Statistical design and analysis of label-free LC-MS proteomic experiments: A case study of coronary artery disease

Timothy Clough, Siegmund Braun, Vladimir Fokin, Ilka Ott, Susanne Ragg, Gunther Schadow, Olga Vitek

Research output: Chapter in Book/Report/Conference proceedingChapter

6 Scopus citations

Abstract

This chapter presents a case study, which applies statistical design and analysis to an LC-MS-based -investigation of subjects with coronary artery disease. First, we discuss the principles of statistical -experimental design, and the specification of an Analysis of Variance (ANOVA) model that describes the major sources of variation in the data. Second, we discuss procedures for detecting differentially abundant proteins, estimating protein abundance in individual samples, testing predefined groups of proteins for enrichment in differential abundance, and calculating sample size for a future experiment. The discussion is accompanied by examples of computer code implemented in the open-source statistical software R, which can be followed for an independent implementation of a similar investigation.

Original languageEnglish (US)
Title of host publicationSerum/Plasma Proteomics
Subtitle of host publicationMethods and Protocols
EditorsRichard Simpson, David Greening
Pages293-319
Number of pages27
DOIs
StatePublished - Dec 1 2011

Publication series

NameMethods in Molecular Biology
Volume728
ISSN (Print)1064-3745

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Keywords

  • Analysis of Variance
  • Blocking
  • Coronary artery disease.
  • Gene set enrichment
  • LC-MS
  • Protein quantification
  • Quantitative proteomics
  • Randomization
  • Replication
  • Sample size
  • Statistical design of experiments

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Clough, T., Braun, S., Fokin, V., Ott, I., Ragg, S., Schadow, G., & Vitek, O. (2011). Statistical design and analysis of label-free LC-MS proteomic experiments: A case study of coronary artery disease. In R. Simpson, & D. Greening (Eds.), Serum/Plasma Proteomics: Methods and Protocols (pp. 293-319). (Methods in Molecular Biology; Vol. 728). https://doi.org/10.1007/978-1-61779-068-3_20