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This review considers the available and ready to use tools that can help end\u2010users to interpret, validate and generate biological information from their experimental data. It concentrates on bioinformatics tools for 2\u2010DE analysis, for LC followed by MS analysis, for protein identification by PMF, by peptide fragment fingerprinting and by <jats:italic>de\u2005novo<\/jats:italic> sequencing and for data quantitation with MS data. 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