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Review

Contribution of mass spectrometry-based proteomics to immunology

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Pages 653-664 | Published online: 09 Jan 2014

References

  • Wasinger VC, Cordwell SJ, Cerpa-Poljak A et al. Progress with gene-product mapping of the Mollicutes: mycoplasma genitalium. Electrophoresis16(7), 1090–1094 (1995).
  • Rammensee HG, Weinschenk T, Gouttefangeas C, Stevanovic S. Towards patient-specific tumor antigen selection for vaccination. Immunol. Rev.188, 164–176 (2002).
  • Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature422(6928), 198–207 (2003).
  • Cresswell P, Ackerman AL, Giodini A et al. Mechanisms of MHC class I-restricted antigen processing and cross-presentation. Immunol. Rev.207, 145–157 (2005).
  • Li P, Gregg JL, Wang N et al. Compartmentalization of class II antigen presentation: contribution of cytoplasmic and endosomal processing. Immunol. Rev.207, 206–217 (2005).
  • Snyder HL, Yewdell JW, Bennink JR. Trimming of antigenic peptides in an early secretory compartment. J. Exp. Med.180(6), 2389–2394 (1994).
  • Serwold T, Gonzalez F, Kim J et al. ERAAP customizes peptides for MHC class I molecules in the endoplasmic reticulum. Nature419(6906), 480–483 (2002).
  • Yewdell JW. Not such a dismal science: the economics of protein synthesis, folding, degradation and antigen processing. Trends Cell Biol.11(7), 294–297 (2001).
  • Reits E, Griekspoor A, Neijssen J et al. Peptide diffusion, protection, and degradation in nuclear and cytoplasmic compartments before antigen presentation by MHC class I. Immunity18(1), 97–108 (2003).
  • Princiotta MF, Finzi D, Qian SB et al. Quantitating protein synthesis, degradation, and endogenous antigen processing. Immunity18(3), 343–354 (2003).
  • Ben Shahar S, Komlosh A, Nadav E et al. 26S proteasome-mediated production of an authentic major histocompatibility class I-restricted epitope from an intact protein substrate. J. Biol. Chem.274(31), 21963–21972 (1999).
  • Cascio P, Hilton C, Kisselev AF et al. 26S proteasomes and immunoproteasomes produce mainly N-extended versions of an antigenic peptide. EMBO J.20(10), 2357–2366 (2001).
  • Montoya M, Del Val M. Intracellular rate-limiting steps in MHC class I antigen processing. J. Immunol.163(4), 1914–1922 (1999).
  • Bjorkman PJ, Parham P. Structure, function, and diversity of class I major histocompatibility complex molecules. Annu. Rev. Biochem.59, 253–288 (1990).
  • Stevanovic S, Schild H. Quantitative aspects of T cell activation – peptide generation and editing by MHC class I molecules. Semin. Immunol.11(6), 375–384 (1999).
  • Hickman HD, Luis AD, Bardet W et al. Cutting edge: class I presentation of host peptides following HIV infection. J. Immunol.171(1), 22–26 (2003).
  • Weinschenk T, Gouttefangeas C, Schirle M et al. Integrated functional genomics approach for the design of patient-individual antitumor vaccines. Cancer Res.62(20), 5818–5827 (2002).
  • Storkus WJ, Zeh HJ, III, Salter RD, Lotze MT. Identification of T-cell epitopes: rapid isolation of class I-presented peptides from viable cells by mild acid elution. J. Immunother.14(2), 94–103 (1993).
  • Falk K, Rötzschke O, Stevanovic S et al. Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature351(6324), 290–296 (1991).
  • Bluestone JA, Jameson S, Miller S, Dick R. Peptide-induced conformational changes in class I heavy chains alter major histocompatibility complex recognition. J. Exp. Med.176(6), 1757–1761 (1992).
  • Solheim JC, Carreno BM, Smith JD et al. Binding of peptides lacking consensus anchor residue alters H-2Ld serologic recognition. J. Immunol.151(10), 5387–5397 (1993).
