State-of-the-art techniques such as liquid-chromatography-electrospray-ionisation tandem mass spectrometry have, in conjunction with database-searching computer algorithms, revolutionised the analysis of biochemical species from complex biological mixtures. With these techniques, it is now possible to perform high-throughput protein identification at picomolar to subpicomolar levels from protein mixtures. This article provides an overview of the techniques and methodologies available for the structural elucidation and identification of proteins and peptides from complex biological samples.