1,2,3, MHC: a Review of Mass-spectrometry-based Immunopeptidomics Methods for Relative and Absolute Quantification of PMHCs

Overview

Journal Immunooncol Technol

Specialty Allergy & Immunology

Date 2022 Jun 27

PMID 35756972

Authors

L E Stopfer

A D DSouza

F M White

Affiliations

Soon will be listed here.

Abstract

Quantitative mass-spectrometry-based methods to perform relative and absolute quantification of peptides in the immunopeptidome are growing in popularity as researchers aim to measure the dynamic nature of the peptide major histocompatibility complex repertoire and make copies-per-cell estimations of target antigens of interest. Multiple methods to carry out these experiments have been reported, each with unique advantages and limitations. This article describes existing methods and recent applications, offering guidance for improving quantitative accuracy and selecting an appropriate experimental set-up to maximize data quality and quantity.

Citing Articles

Immunopeptidomics for autoimmunity: unlocking the chamber of immune secrets.

Arshad S, Cameron B, Joglekar A NPJ Syst Biol Appl. 2025; 11(1):10.

PMID: 39833247 PMC: 11747513. DOI: 10.1038/s41540-024-00482-x.

Ribosome profiling shows variable sensitivity to detect open reading frames for conventional and different types of cryptic T cell antigens.

Fuchs K, Thomaidou S, van der Slik A, van de Meent M, t Hoen P, Falkenburg J Mol Ther Methods Clin Dev. 2025; 33(1):101391.

PMID: 39811688 PMC: 11731205. DOI: 10.1016/j.omtm.2024.101391.

Immunopeptidomics of Serovar -Infected Pig Macrophages Genotyped for Class II Molecules.

Celis-Giraldo C, Suarez C, Agudelo W, Ibarrola N, Degano R, Diaz J Biology (Basel). 2024; 13(10).

PMID: 39452141 PMC: 11505383. DOI: 10.3390/biology13100832.

Validation and quantification of peptide antigens presented on MHCs using SureQuant.

Leddy O, Cui Y, Ahn R, Stopfer L, Choe E, Kim D Nat Protoc. 2024; .

PMID: 39438697 DOI: 10.1038/s41596-024-01076-x.

Unlocking the potential of microfluidics in mass spectrometry-based immunopeptidomics for tumor antigen discovery.

Stutzmann C, Peng J, Wu Z, Savoie C, Sirois I, Thibault P Cell Rep Methods. 2023; 3(6):100511.

PMID: 37426761 PMC: 10326451. DOI: 10.1016/j.crmeth.2023.100511.

References

Kruger M, Moser M, Ussar S, Thievessen I, Luber C, Forner F . SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell. 2008; 134(2):353-64. DOI: 10.1016/j.cell.2008.05.033. View

Li D, Bentley C, Anderson A, Wiblin S, Cleary K, Koustoulidou S . Development of a T-cell Receptor Mimic Antibody against Wild-Type p53 for Cancer Immunotherapy. Cancer Res. 2017; 77(10):2699-2711. DOI: 10.1158/0008-5472.CAN-16-3247. View

Schweppe D, Prasad S, Belford M, Navarrete-Perea J, Bailey D, Huguet R . Characterization and Optimization of Multiplexed Quantitative Analyses Using High-Field Asymmetric-Waveform Ion Mobility Mass Spectrometry. Anal Chem. 2019; 91(6):4010-4016. PMC: 6993951. DOI: 10.1021/acs.analchem.8b05399. View

Tan C, Croft N, Dudek N, Williamson N, Purcell A . Direct quantitation of MHC-bound peptide epitopes by selected reaction monitoring. Proteomics. 2011; 11(11):2336-40. DOI: 10.1002/pmic.201000531. View

Wang Q, Douglass J, Hwang M, Hsiue E, Mog B, Zhang M . Direct Detection and Quantification of Neoantigens. Cancer Immunol Res. 2019; 7(11):1748-1754. PMC: 6825591. DOI: 10.1158/2326-6066.CIR-19-0107. View

Ong S, Blagoev B, Kratchmarova I, Kristensen D, Steen H, Pandey A . Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics. 2002; 1(5):376-86. DOI: 10.1074/mcp.m200025-mcp200. View

