Chapter 11. A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy

  1. Prof. Dr. Gilbert S. Omenn
  1. Joshua N. Adkins,
  2. Matthew E. Monroe,
  3. Kenneth J. Auberry,
  4. Yufeng Shen,
  5. Jon M. Jacobs,
  6. David G. Camp II,
  7. Frank Vitzthum,
  8. Karin D. Rodland,
  9. Richard C. Zangar,
  10. Richard D. Smith and
  11. Dr. Joel G. Pounds

Published Online: 2 NOV 2006

DOI: 10.1002/9783527609482.ch11

Exploring the Human Plasma Proteome

Exploring the Human Plasma Proteome

How to Cite

Adkins, J. N., Monroe, M. E., Auberry, K. J., Shen, Y., Jacobs, J. M., Camp, D. G., Vitzthum, F., Rodland, K. D., Zangar, R. C., Smith, R. D. and Pounds, J. G. (2006) A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy, in Exploring the Human Plasma Proteome (ed G. S. Omenn), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527609482.ch11

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. Biological Sciences Division, Pacific Northwest National Laboratory, Box 999 MSIN: P7-58, Richland, WA 99352, USA

  1. Originally published in Proteomics 2005, 13, 3454–3466

Publication History

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

ISBN Information

Print ISBN: 9783527317578

Online ISBN: 9783527609482

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Keywords:

  • human plasma proteome;
  • proteomic study of HUPO plasma proteome project's pilot samples;
  • accurate mass strategy;
  • accurate time tag strategy;
  • human blood serum and plasma;
  • SEQUEST identification of peptides;
  • putative mass and time tag (PuMT) database

Summary

This chapter contains sections titled:

  • Introduction

  • Materials and methods

    • Human blood serum and plasma

    • Depletion of Igs and trypsin digestion

    • Peptide cleanup

    • Capillary RP-LC

    • IT-MS

    • SEQUEST identification of peptides

    • Putative mass and time tag database from SEQUEST results

    • FT-ICR-MS

    • cLC-FT-ICR MS data analysis

    • OmniViz cluster and visual analysis

  • Results

    • PuMT tag database

    • Summary of peptide/protein identifications by AMT tags

    • Protein concentration estimates from ion current

    • Global protein analysis

  • Discussion

    • Application of FT-ICR MS as a proteomic technology bridge

    • Confidence in any MS-based proteomic approach

    • Peptide/protein redundancy

    • Identification sensitivity versus specificity

    • Throughput and differential analysis

  • References