Proteomic technologies are important because they link genes, proteins and disease. The identification of proteins and peptides has been revolutionized in the last decade by the use of mass spectrometry. This method is highly sensitive and much faster than the chemical reactions used previously because it can fragment peptides in seconds rather than in hours or days. Proteins are digested with an enzyme, usually trypsin, and the resulting peptides are fragmented in a tandem mass spectrometer (MS/MS). The masses of the fragment ions formed in the MS/MS can be used to identify the sequence of amino acids in the peptides. However, a number of different factors have been found to influence the amount of the various types of fragment ion formed. In this article, we review these factors and their interrelation together with the statistical methods used to discover them. Information on the number of fragment ions formed is at present underused in peptide identification algorithms, and fully utilizing this information could improve current algorithms.