Background: Although immune responses to “cancer neoantigens” have been known for decades, the first neoantigen vaccines emerged only very recently. Current developments in genomics and proteomics have enabled descriptions of tumor mutational landscapes, and the immunogenicity of corresponding neoantigens can now be predicted either in silico or in vitro. Cancer regression could be achieved via a combination of neoantigen vaccination and an appropriate immunology approach. Research in model organisms and the results of initial clinical trials of neoantigen vaccines have shown them to be effective. Purpose: We aim to emphasize the importance of neoantigen vaccines in personalized cancer treatment and describe their preparation. We summarize mutations leading to expression of an immunogenic antigen necessary for vaccine development. The processes leading to activation of T-cell anticancer immunity in a patient are briefly introduced. We especially focus on the identification of high confidence neoantigens by next-generation sequencing (NGS) and mass spectrometry (MS), which is key element in the process of designing neoantigen vaccines. Briefly, we describe a proteogenomic platform for confident identification of mutant peptides in biological material. We mention the possibility of neoantigen quantification in biological material using mass spectrometry such as SRM (selected reaction monitoring) and SWATH (sequential windowed acquisition of all theoretical fragment ion spectra). Successful clinical studies demonstrating the potential of neoantigen vaccination in personalized cancer treatment are summarized at the end of the paper.