Proteomics technologies are under continuous improvements and new technologies are introduced. Nowadays high throughput acquisition of proteome data is possible. The young and rapidly emerging field of bioinformatics in proteomics is introducing new algorithms to handle large and heterogeneous data sets and to improve the knowledge discovery process. For example new algorithms for image analysis of two dimensional gels have been developed within the last five years. Within mass spectrometry data analysis algorithms for peptide mass fingerprinting (PMF) and peptide fragmentation fingerprinting (PFF) have been developed. Local proteomics bioinformatics platforms emerge as data management systems and knowledge bases in Proteomics. We review recent developments in bioinformatics for proteomics with emphasis on expression proteomics.