Fig. 1.

Left: Search, analysis, and validation steps for each LC-MS/MS experiment. Spectra were searched against a spectral library or sequence database. The resulting PSMs were then processed using the TPP, including a new component, iProphet, to improve discrimination (see text for details). Right: The PeptideAtlas build process. ProteinProphet combines PSMs passing the FDR threshold for all experiments to create lists of distinct peptides, protein identifications, and protein groups. These data, along with supporting information such as consensus spectra, genome mappings, and proteotypic peptides, comprise a PeptideAtlas build.