To date, most peptide-based vaccines evaluated for the treatment of cancer have consisted of one or few peptides. However, as a greater number of peptide antigens become available for use in experimental therapies, it is important to establish the feasibility of combining multi-peptide reagents as individual peptide mixtures. We have found that mixtures of up to 12 peptides can be analyzed accurately for identity, purity, and stability (for at least 5 years) using a combination of high-performance liquid chromatography (HPLC) and mass spectrometry and these complex peptide mixtures have been acceptable for use in human clinical trials. We have also identified some specific concerns for degradation products that should be considered in multi-peptide vaccine preparation and follow-up quality assurance studies. Results from these analyses have implications for changing the way peptide-based vaccines are manufactured and demonstrate that multi-peptide vaccines are reliable reagents for use in peptide-based immune therapies.