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.
引用
收藏
页数:14
相关论文
共 50 条
  • [41] Predictive Liquid Chromatography of Peptides Based on Hydrophilic Interactions for Mass Spectrometry-Based Proteomics
    Lobas, A. A.
    Levitsky, L. I.
    Fichtenbaum, A.
    Surin, A. K.
    Pridatchenko, M. L.
    Mitulovic, G.
    Gorshkov, A. V.
    Gorshkov, M. V.
    JOURNAL OF ANALYTICAL CHEMISTRY, 2017, 72 (14) : 1375 - 1382
  • [42] Predictive Liquid Chromatography of Peptides Based on Hydrophilic Interactions for Mass Spectrometry-Based Proteomics
    Gorshkov, M.V. (mike.gorshkov@gmail.com), 1600, Pleiades journals (72):
  • [43] Predictive Liquid Chromatography of Peptides Based on Hydrophilic Interactions for Mass Spectrometry-Based Proteomics
    A. A. Lobas
    L. I. Levitsky
    A. Fichtenbaum
    A. K. Surin
    M. L. Pridatchenko
    G. Mitulovic
    A. V. Gorshkov
    M. V. Gorshkov
    Journal of Analytical Chemistry, 2017, 72 : 1375 - 1382
  • [44] Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats
    Petras, Daniel
    Nothias, Louis-Felix
    Quinn, Robert A.
    Alexandrov, Theodore
    Bandeira, Nuno
    Bouslimani, Amina
    Castro-Falcon, Gabriel
    Chen, Liangyu
    Dang, Tam
    Floros, Dimitrios J.
    Hook, Vivian
    Garg, Neha
    Haffner, Nicole
    Jiang, Yike
    Kapono, Clifford A.
    Koester, Irina
    Knight, Rob
    Leber, Christopher A.
    Ling, Tie-Jun
    Luzzatto-Knaan, Tal
    McCall, Laura-Isobel
    McGrath, Aaron P.
    Meehan, Michael J.
    Merritt, Jonathan K.
    Mills, Robert H.
    Morton, Jamie
    Podvin, Sonia
    Protsyuk, Ivan
    Purdy, Trevor
    Satterfield, Kendall
    Searles, Stephen
    Shah, Sahil
    Shires, Sarah
    Steffen, Dana
    White, Margot
    Todoric, Jelena
    Tuttle, Robert
    Wojnicz, Aneta
    Sapp, Valerie
    Vargas, Fernando
    Yang, Jin
    Zhang, Chao
    Dorrestein, Pieter C.
    ANALYTICAL CHEMISTRY, 2016, 88 (22) : 10775 - 10784
  • [45] Mass spectrometry-based characterization of endogenous peptides and metabolites in small volume samples
    Ong, Ta-Hsuan
    Tillmaand, Emily G.
    Makurath, Monika
    Rubakhin, Stanislav S.
    Sweedler, Jonathan V.
    BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 2015, 1854 (07): : 732 - 740
  • [46] IDENTIFICATION OF MHC PEPTIDES USING MASS SPECTROMETRY FOR NEOANTIGEN DISCOVERY AND CANCER VACCINE DEVELOPMENT
    Chen, Rui
    Fulton, Kelly M.
    Twine, Susan M.
    Li, Jianjun
    MASS SPECTROMETRY REVIEWS, 2021, 40 (02) : 110 - 125
  • [47] MHC-TreASUre_Hunt: a computational pipeline for the identification of MHC-I peptides from mass spectrometry
    Wilson, Eric A.
    Wilson, Melissa A.
    Anderson, Karen S.
    MOLECULAR & CELLULAR PROTEOMICS, 2019, 18 (08) : S74 - S74
  • [48] Mass spectrometry-based proteomics strategies for protease cleavage site identification
    van den Berg, Bart H. J.
    Tholey, Andreas
    PROTEOMICS, 2012, 12 (4-5) : 516 - 529
  • [49] Mass spectrometry-based candidate substrate and site identification of PTM enzymes
    Chen, Weiyu
    Ji, Guanghui
    Wu, Roujun
    Fang, Caiyun
    Lu, Haojie
    TRAC-TRENDS IN ANALYTICAL CHEMISTRY, 2023, 160
  • [50] Applications of mass spectrometry-based proteomics in food authentication and quality identification
    Tian Yujing
    Zhang Jiukai
    Cheng Haiyan
    Li Xian
    Chen Ying
    CHINESE JOURNAL OF CHROMATOGRAPHY, 2018, 36 (07) : 588 - 598