  • Margulies DH, Ramsey AL, Boyd LF, McCluskey J. Genetic engineering of an H-2Dd/Q10b chimeric histocompatibility antigen: purification of soluble protein from transformant cell supernatants. Proc. Natl Acad. Sci. USA83(14), 5252–5256 (1986).
  • Prilliman K, Lindsey M, Zuo Y et al. Large-scale production of class I bound peptides: assigning a signature to HLA-B*1501. Immunogenetics45(6), 379–385 (1997).
  • Krüger T, Schoor O, Lemmel C et al. Lessons to be learned from primary renal cell carcinomas: novel tumor antigens and HLA ligands for immunotherapy. Cancer Immunol. Immunother.54(9), 826–836 (2005).
  • Falk K, Rötzschke O, Deres K et al. Identification of naturally processed viral nonapeptides allows their quantification in infected cells and suggests an allele-specific T cell epitope forecast. J. Exp. Med.174(2), 425–434 (1991).
  • Hunt DF, Henderson RA, Shabanowitz J et al. Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry. Science255(5049), 1261–1263 (1992).
  • Hofmann S, Glückmann M, Kausche S et al. Rapid and sensitive identification of major histocompatibility complex class I-associated tumor peptides by Nano-LC MALDI MS/MS. Mol. Cell Proteomics4(12), 1888–1897 (2005).
  • Macdonald W, Williams DS, Clements CS et al. Identification of a dominant self-ligand bound to three HLA B44 alleles and the preliminary crystallographic analysis of recombinant forms of each complex. FEBS Lett.527(1–3), 27–32 (2002).
  • de Jong A. Contribution of mass spectrometry to contemporary immunology. Mass Spectrom. Rev.17(5), 311–335 (1998).
  • Lemmel C, Stevanovic S. The use of HPLC-MS in T-cell epitope identification. Methods29(3), 248–259 (2003).
  • Bodnar WM, Blackburn RK, Krise JM, Moseley MA. Exploiting the complementary nature of LC/MALDI/MS/MS and LC/ESI/MS/MS for increased proteome coverage. J. Am. Soc. Mass Spectrom.14(9), 971–979 (2003).
  • Chen HS, Rejtar T, Andreev V et al. Enhanced characterization of complex proteomic samples using LC-MALDI MS/MS: exclusion of redundant peptides from MS/MS analysis in replicate runs. Anal. Chem.77(23), 7816–7825 (2005).
  • Sickmann A, Bluggel M, Kulke M et al. Identification of major histocompatibility complex class II-associated peptides derived from freshly prepared rat Langerhans cells using MALDI-PSD and Edman degradation. Analyst125(4), 569–573 (2000).
  • Domon B, Aebersold R. Mass spectrometry and protein analysis. Science312(5771), 212–217 (2006).
  • Guerrera IC, Kleiner O. Application of mass spectrometry in proteomics. Biosci. Rep.25(1–2), 71–93 (2005).
  • Dengjel J, Schoor O, Fischer R et al. Autophagy promotes MHC class II presentation of peptides from intracellular source proteins. Proc. Natl Acad. Sci. USA102(22), 7922–7927 (2005).
  • Dongre AR, Kovats S, deRoos P et al. In vivo MHC class II presentation of cytosolic proteins revealed by rapid automated tandem mass spectrometry and functional analyses. Eur. J. Immunol.31(5), 1485–1494 (2001).
  • Hickman HD, Luis AD, Buchli R et al. Toward a definition of self: proteomic evaluation of the class I peptide repertoire. J. Immunol.172(5), 2944–2952 (2004).
  • Gygi SP, Corthals GL, Zhang Y et al. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl Acad. Sci. USA97(17), 9390–9395 (2000).
  • Southan C. Has the yo-yo stopped? An assessment of human protein-coding gene number. Proteomics4(6), 1712–1726 (2004).
  • Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell Proteomics1(11), 845–867 (2002).
