With the advent of recombinant deoxyribonucleic acid (DNA) technology which allows a wide range of manipulation of genes and their expression in cell lines other than the natural ones, many aspects of protein structure have become more important than ever. In addition to the determination of the amino acid sequence questions relating to homogeneity, the nature of post-translational modifications, the verification of the structure of a protein produced by a synthetically modified gene or the detection of a natural mutant are all questions that are more and more frequently asked and with the demand for more detail. Mass spectrometry has emerged as an important contributor to this field, particularly since the advent of fast atom bombardment (FAB) ionization, which makes it possible to ionize directly large polar molecules such as peptides and small proteins. As such, FAB mass spectrometry provides mainly molecular weight information which, in itself, often suffices to answer certain questions, particularly because the mass of many peptides can be determined directly from a single mass spectrum of a mixture. However, in order to obtain detailed structural information, such as the amino acid sequence, fragmentation has to be induced by collision processes and the product ions separated, preferably in the second mass spectrometer of a tandem system. This approach is particularly suited for the determination of the sequence of N-blocked peptides and the nature of the blocking group; the type and location of modified (i.e. phosphorylated, sulfated, glycosylated) amino acids; detection or verification of amino acid replacements; confirmation of the structure of synthetic peptides; and last but not least, the determination of the primary structure of proteins.