Recent advances in protein separation technology and mass spectrometry (MS) have enabled the systematic identification and quantification of large sets of proteins from an organelle, cell type or organism. In principle, protein isoforms, enzymically modified variants and protein complexes can be studied, for instance, at a certain stage in development or in response to stress or more subtle changes of the environment. An important pre-clinical application is the search for protein markers in body fluids for diagnostic purposes. Such proteomics studies can be performed increasingly at high-throughput rates that are reminiscent of those of genomic sequencing or the monitoring of messenger RNA levels. Thus, large sets of proteins can be monitored simultaneously in a single experiment. Proteomics data will increasingly be followed up by investigations of the three-dimensional structures of proteins and protein complexes at atomic detail in large-scale structural proteomics projects. We attempt in this article to give a flavour of what to us seem important experimental developments and to point to links with bioinformatics resources where appropriate.

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