  • Corthals GL, Wasinger VC, Hochstrasser DF, Sanchez JC. The dynamic range of protein expression: a challenge for proteomic research. Electrophoresis21(6), 1104–1115 (2000).
  • Washburn MP, Wolters D, Yates JR 3rd. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol.19(3), 242–247 (2001).
  • Gygi SP, Rist B, Griffin TJ et al. Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags. J. Proteome Res.1(1), 47–54 (2002).
  • Mann M, Hendrickson RC, Pandey A. Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem.70,437–473 (2001).
  • Ellis DI, O'Hagan S, Dunn WB et al. From genomes to systems. Genome Biol.5(11), 354 (2004).
  • Küster B, Schirle M, Mallick P, Aebersold R. Scoring proteomes with proteotypic peptide probes. Nat. Rev. Mol. Cell Biol.6(7), 577–583 (2005).
  • Jensen ON. Interpreting the protein language using proteomics. Nat. Rev. Mol. Cell Biol.7(6), 391–403 (2006).
  • Mann M, Jensen ON. Proteomic analysis of post-translational modifications. Nat. Biotechnol.21(3), 255–261 (2003).
  • Dengjel J, Rammensee HG, Stevanovic S. Glycan side chains on naturally presented MHC class II ligands. J. Mass Spectrom.40(1), 100–104 (2005).
  • Kastrup IB, Stevanovic S, Arsequell G et al. Lectin purified human class I MHC-derived peptides: evidence for presentation of glycopeptides in vivo. Tissue Antigens56(2), 129–135 (2000).
  • Haurum JS, Arsequell G, Lellouch AC et al. Recognition of carbohydrate by major histocompatibility complex class I-restricted, glycopeptide-specific cytotoxic T lymphocytes. J. Exp. Med.180(2), 739–744 (1994).
  • Engelhard VH, Altrich-Vanlith M, Ostankovitch M, Zarling AL. Post-translational modifications of naturally processed MHC-binding epitopes. Curr. Opin. Immunol.18(1), 92–97 (2006).
  • Veenstra TD, Conrads TP, Issaq HJ. What to do with ‘one-hit wonders’? Electrophoresis25(9), 1278–1279 (2004).
  • Reinders J, Lewandrowski U, Moebius J et al. Challenges in mass spectrometry-based proteomics. Proteomics4(12), 3686–3703 (2004).
  • Hanada K, Yewdell JW, Yang JC. Immune recognition of a human renal cancer antigen through post-translational protein splicing. Nature427(6971), 252–256 (2004).
  • Schuler MM, Dönnes P, Nastke MD et al. SNEP: SNP-derived epitope prediction program for minor H antigens. Immunogenetics57(11), 816–820 (2005).
  • Vigneron N, Stroobant V, Chapiro J et al. An antigenic peptide produced by peptide splicing in the proteasome. Science304(5670), 587–590 (2004).
  • Friede T, Gnau V, Jung G et al. Natural ligand motifs of closely related HLA-DR4 molecules predict features of rheumatoid arthritis associated peptides. Biochim. Biophys. Acta1316(2), 85–101 (1996).
  • Zhang Y, Chaux P, Stroobant V et al. A MAGE-3 peptide presented by HLA-DR1 to CD4+ T cells that were isolated from a melanoma patient vaccinated with a MAGE-3 protein. J. Immunol.171(1), 219–225 (2003).
  • Tewari MK, Sinnathamby G, Rajagopal D, Eisenlohr LC. A cytosolic pathway for MHC class II-restricted antigen processing that is proteasome and TAP dependent. Nat. Immunol.6(3), 287–294 (2005).
  • Dörfel D, Appel S, Grünebach F et al. Processing and presentation of HLA class I and II epitopes by dendritic cells after transfection with in vitro-transcribed MUC1 RNA. Blood105(8), 3199–3205 (2005).
  • Nimmerjahn F, Milosevic S, Behrends U et al. Major histocompatibility complex class II-restricted presentation of a cytosolic antigen by autophagy. Eur. J. Immunol.33(5), 1250–1259 (2003).
