Absolute protein quantification for cytosolic proteins of B. subtilis growing on a carbon source (condition S) or on an amino acid source (condition CH). Data for 3 biological replicates and 3 technical replicates each for each condition are provided. For data processing and protein identification, raw data were imported into ProteinLynx Global Server 2.4(PLGS, Waters) and processed via Apex3D algorithm with following parameters:chromatographic peak width:automatic, MS ToF resolution: automatic, lock mass for charge 2:785.8426Da/e, lock mass window: 0.25Da, low energy threshold: 250cts, elevated energy threshold: 30cts, retention time window: automatic, intensity threshold of precursor/fragment ion cluster:1000cts. Database search was carried out by the ion accounting algorithm against randomized _B. subtilis_ 168 database with added common laboratory contaminants and yeast ADH1 sequence (8,438 entries) using following parameters: peptide tolerance:automatic, protein tolerance: automatic, min fragment ions matches per peptide: 1, min fragment ions matches per protein: 5, min peptide matches per protein: 2, primary digest reagent: trypsin, missed cleavages: 2, variable modifications: carbamidomethylation C (+57.0215), deamidation N, Q (+0.9840),oxidation M (+15.9949), pyrrolidonecarboxylacid N-TERM (-27.9949), false discovery rate (FDR): 5%, calibration protein: yeast ADH1. With PLGS absolute protein quantification is based on comparison of the summed signal intensities of the three most intense peptides of a protein to these of ADH1 (Hi3 approach).