Cancer neo-antigens are considered important targets for personalized cancer immunotherapy. However, development and application of patient-specific cancer therapies pose a challenge to fast, flexible and cost effective ways to monitor the immune response to these treatments. Overlapping neo-epitope spanning peptide libraries, pools and arrays represent efficient immune monitoring tools for both humoral and cellular immune responses. Because each patient requires a different, individually synthesized set of peptides, standard commercial approaches to peptide synthesis deliver neither the speed nor the capacity required for large trials. We bridge this gap by offering unique peptide formats for the specific needs of immune monitoring when developing neo-epitope based therapies. Our high-throughput peptide synthesis approach paired with automated liquid handling as well as a proprietary peptide microarray technology provide access to a large selection of peptide formats. This enables cellular and humoral immune monitoring for individualized neo-epitope based immunotherapy trials.