  • Crotzer VL, Blum JS. Autophagy and intracellular surveillance: Modulating MHC class II antigen presentation with stress. Proc. Natl Acad. Sci. USA102(22), 7779–7780 (2005).
  • Klionsky DJ, Emr SD. Autophagy as a regulated pathway of cellular degradation. Science290(5497), 1717–1721 (2000).
  • Stoltze L, Schirle M, Schwarz G et al. Two new proteases in the MHC class I processing pathway. Nat. Immunol.1(5), 413–418 (2000).
  • Osterloh P, Linkemann K, Tenzer S et al. Proteasomes shape the repertoire of T cells participating in antigen-specific immune responses. Proc. Natl Acad. Sci. USA103(13), 5042–5047 (2006).
  • Luckey CJ, Marto JA, Partridge M et al. Differences in the expression of human class I MHC alleles and their associated peptides in the presence of proteasome inhibitors. J. Immunol.167(3), 1212–1221 (2001).
  • Purcell AW, Gorman JJ, Garcia-Peydro M et al. Quantitative and qualitative influences of tapasin on the class I peptide repertoire. J. Immunol.166(2), 1016–1027 (2001).
  • Wei ML, Cresswell P. HLA-A2 molecules in an antigen-processing mutant cell contain signal sequence-derived peptides. Nature356(6368), 443–446 (1992).
  • Henderson RA, Michel H, Sakaguchi K et al. HLA-A2.1-associated peptides from a mutant cell line: a second pathway of antigen presentation. Science255(5049), 1264–1266 (1992).
  • Weinzierl AO, Sigurdardottir D, Rammensee HG, Stevanovic S. TAP-independent HLA ligands: characterization and quantification by differential mass spectrometry. Presented at: Conference proceedings Joint Annual Meeting of the German and Scandinavian Societies, Kiel, Germany (2005).
  • Muntasell A, Carrascal M, Alvarez I et al. Dissection of the HLA-DR4 peptide repertoire in endocrine epithelial cells: strong influence of invariant chain and HLA-DM expression on the nature of ligands. J. Immunol.173(2), 1085–1093 (2004).
  • Bubenik J. MHC class I down-regulation: tumour escape from immune surveillance? (review). Int. J. Oncol.25(2), 487–491 (2004).
  • Lilley BN, Ploegh HL. Viral modulation of antigen presentation: manipulation of cellular targets in the ER and beyond. Immunol. Rev.207, 126–144 (2005).
  • Reits EA, Hodge JW, Herberts CA et al. Radiation modulates the peptide repertoire, enhances MHC class I expression, and induces successful antitumor immunotherapy. J. Exp. Med.203(5), 1259–1271 (2006).
  • Schag K, Schmidt SM, Müller MR et al. Identification of C-met oncogene as a broadly expressed tumor-associated antigen recognized by cytotoxic T-lymphocytes. Clin. Cancer Res.10(11), 3658–3666 (2004).
  • Schmidt SM, Schag K, Müller MR et al. Induction of adipophilin-specific cytotoxic T lymphocytes using a novel HLA-A2-binding peptide that mediates tumor cell lysis. Cancer Res.64(3), 1164–1170 (2004).
  • Cox AL, Skipper J, Chen Y et al. Identification of a peptide recognized by five melanoma-specific human cytotoxic T cell lines. Science264(5159), 716–719 (1994).
  • Slingluff CL Jr, Yamshchikov G, Neese P et al. Phase I trial of a melanoma vaccine with gp100(280–288) peptide and tetanus helper peptide in adjuvant: immunologic and clinical outcomes. Clin. Cancer Res.7(10), 3012–3024 (2001).
  • Slingluff CL, Jr., Petroni GR, Yamshchikov GV et al. Clinical and immunologic results of a randomized Phase II trial of vaccination using four melanoma peptides either administered in granulocyte-macrophage colony-stimulating factor in adjuvant or pulsed on dendritic cells. J. Clin. Oncol.21(21), 4016–4026 (2003).
