A Novel MS-Cleavable Azo Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS)

Research Article

Abstract

The chemical cross-linking/mass spectrometry (MS) approach is a growing research field in structural proteomics that allows gaining insights into protein conformations. It relies on creating distance constraints between cross-linked amino acid side chains that can further be used to derive protein structures. Currently, the most urgent task for designing novel cross-linking principles is an unambiguous and automated assignment of the created cross-linked products. Here, we introduce the homobifunctional, amine-reactive, and water soluble cross-linker azobisimidoester (ABI) as a prototype of a novel class of cross-linkers. The ABI-linker possesses an innovative modular scaffold combining the benefits of collisional activation lability with open shell chemistry. This MS-cleavable cross-linker can be efficiently operated via free radical initiated peptide sequencing (FRIPS) in positive ionization mode. Our proof-of-principle study challenges the gas phase behavior of the ABI-linker for the three amino acids, lysine, leucine, and isoleucine, as well as the model peptide thymopentin. The isomeric amino acids leucine and isoleucine could be discriminated by their characteristic side chain fragments. Collisional activation experiments were conducted via positive electrospray ionization (ESI) on two Orbitrap mass spectrometers. The ABI-mediated formation of odd electron product ions in MS/MS and MS3 experiments was evaluated and compared with a previously described azo-based cross-linker. All cross-linked products were amenable to automated analysis by the MeroX software, underlining the future potential of the ABI-linker for structural proteomics studies.

Graphical Abstract

Keywords

Azobisimidoester Chemical cross-linking Collisional activation Free radical initiated peptide sequencing (FRIPS) Peptides 

Supplementary material

13361_2017_1744_MOESM1_ESM.docx (1.1 mb)
ESM 1(DOCX 1145 kb)

