SMAQC computes quality metrics for a LC-MS/MS dataset. The quality metrics are based on the metrics proposed by Rudnick and Stein, as described in "Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses.", Mol Cell Proteomics. 2010 Feb;9(2):225-41.  SMAQC requires that the dataset first be processed with MASIC, then processed with MSGF+ or X!Tandem.  The MSGF+ or X!Tandem results must be post-processed with the PeptideHitResultsProcessor (PHRP).