Nonribosomal peptides are a prolific source of bioactive molecules biosynthesized on large, modular assembly-line synthetases. Synthetic biologists seek to obtain tailored peptides with tuned or novel bioactivities by engineering modules and domains of thesenonribosomal peptide synthetases. The activation step catalyzed by adenylation domains primarily selectswhich amino acids are incorporated into nonribosomal peptides.Here,we review experimental protocols for probing the adenylation reaction that are applicable in natural product discovery and engineering. Several alternatives to the established pyrophosphate exchange assay will be compared and potential pitfalls pointed out. Binding pocket mutagenesis of adenylation domains has been successfully conducted to adjust substrate preferences. Novel screening methods relying on yeast surface display, for instance, search a larger sequence space for improved mutants and thus allow more substantial changes in peptide structure.