Lippolis J, White F, Marto J, Luckey C, Bullock T, Shabanowitz J . Analysis of MHC class II antigen processing by quantitation of peptides that constitute nested sets. J Immunol. 2002; 169(9):5089-97. DOI: 10.4049/jimmunol.169.9.5089. View

Stopfer L, Mesfin J, Joughin B, Lauffenburger D, White F . Multiplexed relative and absolute quantitative immunopeptidomics reveals MHC I repertoire alterations induced by CDK4/6 inhibition. Nat Commun. 2020; 11(1):2760. PMC: 7265461. DOI: 10.1038/s41467-020-16588-9. View

Murphy J, Yu Q, Konda P, Paulo J, Jedrychowski M, Kowalewski D . Multiplexed Relative Quantitation with Isobaric Tagging Mass Spectrometry Reveals Class I Major Histocompatibility Complex Ligand Dynamics in Response to Doxorubicin. Anal Chem. 2019; 91(8):5106-5115. PMC: 7302430. DOI: 10.1021/acs.analchem.8b05616. View

10.

Bozzacco L, Yu H, Zebroski H, Dengjel J, Deng H, Mojsov S . Mass spectrometry analysis and quantitation of peptides presented on the MHC II molecules of mouse spleen dendritic cells. J Proteome Res. 2011; 10(11):5016-30. PMC: 3270889. DOI: 10.1021/pr200503g. View

11.

Huang J, Brameshuber M, Zeng X, Xie J, Li Q, Chien Y . A single peptide-major histocompatibility complex ligand triggers digital cytokine secretion in CD4(+) T cells. Immunity. 2013; 39(5):846-57. PMC: 3846396. DOI: 10.1016/j.immuni.2013.08.036. View

12.

Demmers L, Kretzschmar K, Van Hoeck A, Bar-Epraim Y, van den Toorn H, Koomen M . Single-cell derived tumor organoids display diversity in HLA class I peptide presentation. Nat Commun. 2020; 11(1):5338. PMC: 7577990. DOI: 10.1038/s41467-020-19142-9. View

13.

Pfammatter S, Bonneil E, Lanoix J, Vincent K, Hardy M, Courcelles M . Extending the Comprehensiveness of Immunopeptidome Analyses Using Isobaric Peptide Labeling. Anal Chem. 2020; 92(13):9194-9204. DOI: 10.1021/acs.analchem.0c01545. View

14.

Caron E, Vincent K, Fortier M, Laverdure J, Bramoulle A, Hardy M . The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation. Mol Syst Biol. 2011; 7:533. PMC: 3202804. DOI: 10.1038/msb.2011.68. View

15.

Shao W, Pedrioli P, Wolski W, Scurtescu C, Schmid E, Vizcaino J . The SysteMHC Atlas project. Nucleic Acids Res. 2017; 46(D1):D1237-D1247. PMC: 5753376. DOI: 10.1093/nar/gkx664. View

16.

Rodenko B, Toebes M, Hadrup S, van Esch W, Molenaar A, Schumacher T . Generation of peptide-MHC class I complexes through UV-mediated ligand exchange. Nat Protoc. 2007; 1(3):1120-32. DOI: 10.1038/nprot.2006.121. View

17.

Hogrebe A, von Stechow L, Bekker-Jensen D, Weinert B, Kelstrup C, Olsen J . Benchmarking common quantification strategies for large-scale phosphoproteomics. Nat Commun. 2018; 9(1):1045. PMC: 5849679. DOI: 10.1038/s41467-018-03309-6. View

18.

Zanivan S, Krueger M, Mann M . In vivo quantitative proteomics: the SILAC mouse. Methods Mol Biol. 2011; 757:435-50. DOI: 10.1007/978-1-61779-166-6_25. View

19.

Chong C, Marino F, Pak H, Racle J, Daniel R, Muller M . High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferonγ-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome. Mol Cell Proteomics. 2017; 17(3):533-548. PMC: 5836376. DOI: 10.1074/mcp.TIR117.000383. View

20.

Abelin J, Harjanto D, Malloy M, Suri P, Colson T, Goulding S . Defining HLA-II Ligand Processing and Binding Rules with Mass Spectrometry Enhances Cancer Epitope Prediction. Immunity. 2019; 51(4):766-779.e17. DOI: 10.1016/j.immuni.2019.08.012. View