This dataset contains the additional supplementary data belonging to the PhD thesis of Fleur Ruijne titled 'Combinatorial RiPP biosynthesis for the generation of gene-encoded new-to-nature peptide antimicrobials'. In this thesis we constructed several new biosynthetic pathways, combining RiPP post-translational modification enzymes to act on a single peptide to synthesize new-to-nature antimicrobial peptides that mimic several potent non-ribosomal peptide antibiotics. These files contains data belonging to the three experimental chapters of the thesis and include mass spectrometry figures, LC-MS analysis figures, precursor peptide sequences, primer sequences and the supplementary information references.