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Following the succesful publication of "Proteome and Protein Analysis" in 2000, which was based on a former MPSA (Methods in Protein Structure Analysis) conference, "Methods in Proteome and Protein Analysis" presents the most interesting papers from the 14th MPSA meeting.§Selected contributions discuss the latest techniques and approaches for analysing protein and proteome structures. Major topics include: §protein and peptide sample preparation and separation §new reagent for protein sequence analysis §mass spectrometry in protein research §analysis of posttranslational modification §protein-protein interaction using MALDI-MS §manipulation of genome or functional compositon trap §structure-function correlation study using optical biosensors of microcolorimetrical techniques §structural proteomics as NMR or fluorescence polarization study §the classification and prediction of structure or functional sites §in silico analysis of proteins and proteomes §increasing throughput and data quality for proteomics