Software for computational peptide identification from MS–MS data

Protein identification in biological samples is an important task in drug discovery research. Protein identification is nowadays regularly performed by tandem mass spectrometry (MS–MS). Because of the difficulty of measuring intact proteins using MS–MS, typically a protein is enzymically digested into peptides and the MS–MS spectrum of each peptide is measured. Computational methods are then invoked to identify the peptides, which are later combined together to identify the protein. The most recognized peptide identification software packages can be classified into four categories: database searching, de novo sequencing, sequence tagging and consensus of multiple engines.