title: Statistical analysis of image data provided by two-dimensional gel electrophoresis for discovery proteomics.
abstract: Standardized methods for the solubilization of proteins prior to proteomics analyses incorporating two-dimensional gel electrophoresis (2-DE) are essential for providing reproducible data that can be subjected to rigorous statistical interrogation for comparative studies investigating disease-genesis. In this chapter, we discuss the imaging and image analysis of proteins separated by 2-DE, in the context of determining protein abundance alterations related to a change in biochemical or biophysical conditions. We then describe the principles behind 2-DE gel statistical analysis, including subtraction of background noise, spot detection, gel matching, spot quantitation for data comparison, and statistical requirements to create meaningful gel data sets. We also emphasize the need to develop reproducible and robust protocols for protein sample preparation and 2-DE itself.
authors.affiliation: School of Molecular and Microbial Biosciences, University of Sydney, New South Wales, Australia.
authors.forename: Ben
authors.initials: B
authors.lastname: Crossett
authors.forename: Alistair V G
authors.initials: AV
authors.lastname: Edwards
authors.forename: Melanie Y
authors.initials: MY
authors.lastname: White
authors.forename: Stuart J
authors.initials: SJ
authors.lastname: Cordwell
mesh_terms: D000818:Animals; D003627:Data Interpretation, Statistical; D015180:Electrophoresis, Gel, Two-Dimensional; D006801:Humans; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D011786:Quality Control