Chapter 2. Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project

  1. Prof. Dr. Gilbert S. Omenn
  1. Marcin Adamski,
  2. Thomas Blackwell,
  3. Rajasree Menon,
  4. Dr. Lennart Martens1,
  5. Henning Hermjakob,
  6. Chris Taylor,
  7. Dr. Gilbert S. Omenn3 and
  8. Dr. David J. States2

Published Online: 2 NOV 2006

DOI: 10.1002/9783527609482.ch2

Exploring the Human Plasma Proteome

Exploring the Human Plasma Proteome

How to Cite

Adamski, M., Blackwell, T., Menon, R., Martens, L., Hermjakob, H., Taylor, C., Omenn, G. S. and States, D. J. (2006) Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project, in Exploring the Human Plasma Proteome (ed G. S. Omenn), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527609482.ch2

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

    Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium

  2. 2

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

  3. 3

    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, 3246-3261

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;
  • data management;
  • preliminary data analysis;
  • pilot phase of the HUPO plasma proteome project;
  • materials and methods;
  • inference from peptide level to protein level;
  • summary of contributed data;
  • false-positive identifications;
  • data dissemination;
  • computer technologies applied

Summary

This chapter contains sections titled:

  • Introduction

  • Materials and methods

    • Development of the data model

      • Laboratory

      • Experimental protocol

      • Protein identification data set

      • Peak list

      • Summary of technologies and resources

      • MS/MS spectra

      • SELDI peak list

    • Data submission process

    • Design of the data repository

    • Receipt of the data

  • Inference from peptide level to protein level

  • Summary of contributed data

    • Cross-laboratory comparison, confidence of the identifications

  • False-positive identifications

  • Data dissemination

  • Discussion

  • Concluding remarks

  • Computer technologies applied

  • References