Proteomics has made tremendous progress, attaining throughput and comprehensiveness so far only seen in genomics technologies. The consequent avalanche of proteome level data poses great analytical challenges for downstream interpretation. We review bioinformatic analysis of qualitative and quantitative proteomic data, focusing on current and emerging paradigms employed for functional analysis, data mining and knowledge discovery from high resolution quantitative mass spectrometric data. Many bioinformatics tools developed for microarrays can be reused in proteomics, however, the uniquely quantitative nature of proteomics data also offers entirely novel analysis possibilities, which directly suggest and illuminate biological mechanisms.