title: Proteogenomics meets cancer immunology: mass spectrometric discovery and analysis of neoantigens.
abstract: Cancer proteogenomics is an emerging field that aims to identify and quantify protein sequence changes associated with the cancer genome. Besides being involved in cancer development and progression, such protein variants may serve as neoantigens, which provide the T-cell response against tumors. Mass spectrometry-based proteogenomics may be a promising tool for finding neoantigens in individual specimens. It is partly based on a technical background accumulated from mass spectrometric studies of peptide ligands of major histocompatibility complex proteins. Examples of the use of mass spectrometry in neoantigen identification are reviewed in this article. Some experimental workflows are discussed, which may use shotgun and targeted proteomics for translational human studies of neoepitopes, such as cancer vaccine development and checkpoint therapy response prediction.
authors.affiliation: a Institute of Biomedical Chemistry - Personalized Medicine, Pogodinskaya Street 10, Moscow 119121, Russian Federation.
authors.forename: Anna
authors.initials: A
authors.lastname: Polyakova
authors.affiliation: a Institute of Biomedical Chemistry - Personalized Medicine, Pogodinskaya Street 10, Moscow 119121, Russian Federation.
authors.forename: Ksenia
authors.initials: K
authors.lastname: Kuznetsova
authors.forename: Sergei
authors.initials: S
authors.lastname: Moshkovskii
mesh_terms: D000818:Animals; D000951:Antigens, Neoplasm / Q000737:chemistry* / Q000235:genetics / Q000276:immunology; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D009369:Neoplasms / Q000235:genetics* / Q000276:immunology; D020543:Proteome / Q000235:genetics* / Q000276:immunology
chemical_list: D000951:Antigens, Neoplasm; D020543:Proteome
keywords: T-cell epitope; cancer genome; cytotoxic T-lymphocyte; major histocompatibility complex; mass spectrometry; neoantigen; proteogenomics