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The elucidation of the entire genomic sequence of various organisms, from viruses to complex metazoans, most recently man, is undoubtedly the greatest triumph of molecular biology since the discovery of the DNA double helix. Over the past two decades, the focus of molecular biology has gradually moved from genomes to proteomes, the intention being to discover the functions of the genes themselves. The postgenomic era stimulated the development of new techniques (e.g. 2‐DE and MS) and bioinformatics tools to identify the functions, reactions, interactions and location of the gene products in tissues and/or cells of living organisms. Both 2‐DE and MS have been very successfully employed to identify proteins involved in biological phenomena (e.g. immunity, cancer, host–parasite interactions, etc.), although recently, several papers have emphasised the pitfalls of 2‐DE experiments, especially in relation to …