The most recent algorithms based on the use of modern analytical techniques for the assessment of structural peptide and protein features have been reviewed. No algorithm devoted to the realization of predictive models or statistical analysis has been discussed, but only methods furnishing information on the real structure of the molecules. In particular, the procedures designed for handling sequence and mass spectrometric data obtained from the analysis of unfractionated digestion mixtures allow the user to get rapid information on the structure of the target polypeptide. Two classes of methods are illustrated: the first regards the determination of the amino acid sequence, whereas the second used its knowledge to supply data on the localization, function and three-dimensional structure of disulphides.