The routine production of peptides by manual or automated solid-phase synthesis protocols has gained widespread usage among a variety of biological scientists as new synthetic procedures have been introduced over the past several years. We report here a detailed analysis of Fmoc synthesis procedures to identify problematic reactions and to evaluate analytical procedures for monitoring the quality of peptides during and after synthesis. The results of these studies demonstrate double additions of particular amino acids during single coupling cycles, frequent incomplete deblocking of peptides by standard piperidine reactions, and the failure of the Kaiser ninhydrin test to detect free amino groups of certain amino acids at the N-terminus of synthetic peptides. These results suggest the need for more careful monitoring of Fmoc synthesis reactions than previously recognized or recommended in standard protocols. We demonstrate the utility of plasma desorption mass spectrometry (PDMS) in analyzing peptide products and recommend a minimum sequence of analytical quality control including HPLC and PDMS.