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Statistical Analysis of Spectral Count Data Generated by Label-Free Tandem Mass Spectrometry-Based Proteomics

  • Thang V. PhamEmail author
  • Connie R. Jimenez
Protocol
Part of the Neuromethods book series (NM, volume 57)

Abstract

Label-free strategies for quantitative proteomics provide a versatile and economical alternative to labeling-based proteomics strategies. We have shown for different types of biological samples that spectral counting-based label-free quantitation is a promising avenue for biomarker discovery. Analyzing spectral count data generated from these studies is, however, not straightforward, as commonly used techniques for genomics data analysis are not suitable. In this book chapter, we describe three methods to analyze spectral count data, namely, cluster analysis, significance analysis of independent samples, and significance analysis of paired samples. For cluster analysis, we devise a novel distance measure between samples based on the Jeffrey divergence. This measure prevents highly abundant proteins from dominating others in contribution to the total sample difference. We employ the beta-binomial distribution for significance analysis of independent samples, which integrates both within-sample variation and between-sample variation into a single statistical model. Finally, the Mantel–Haenszel test is used for significance analysis of paired samples. We provide detailed illustrations of the steps involved in the analyses.

Key words

Beta-binomial distribution Biomarker discovery Cluster analysis Comparative analysis Label-free tandem mass spectrometry-based proteomics Spectral counting 

Notes

Acknowledgments

This work is supported by the VUmc Cancer Center, Amsterdam.

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.OncoProteomics Laboratory, Department of Medical OncologyVU University Medical Center-Cancer Center AmsterdamAmsterdamThe Netherlands

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