Robert E. Gerszten,
  19. Haifeng Wu,
  20. Mark Raftery,
  21. Valerie Wasinger,
  22. Peter Schulz-Knappe,
  23. Samir M. Hanash,
  24. Professor Young-Ki Paik2,
  25. Professor William S. Hancock3,
  26. Dr. David J. States4,
  27. Dr. Gilbert S. Omenn6 and
  28. Dr. Akhilesh Pandey5

Published Online: 2 NOV 2006

DOI: 10.1002/9783527609482.ch16

Exploring the Human Plasma Proteome

Exploring the Human Plasma Proteome

How to Cite

Ping, P., Vondriska, T. M., Creighton, C. J., Gandhi, T. K. B., Yang, Z., Menon, R., Kwon, M.-S., Cho, S. Y., Drwal, G., Kellmann, M., Peri, S., Suresh, S., Gronborg, M., Molina, H., Chaerkady, R., Rekha, B., Shet, A. S., Gerszten, R. E., Wu, H., Raftery, M., Wasinger, V., Schulz-Knappe, P., Hanash, S. M., Paik, Y.-K., Hancock, W. S., States, D. J., Omenn, G. S. and Pandey, A. (2006) A functional annotation of subproteomes in human plasma, in Exploring the Human Plasma Proteome (ed G. S. Omenn), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527609482.ch16

Editor Information

  1. Internal Medicine, University of Michigan, A520 MSRB 1 Bldg, 1150 West Medical Center Dr. Ann Arbor, MI 48109–0626, USA

Author Information

  1. 1

    Cardiovascular Research Laboratories, Departments of Physiology and Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, Room 1619, MRL Building, Los Angeles, CA 90095, USA

  2. 2

    Yonsei Proteome Research Center and Biomedical Proteome Research Center, Yonsei University, 134 Shinchon-dong, Sudaemoon-ku, Seoul 120-749, Korea

  3. 3

    Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA

  4. 4

    University of Michigan, 2017 Palmer Commons, 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218, USA

  5. 5

    McKusick-Nathans Institute of Genetic Medicine, 733 N. Broadway, BRB 569, Johns Hopkins University, Baltimore, MD 21205, USA

  6. 6

    Internal Medicine, University of Michigan, A520 MSRB 1 Bldg, 1150 West Medical Center Dr. Ann Arbor, MI 48109–0626, USA

  1. Originally published in Proteomics 2005, 13, 3506–3519

Publication History

  1. Published Online: 2 NOV 2006
  2. Published Print: 6 OCT 2006

ISBN Information

Print ISBN: 9783527317578

Online ISBN: 9783527609482



  • human plasma proteome;
  • subproteomes in human plasma;
  • coagulation pathway;
  • protein interaction network analysis;
  • bioinformatic analyses;
  • functional subproteomes;
  • proteins potentially derived from mononuclear phagocytes;
  • proteins involved in inflammation;
  • liver related plasma proteins;
  • cardiovascular system related plasma proteins;
  • glycoproteins;
  • DNA-binding proteins


This chapter contains sections titled:

  • Introduction

  • Materials and methods

    • Coagulation pathway and protein interaction network analysis

    • Gene ontology annotations

    • Analysis of MS-derived data for identification of proteolytic events and post-translational modifications

  • Results and discussion

    • Bioinformatic analyses of the functional subproteomes

      • An interaction map of human plasma proteins

      • Gene Ontology annotation of protein function

    • Proteins involved in the blood coagulation pathway

    • Proteins potentially derived from mononuclear phagocytes

    • Proteins involved in inflammation

    • Analyzing the peptide subproteome of human plasma

    • Liver related plasma proteins

    • Cardiovascular system related plasma proteins

    • Glycoproteins

    • DNA-binding proteins

      • Histones

      • Helicases

      • Zinc finger proteins

    • Annotation through reanalysis of mass spectrometry data

      • Cleavage of signal peptides and transmembrane domains

      • Identification of PTMs

  • Concluding remarks

  • References