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Letter

Impact of Replicate Types on Proteomic Expression Analysis

Supporting Info

Natasha A. Karp,^† Matthew Spencer,^‡ Helen Lindsay,^§ Kevin O'Dell,^§ and Kathryn S. Lilley*^†

Biochemistry Department, University of Cambridge, Cambridge, England, Department of Mathematics and Statistics and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada, and IBLS Division of Molecular Genetics, University of Glasgow, Glasgow, Scotland

J. Proteome Res., 2005, 4 (5), pp 1867–1871

DOI: 10.1021/pr050084g

Publication Date (Web): August 17, 2005

†

University of Cambridge.

‡

Dalhousie University.

University of Glasgow.

To whom correspondence should be addressed. E-mail: KSL23@ cam.ac.uk.

Abstract

In expression proteomics, the samples utilized within an experimental design may include technical, biological, or pooled replicates. This manuscript discusses various experimental designs and the conclusions that can be drawn from them. Specifically, it addresses the impact of mixing replicate types on the statistical analysis which can be performed. This study focuses on difference gel electrophoresis (DiGE), but the issues are equally applicable to all quantitative methodologies assessing relative changes in protein expression.

Keywords: expression analysis • proteomics • differential gel electrophoresis • replication • nested ANOVA

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