Protein mass spectrometry refers the use of mass spectrometry in studying the properties of proteins. Today mass spectrometry became an important tool for the characterization of proteins. Electrospray ionization and matrix-assisted laser desorption/ionization are the two important primary methods for ionization of whole proteins. Mass Spectrometer measure mass/charge ratio of an ion. Mass Spectrometry mainly generates partial N- and C-terminal peptides. Spectrum consists of different ion types because proteins can be broken in several places. The advantages of tandem mass spectrometry are, gets the sequences that are not necessarily in the database and an additional similarity search step using these sequences may identify the related proteins in the database.