Mass spectrometry-based identification of MHC-associated peptides

Sachin Kote , Artur Piróg , Georges Bedran , Javier Alfaro , Irena Dapic

Abstract

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.
Author Sachin Kote (ICCVS)
Sachin Kote,,
- International Centre for Cancer Vaccine Science
, Artur Piróg (IFB / M020 / DMCB)
Artur Piróg,,
- Department of Molecular and Cellular Biology
, Georges Bedran (ICCVS)
Georges Bedran,,
- International Centre for Cancer Vaccine Science
, Javier Alfaro (ICCVS)
Javier Alfaro,,
- International Centre for Cancer Vaccine Science
, Irena Dapic (ICCVS)
Irena Dapic,,
- International Centre for Cancer Vaccine Science
Journal seriesCancers, ISSN 2072-6694, (N/A 140 pkt)
Issue year2020
Vol12
No3
Pages1-14
Publication size in sheets0.65
Article number535
Keywords in Englishneoantigens, mild acid elution, immunoprecipitation, mass spectrometry, cancer
ASJC Classification2730 Oncology; 1306 Cancer Research
DOIDOI:10.3390/cancers12030535
URL https://doi.org/10.3390/cancers12030535
Languageen angielski
LicenseJournal (articles only); published final; Uznanie Autorstwa (CC-BY); with publication
Score (nominal)140
Score sourcejournalList
ScoreMinisterial score = 140.0, 30-04-2020, ArticleFromJournal
Publication indicators Scopus SNIP (Source Normalised Impact per Paper): 2018 = 1.44; WoS Impact Factor: 2018 = 6.162 (2)
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