2. Types of Sample and Experimental Planning

  1. P. David Eckersall2 and
  2. Phillip D. Whitfield3
  1. Christine Olver

Published Online: 5 AUG 2011

DOI: 10.1002/9780470960660.ch2

Methods in Animal Proteomics

Methods in Animal Proteomics

How to Cite

Olver, C. (2011) Types of Sample and Experimental Planning, in Methods in Animal Proteomics (eds P. D. Eckersall and P. D. Whitfield), Wiley-Blackwell, Oxford, UK. doi: 10.1002/9780470960660.ch2

Editor Information

  1. 2

    University of Glasgow, UK

  2. 3

    University of the Highlands and Islands, UK

Author Information

  1. Colorado State University, CO, USA

Publication History

  1. Published Online: 5 AUG 2011
  2. Published Print: 19 AUG 2011

ISBN Information

Print ISBN: 9780813817910

Online ISBN: 9780470960660



  • sample types, and experimental planning - proteome, full complement of proteins at any given time or environmental condition;
  • experiments, planned carefully with goals - and analytical methods in mind;
  • sample types, collection and processing - cell lysis and solubilization, for mass spectrometry;
  • sample preparation for proteomics experiments - biological samples prepared crudely;
  • whole tissue, and tumor biopsies - whole organs and whole organ sections;
  • plasma or serum, source of potential biomarkers - blood circulation in body;
  • homogenization, clarification and simplification – protein handling precautions;
  • protein solubilization during homogenization - aided by chaotropic agents, reducing agents;
  • recommended reagents - for initial protein solubilization;
  • qualification phase, translating methods for candidate marker detection - and targeted mass spectrometry-based assays, using multiple reaction monitoring (MRM)


This chapter contains sections titled:

  • Introduction

  • Types of Samples and Their Collection

  • General Preparation of Body Fluids, Cultured Cells in Suspension, and Blood

  • Homogenization, Clarification, and Simplification

  • Determination of Protein Concentration in Proteomic Samples

  • Enzymatic Digestion

  • Experimental Design: Strategies for Simplification and Enrichment

  • Specialized Techniques for Sample Preparation

  • Experimental Planning and Design: General Guidelines

  • Biomarker Discovery: Special Considerations for Experimental Planning

  • Concluding Remarks

  • References