High‐throughput analysis for purity and molecular weight determination of synthetic peptides including characterisation of any peptidic byproducts arising from synthesis is described. The data from electrospray mass spectrometry are processed with an algorithm that calculates the contribution of the target peptide and each of the identifiable contaminants to the total ionizable material in a sample of synthetic peptide. All essential data are obtained by one instrumental technique in<3 min per sample. The technique has distinct advantages in the rapid analysis of the many hundreds of peptides/peptidomimetics required in systematic quantitative structure‐activity relationship and other investigations. ©Munksgaard