Updated project metadata. This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms after labeling them with stable isotope-labeled substrates. In this dataset Escherichia coli and Bacillus subtilis cultures were labeled with different percentages of fully labeled 13C glucose (13C6). Cultures of B. subtilis and E. coli were grown in Bacillus minimal medium or M9 minimal medium (E. coli) in which a percentage of the glucose was replaced with 13C6 glucose for >10 generations to achieve close to complete labeling of cells. The following percentages of 13C6 glucose were added 0, 0.01, 0.025, 0.1, 0.25, 1, 5 and 10%. Triplicate cultures were grown for each percentage. Please note that the unlabeled glucose that was used of course had a natural content of 13C of around 1.1%, thus the 0% added label samples have an actual 13C content of 1.1% and all added label is on top of this value. We included a tab delimited table with this submission providing details on all raw files.