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 Citations (Scopus)

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 publicationMethods in Molecular Biology
Pages293-319
Number of pages27
Volume728
DOIs
StatePublished - 2011
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume728
ISSN (Print)10643745

Fingerprint

Proteomics
Coronary Artery Disease
Proteins
Sample Size
Analysis of Variance
Research Design
Software

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
  • Medicine(all)

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 Methods in Molecular Biology (Vol. 728, pp. 293-319). (Methods in Molecular Biology; Vol. 728). https://doi.org/10.1007/978-1-61779-068-3_20

Statistical design and analysis of label-free LC-MS proteomic experiments : A case study of coronary artery disease. / Clough, Timothy; Braun, Siegmund; Fokin, Vladimir; Ott, Ilka; Ragg, Susanne; Schadow, Gunther; Vitek, Olga.

Methods in Molecular Biology. Vol. 728 2011. p. 293-319 (Methods in Molecular Biology; Vol. 728).

Research output: Chapter in Book/Report/Conference proceedingChapter

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 Methods in Molecular Biology. vol. 728, Methods in Molecular Biology, vol. 728, pp. 293-319. https://doi.org/10.1007/978-1-61779-068-3_20
Clough T, Braun S, Fokin V, Ott I, Ragg S, Schadow G et al. Statistical design and analysis of label-free LC-MS proteomic experiments: A case study of coronary artery disease. In Methods in Molecular Biology. Vol. 728. 2011. p. 293-319. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-61779-068-3_20
Clough, Timothy ; Braun, Siegmund ; Fokin, Vladimir ; Ott, Ilka ; Ragg, Susanne ; Schadow, Gunther ; Vitek, Olga. / Statistical design and analysis of label-free LC-MS proteomic experiments : A case study of coronary artery disease. Methods in Molecular Biology. Vol. 728 2011. pp. 293-319 (Methods in Molecular Biology).
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