PEPscreen peptide synthesis platform facilitates high throughput synthesis of custom peptide libraries (6-20 amino acids) comprising thousands of peptides at 70% purity. Higher purity development is also available. Peptides are synthesized in quantities from 0.5 - 3 mg, in which 100% of the peptides are analyzed by MALDI-TOF mass spectroscopy. Peptide libraries can be synthesized, analyzed and delivered in less than 7 days. The libraries can be used in applications such as: epitope mapping, interaction profiling, substrate specificity profiling, vaccine development, immunogen detection, peptide microarray production, protein-protein (or receptor-ligand interactions) and alanine scans.