title: Numerical approaches for quantitative analysis of two-dimensional maps: a review of commercial software and home-made systems.
abstract: The present review attempts to cover a number of methods that have appeared in the last few years for performing quantitative proteome analysis. However, due to the large number of methods described for both electrophoretic and chromatographic approaches, we have limited this review to conventional two-dimensional (2-D) map analysis which couples orthogonally a charge-based step (isoelectric focusing) to a size-based separation step (sodium dodecyl sulfate-electrophoresis). The first and oldest method applied to 2-D map data reduction is based on statistical analysis performed on sets of gels via powerful software packages, such as Melanie, PDQuest, Z3 and Z4000, Phoretix and Progenesis. This method calls for separately running a number of replicas for control and treated samples. The two sets of data are then merged and compared via a number of software packages which we describe. In addition to commercially-available systems, a number of home made approaches for 2-D map comparison have been recently described and are also reviewed. They are based on fuzzyfication of the digitized 2-D gel image coupled to linear discriminant analysis, three-way principal component analysis or a combination of principal component analysis and soft-independent modeling of class analogy. These statistical tools appear to perform well in differential proteomic studies.
authors.affiliation: Department of Environmental and Life Sciences, University of Eastern Piedmont, Alessandria, Italy.
authors.forename: Emilio
authors.initials: E
authors.lastname: Marengo
authors.forename: Elisa
authors.initials: E
authors.lastname: Robotti
authors.forename: Francesca
authors.initials: F
authors.lastname: Antonucci
authors.forename: Daniela
authors.initials: D
authors.lastname: Cecconi
authors.forename: Natascia
authors.initials: N
authors.lastname: Campostrini
authors.forename: Pier Giorgio
authors.initials: PG
authors.lastname: Righetti
mesh_terms: D016000:Cluster Analysis; D016002:Discriminant Analysis; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods*; D017143:Fuzzy Logic; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D025341:Principal Component Analysis; D020543:Proteome / Q000032:analysis*; D012984:Software
chemical_list: D020543:Proteome