Purcell, A.W., Ramarathinam, S.H. & Ternette, N. Mass spectrometry–based identification of MHC-bound peptides for immunopeptidomics. Nat Protoc 14, 1687–1707 (2019). https://doi.org/10.1038/s41596-019-0133-y
Prof. Anthony W. Purcell et al. published their research of neoantigens in the Nature Protocols, highlighted the advantages of PEAKS software for neoantigens identification. Exogenous antigens can be degraded in the endosomal compartments of the cell and the resultant peptides will be presented on the surface of the cell by MHCs. MHC-bound peptides were enriched by MHC antibodies and released by mild acid. Identification of unspecific cleaved neoantigens relies on the de novo sequencing algorithm such as PEAKS Studio. Prof. Anthony W. Purcell described a robust and universal protocol for MHC-bound peptides purification. With this protocol, several thousand peptides can be identified from a wide variety of cell types, including cancerous and infected cells and those from tissues, with a turnaround time of 2–3 d. The PEAKS de novo sequencing algorithm along with scoring functions, were employed to accurately identify novel peptides, improved data mining and discovering neoantigens for immunopeptidomics research. Immunopeptidomics is turning more and more important in cancer research since neoantigens are potential targets for cancer immunotherapy. Researchers would be able to customize antineoplastic Protocols for specific patient. PEAKS de novo function provided a robust tool for researchers to discover new targets.