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Delta2D - difference analysis of 2D electrophoresis gels. Produce dual channel images that show clearly the differences and similarities between two gels.
http://www.decodon.com/Products/Delta2D/

GeneData Impressionist 231 is a scientific software system for the computational analysis of protein expression data. It facilitates and automates the analysis of large amounts of complex expression data derived from 2D gels and mass spectrometry.
http://www.genedata.com/products_template.php?basename=impressionist

Melanie 3 - 2D Gel Analysis Software.
http://www.expasy.ch/melanie/Melanie.htm

ProteinProspector - Tools for mining sequence databases in conjunction with Mass Proteometry experiments.
http://prospector.ucsf.edu/