A powerful proteomics methodology couples high-performance liquid chromatography (HPLC) with tandem mass spectrometry and database-search software, such as SEQUEST. Such a set-up, however, produces a large number of spectra, many of which are of too poor quality to be useful. Hence a filter that eliminates poor spectra before the database search can significantly improve throughput and robustness. Moreover, spectra judged to be of high quality, but that cannot be identified by database search, are prime candidates for still more computationally intensive methods, such as de novo sequencing or wider database searches including post-translational modifications.