SpectraST: An open-source MS/MS spectra-matching search tool for targeted proteomics

SpectraST is able to obtain better score separation between the good and bad hits, hence better separation between the sensitivity and error curves, than SEQUEST, in all cases. SpectraST is able to obtain considerably more highly-confident IDs than SEQUEST for the LCQ-generated datasets (Dataset 1 & 2). The extra hits that are missed by SEQUEST are manually verified to be correct (labeled F). False positives (labeled G) are extremely rare.