Mass spectrometry has become the pre-eminent analytical method for the study of proteins and proteomes in post-genome science. The high volumes of complex spectra and data generated from such experiments represent new challenges for the field of bioinformatics. The past decade has seen an explosion of informatics tools targeted towards the processing, analysis, storage, and integration of mass spectrometry based proteomic data. In this review, some of the more recent developments in proteome informatics will be discussed. This includes new tools for predicting the properties of proteins and peptides which can be exploited in experimental proteomic design, and tools for the identification of peptides and proteins from their mass spectra. Similarly, informatics approaches are required for the move towards quantitative proteomics which are also briefly discussed. Finally, the growing number of proteomic data repositories and emerging data standards developed for the field are highlighted. These tools and technologies point the way towards the next phase of experimental proteomics and informatics challenges that the proteomics community will face.