To discuss performance is always a difficult exercise because performance is data-dependent and, pure TP/FP performance considerations must be weighed against tool functionalities. We believe to have demonstrated superior performance of advanced statistics-founded scoring functions (Phenyx) compared to heuristic or simpler functions , but, admittedly, this sort of advantage diminishes with excellent data quality and mass accuracy (~10 ppm on peptide masses). Since these two conditions are not always satisfied, scoring functions are not anonymous components. It is also a common belief that Mascot achieves better results than Sequest with TOF data, and Sequest performs better than Mascot with ion trap data. OMSSA and X!Tandem performance is usually reported comparable to Mascot and Sequest. X!Tandem was designed to be very fast, and it comes with a concept of data representation and sharing (the global proteome machine). We also stress that no scoring function is general enough and exhaustivity can be achieved by using more than one search tool only .
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