Automated Analysis of Peptide Mass Spectra This Web site runs ByOnic and ComByne, programs for automated analysis of shotgun proteomics experiments. ByOnic identifies the peptides found in CID MS/MS spectra, and ComByne integrates the peptide identifications into a list of protein identifications, ranked by confidence. We invite you to compare ByOnic's results with those given by SEQUEST, Mascot, X!Tandem, etc. You can submit spectra in either .dta or .mgf format. Spectra in .dta format should be concatenated with blank lines separating successive spectra. A spectrum can start with an optional comment line with first character #, giving a spectrum identifier such as retention time. We recommend that you submit 100 to 10,000 spectra per run, so that ComByne can compute a reasonable protein ranking. The system will notify you by e-mail when your results are ready; big data sets may take overnight. You can check percent completion at the results page.