This dataset contains the full supporting material belonging to the PhD thesis of Marcel Eleveld titled “Departure From Randomness: Expanding the Structure Space of Self-Replicating Molecules”. The supplementary material is available as separate PDF documents per thesis chapter. The mass spectra corresponding to the LC-MS analyses of DCLs in Chapter 6 are available (in “Mass Spectra Chapter 6.zip”) as separate PNG images of the raw data.