Mass Spectrometry-Based Identification of MHC-Associated Peptides

被引:27
|
作者
Kote, Sachin [1 ]
Pirog, Artur [1 ]
Bedran, Georges [1 ]
Alfaro, Javier [1 ]
Dapic, Irena [1 ]
机构
[1] Univ Gdansk, Int Ctr Canc Vaccine Sci, PL-80308 Gdansk, Poland
关键词
Neoantigens; mild acid elution; immunoprecipitation; mass spectrometry; cancer; CLASS-I; ANTIGEN PRESENTATION; PRESENTED PEPTIDES; VIABLE CELLS; GENERATION; DISCOVERY; IMMUNOPEPTIDOMICS; FRAGMENTATION; QUANTITATION; REPERTOIRE;
D O I
10.3390/cancers12030535
中图分类号
R73 [肿瘤学];
学科分类号
100214 ;
摘要
Neoantigen-based immunotherapies promise to improve patient outcomes over the current standard of care. However, detecting these cancer-specific antigens is one of the significant challenges in the field of mass spectrometry. Even though the first sequencing of the immunopeptides was done decades ago, today there is still a diversity of the protocols used for neoantigen isolation from the cell surface. This heterogeneity makes it difficult to compare results between the laboratories and the studies. Isolation of the neoantigens from the cell surface is usually done by mild acid elution (MAE) or immunoprecipitation (IP) protocol. However, limited amounts of the neoantigens present on the cell surface impose a challenge and require instrumentation with enough sensitivity and accuracy for their detection. Detecting these neopeptides from small amounts of available patient tissue limits the scope of most of the studies to cell cultures. Here, we summarize protocols for the extraction and identification of the major histocompatibility complex (MHC) class I and II peptides. We aimed to evaluate existing methods in terms of the appropriateness of the isolation procedure, as well as instrumental parameters used for neoantigen detection. We also focus on the amount of the material used in the protocols as the critical factor to consider when analyzing neoantigens. Beyond experimental aspects, there are numerous readily available proteomics suits/tools applicable for neoantigen discovery; however, experimental validation is still necessary for neoantigen characterization.
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页数:14
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