Utilisation of proteomics datasets generated via multidimensional protein identification technology (MudPIT).

Technological developments in proteomics have had a dramatic impact on biology in recent years. One of these developments--named multidimensional protein identification technology (MudPIT)--couples two-dimensional chromatography of peptides in mass spectrometry-compatible solutions directly to tandem mass spectrometry, allowing for the identification of proteins from highly complex mixtures. Since the initial descriptions of MudPIT, this approach has been implemented in the analysis of whole proteomes, organelles and protein complexes. Key aspects of many of the analyses are the validation of MudPIT datasets with alternate strategies and the integration of MudPIT datasets with other biochemical, cell biology or molecular biology approaches. This paper presents strategies for validating MudPIT datasets and incorporating these datasets into biologically driven experimental design.