In this study, we acquired DDA-MS data and DIA-MS data from peptide extracts of plasma and eleven organs (lung, spleen, adrenal gland, kidney, heart, liver, muscle, pancreas, cerebellum, hippocampus, and cerebral cortex). These data were analyzed using FragPipe v23 to obtain peptide identification results and to construct an empirical spectral library. We also acquired DIA-MS data from plasma peptide extracts and analyzed them with DIA-NN v2.3.1 using three empirical spectral libraries that we constructed, thereby obtaining peptide identification results.