Peptide identification of tandem mass spectra by a variety of available search algorithms forms the foundation for much of modern-day mass spectrometry-based proteomics. Despite the critical importance of proper evaluation and interpretation of the results generated by these algorithms there is still little consistency in their application or understanding of their similarities and differences. A survey is conducted of four tandem mass spectrometry peptide identification search algorithms, including Mascot, OMSSA, Sequest, and X! Tandem. The same input data, search parameters and sequence library are used for the searches. Comparisons are based on commonly used scoring methodologies for each algorithm and on the results of a target-decoy approach to sequence library searching. The results indicate that there is little difference in the output of the algorithms so long as consistent scoring procedures are applied. The results show that some commonly used scoring procedures may lead to excessive false discovery rates. Finally, an alternative method for the determination of an optimal cutoff threshold is proposed.