The pitfalls of proteomics experiments without the correct use of bioinformatics tools

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 experimental design, poor statistical treatment and the high rate of ‘false positive’ results with regard to protein identification. In the light of these perceived problems, we review the advantages and misuses of bioinformatics tools – from realisation of 2‐DE gels to the identification of candidate protein spots – and suggest some useful avenues to improve the quality of 2‐DE experiments. In addition, we present key steps which, in our view, need to be to taken into consideration during such analyses. Lastly, we present novel biological entities named ‘interactomes', and the bioinformatics tools developed to analyse the large protein–protein interaction networks they form, along with several new perspectives of the field.