Comparative Evaluation of Tandem MS Search Algorithms Using a Target-Decoy Search Strategy*□S

Peptide identification of tandemmass spectra by a variety of available search algorithms forms the foundation for much of modern day mass spectrometry-based proteom-ics. Despite the critical importance of proper evaluation and interpretation of the results generated by these algo-rithms there is still little consistency in their application or understanding of their similarities and differences. A sur-vey was conducted of four tandem mass spectrometry peptide identification search algorithms, including Mas-cot, Open Mass Spectrometry Search Algorithm, Sequest, and X! Tandem. The same input data, search parameters, and sequence library were used for the searches. Com-parisons were based on commonly used scoring method-ologies for each algorithm and on the results of a target-decoy approach to sequence library searching. Th