Mass spectrometry has become an important analytical tool in biological and biochemical research. Its speed, accuracy and sensitivity are unmatched by conventional analytical techniques. Identification of proteins and characterisation of their primary structure is a rapidly growing field in the post-genomic era, where matrix-assisted laser desorption/ionisation time-of-flight peptide mass fingerprinting combined with electrospray tandem mass spectrometry can efficiently solve many questions. Many recently determined genomic sequences have not been characterised at the protein level. Analysis of the amino acid sequence and characterisation of post-translational modifications are therefore important steps towards correlation of protein structure with function. This review concerns methods, instrumentation and applications of mass spectrometry in protein and peptide analysis.