  • Banchereau J, Palucka AK, Dhodapkar M et al. Immune and clinical responses in patients with metastatic melanoma to CD34+ progenitor-derived dendritic cell vaccine. Cancer Res.61(17), 6451–6458 (2001).
  • Dudley ME, Wunderlich JR, Yang JC et al. Adoptive cell transfer therapy following non-myeloablative but lymphodepleting chemotherapy for the treatment of patients with refractory metastatic melanoma. J. Clin. Oncol.23(10), 2346–2357 (2005).
  • Pascolo S, Schirle M, Gückel B et al. A MAGE-A1 HLA-A A*0201 epitope identified by mass spectrometry. Cancer Res.61(10), 4072–4077 (2001).
  • Schirle M, Keilholz W, Weber B et al. Identification of tumor-associated MHC class I ligands by a novel T cell-independent approach. Eur. J. Immunol.30(8), 2216–2225 (2000).
  • Planz O, Dumrese T, Hülpüsch S et al. A naturally processed rat major histocompatibility complex class I-associated viral peptide as target structure of borna disease virus-specific CD8+ T cells. J. Biol. Chem.276(17), 13689–13694 (2001).
  • Lemmel C, Weik S, Eberle U et al. Differential quantitative analysis of MHC ligands by mass spectrometry using stable isotope labeling. Nat. Biotechnol.22(4), 450–454 (2004).
  • Weinzierl AO, Stevanovic S. LC-MS based protein and peptide quantification using stable isotope labels: from ICAT in general to differential N-terminal coding (dNIC) in Special. Biotechnol. Genet. Eng. Rev.23 (In Press) (2006).
  • Anderson L, Seilhamer J. A comparison of selected mRNA and protein abundances in human liver. Electrophoresis18(3–4), 533–537 (1997).
  • Gygi SP, Rochon Y, Franza BR, Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol. Cell Biol.19(3), 1720–1730 (1999).
  • Huber M, Bahr I, Kratzschmar JR et al. Comparison of proteomic and genomic analyses of the human breast cancer cell line T47D and the antiestrogen-resistant derivative T47D-r. Mol. Cell Proteomics3(1), 43–55 (2004).
  • Kloetzel PM, Ossendorp F. Proteasome and peptidase function in MHC-class-I-mediated antigen presentation. Curr. Opin. Immunol.16(1), 76–81 (2004).
  • Yewdell JW, Schubert U, Bennink JR. At the crossroads of cell biology and immunology: DRiPs and other sources of peptide ligands for MHC class I molecules. J.Cell Sci.114(Pt 5), 845–851 (2001).
  • Milner E, Barnea E, Beer I, Admon A. The turnover kinetics of MHC peptides of human cancer cells. Mol. Cell Proteomics5(2), 357–365 (2006).
  • Koopmann JO, Albring J, Huter E et al. Export of antigenic peptides from the endoplasmic reticulum intersects with retrograde protein translocation through the Sec61p channel. Immunity13(1), 117–127 (2000).
  • Harrison PM, Kumar A, Lang N et al. A question of size: the eukaryotic proteome and the problems in defining it. Nucleic Acids Res.30(5), 1083–1090 (2002).
  • Carninci P, Kasukawa T, Katayama S et al. The transcriptional landscape of the mammalian genome. Science309(5740), 1559–1563 (2005).
  • Buchsbaum S, Barnea E, Dassau L et al. Large-scale analysis of HLA peptides presented by HLA-Cw4. Immunogenetics55(3), 172–176 (2003).
  • Dengjel J, Decker P, Schoor O et al. Identification of a naturally processed cyclin D1 T-helper epitope by a novel combination of HLA class II targeting and differential mass spectrometry. Eur. J. Immunol.34(12), 3644–3651 (2004).

Websites

  • IMGT/HLA Database www.ebi.ac.uk/imgt/hla/
  • Syfpeithi, A database of MHC ligands and peptide motifs www.syfpeithi.de/

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