Peptide Mass Fingerprinting (PMF) is a technique used to identify proteins by matching their constituent fragment masses (peptide masses) to the theoretical peptide masses generated from a protein or DNA database. The first step in PMF is that an intact, unknown protein is cleaved with a proteolytic enzyme to generate peptides. With PMF, heterogeneity is most commonly imparted to the unknown protein with a trypsin digestion. The premise of peptide mass finger printing is that every unique protein will have a unique set of peptides and hence unique peptide masses. Identification is accomplished by matching the observed peptide masses to the theoretical masses derived from a sequence database. PMF identification relies on observing a large number of peptides, 5+, from the same protein at high mass accuracy. This technique does well with 2D gel spots where the protein purity is high. PMF protein identification can run into difficulties with complex mixtures of proteins. Low level ID also becomes difficult due to commonplace contamination by keratin.