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

  1. Prof. Dr. Gilbert S. Omenn
  1. Dr. Alex J. Rai Assistant Professor and Director of General Chemistry,
  2. Paul M. Stemmer,
  3. Zhen Zhang,
  4. Bao-Ling Adam,
  5. William T. Morgan,
  6. Rebecca E. Caffrey,
  7. Vladimir N. Podust,
  8. Manisha Patel,
  9. Lih-Yin Lim,
  10. Natalia V. Shipulina,
  11. Daniel W. Chan,
  12. O. John Semmes and
  13. Hon-Chiu Eastwood Leung

Published Online: 2 NOV 2006

DOI: 10.1002/9783527609482.ch12

Exploring the Human Plasma Proteome

Exploring the Human Plasma Proteome

How to Cite

Rai, A. J., Stemmer, P. M., Zhang, Z., Adam, B.-L., Morgan, W. T., Caffrey, R. E., Podust, V. N., Patel, M., Lim, L.-Y., Shipulina, N. V., Chan, D. W., Semmes, O. J. and Eastwood Leung, H.-C. (2006) 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, in Exploring the Human Plasma Proteome (ed G. S. Omenn), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527609482.ch12

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. Department of Pathology, Division of Clinical Chemistry, Johns Hopkins University School of Medicine, 600 N. Wolfe St., Meyer B-121, Baltimore, MD 21287-7065, USA

  1. Originally published in Proteomics 2005, 13, 3467–3474

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;
  • analysis of human proteome organization plasma proteome project (HUPO PPP);
  • reference specimens;
  • surface enhanced laser desorption/ionization-time of flight (SELDI-TOF) mass spectrometry;
  • spectra;
  • identification of biomarkers;
  • peptide mass fingerprinting (PMF);
  • Western blot analysis

Summary

This chapter contains sections titled:

  • Introduction

  • Materials and methods

    • Sample preparation

    • Sample preprocessing

    • Target (CM10) chip preparation and sample incubation

    • Scanning protocol

    • Data processing

    • Bioinformatics analysis of data and correlation coefficient matrix

    • Protein purification, SDS-PAGE analysis, and extraction of proteins

    • Peptide mass fingerprinting (PMF)

    • MS/MS analysis

    • Western blot analysis

  • Results

  • Discussion

  • References