References

  1. 1.
    Sinz, A.: Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein–protein interactions. Mass Spectrom. Rev. 25, 663–682 (2006)CrossRefGoogle Scholar
  2. 2.
    Petrotchenko, E.V., Borchers, C.H.: Cross-linking combined with mass spectrometry for structural proteomics. Mass Spectrom. Rev. 29, 862–876 (2010)CrossRefGoogle Scholar
  3. 3.
    Sinz, A.: The advancement of chemical cross-linking and mass spectrometry for structural proteomics: from single proteins to protein interaction networks. Expert Rev. Proteom. 11, 733–743 (2014)CrossRefGoogle Scholar
  4. 4.
    Sinz, A., Arlt, C., Chorev, D., Sharon, M.: Chemical cross-linking and native mass spectrometry: a fruitful combination for structural biology. Prot. Sci. 24, 1193–1209 (2015)CrossRefGoogle Scholar
  5. 5.
    Leitner, A., Faini, M., Stengel, F., Aebersold, R.: Cross-linking and mass spectrometry: an integrated technology to understand the structure and function of molecular machines. Trends Biochem. Sci. 41, 20–32 (2016)CrossRefGoogle Scholar
  6. 6.
    Tran, B.Q., Goodlett, D.R., Goo, Y.A.: Advances in protein complex analysis by chemical cross-linking coupled with mass spectrometry (CXMS) and bioinformatics. Biochem. Biophys. Acta 1864, 123–129 (2016)Google Scholar
  7. 7.
    Yang, L., Zheng, C., Weisbrod, C.R., Tang, X., Munske, G.R., Hoopmann, M.R., Eng, J.K., Bruce, J.E.: In vivo application of photocleavable protein interaction reporter technology. J. Proteome Res. 11, 1027–1041 (2012)CrossRefGoogle Scholar
  8. 8.
    Iacobucci, C., Reale, S., De Angelis, F.: Photoactivable amino acid bioisosteres and mass spectrometry: snapshots of in vivo 3D protein structures. ChemBioChem 14, 181–183 (2013)CrossRefGoogle Scholar
  9. 9.
    Kaake, R.M., Wang, X., Burke, A., Yu, C., Kandur, W., Yang, Y., Novtisky, E.J., Second, T., Duan, J., Kao, A., Guan, S., Vellucci, D., Rychnovsky, S.D., Huang, L.: A new in vivo cross-linking mass spectrometry platform to define protein-protein interactions in living cells. Mol. Cell. Proteomics 13, 3533–3543 (2014)CrossRefGoogle Scholar
  10. 10.
    Agou, F., Véron, M.: In vivo protein cross-linking. In: Meyerkord, L.C., Fu, H. (eds.) Methods Mol. Biol. Springer, New York, NY (2015)Google Scholar
  11. 11.
    Green, N.S., Reisler, E., Houk, K.N.: Quantitative evaluation of the lengths of homobifunctional protein cross-linking reagents used as molecular rulers. Protein Sci. 10, 1293–1304 (2001)CrossRefGoogle Scholar
  12. 12.
    Kalkhof, S., Haehn, S., Paulsson, M., Smyth, N., Meiler, J., Sinz, A.: Computational modeling of laminin N-terminal domains using sparse distance constraints from disulfide bonds and chemical cross-linking. Proteins: Struct. Funct. Bioinf. 78, 3409–3427 (2010)CrossRefGoogle Scholar
  13. 13.
    Kahraman, A., Herzog, F., Leitner, A., Rosenberger, G., Aebersold, R., Malmstrom, L.: Cross-link guided molecular modeling with ROSETTA. PLoS One 8, e73411 (2013)CrossRefGoogle Scholar
  14. 14.
    Hofmann, T., Fischer, A.W., Meiler, J., Kalkhof, S.: Protein structure prediction guided by crosslinking restraints – a systematic evaluation of the impact of the cross-linking spacer length. Methods 89, 79–90 (2015)CrossRefGoogle Scholar
  15. 15.
    Schneider, M., Belsom, A., Rappsilber, J., Brock, O.: Blind testing of cross-linking/mass spectrometry hybrid methods in CASP11. Proteins: Struct. Funct. Bioinf. 84, 152–163 (2016)CrossRefGoogle Scholar
  16. 16.
    Leitner, A., Reischl, R., Walzthoeni, T., Herzog, F., Bohn, S., Forster, F., Aebersold, R.: Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography. Mol. Cell. Proteomics 11, M111.014126 (2012)CrossRefGoogle Scholar
  17. 17.
    Fritzsche, R., Ihling, C.H., Götze, M., Sinz, A.: Optimizing the enrichment of cross-linked products for mass spectrometric protein analysis. Rapid Commun. Mass Spectrom. 26, 653–658 (2012)CrossRefGoogle Scholar
  18. 18.
    Rappsilber, J., Mann, M., Ishihama, Y.: Protocol for micro-purification, enrichment, prefractionation, and storage of peptides for proteomics using StageTips. Nat. Protoc. 2, 1896–1906 (2007)CrossRefGoogle Scholar
  19. 19.
    Trnka, M.J., Baker, P.R., Robinson, P.J., Burlingame, A.L., Chalkley, R.J.: Matching cross-linked peptide spectra: only as good as the worse identification. Mol. Cell. Proteomic 13, 420–434 (2014)CrossRefGoogle Scholar
  20. 20.
    Rasmussen, M.I., Refsgaard, J.C., Peng, L., Houen, G., Hojrup, P.: CrossWork: software-assisted identification of cross-linked peptides. J. Proteome 74, 1871–1883 (2011)CrossRefGoogle Scholar
  21. 21.
    Müller, D.R., Schindler, P., Towbin, H., Wirth, U., Voshol, H., Hoving, S., Steinmetz, M.O.: Isotope-tagged cross-linking reagents. A new tool in mass spectrometric protein interaction analysis. Anal. Chem. 73, 1927–1934 (2001)CrossRefGoogle Scholar
  22. 22.
    Petrotchenko, E.V., Olkhovik, V.K., Borchers, C.H.: Isotopically coded cleavable cross-linker for studying protein–protein interaction and protein complexes. Mol. Cell. Proteomics 4, 1167–1179 (2005)CrossRefGoogle Scholar
  23. 23.
    Ihling, C., Schmidt, A., Kalkhof, S., Schulz, D.M., Stingl, C., Mechtler, K., Haack, M., Beck-Sickinger, A.G., Cooper, D.M., Sinz, A.: Isotope-labeled cross-linkers and Fourier transform ion cyclotron resonance mass spectrometry for structural analysis of a protein/peptide complex. J. Am. Soc. Mass Spectrom. 17, 1100–1113 (2006)CrossRefGoogle Scholar
  24. 24.
    Petrotchenko, E.V., Serpa, J.J., Borchers, C.H.: Use of a combination of isotopically coded cross-linkers and isotopically coded N-terminal modification reagents for selective identification of inter-peptide cross-links. Anal. Chem. 82, 817–823 (2010)CrossRefGoogle Scholar
  25. 25.
    Brodie, N.I., Makepeace, K.A., Petrotchenko, E.V., Borchers, C.H.: Isotopically-coded short-range hetero-bifunctional photo-reactive cross-linkers for studying protein structure. J. Proteome 118, 12–20 (2015)CrossRefGoogle Scholar
  26. 26.
    Spengler, B., Hester, A.: Mass-based classification (MBC) of peptides: highly accurate precursor ion mass values can be used to directly recognize peptide phosphorylation. J. Am. Soc. Mass Spectrom. 19, 1808–1812 (2008)CrossRefGoogle Scholar
  27. 27.
    Ricks, A.M., Amster, I.J., Lie, C., Niehuser, S., Hernandez, H.: Mass defect labeling for enhanced protein identification. Abstr. Pap. Am. Chem. S. 229, U391-U391 (2005)Google Scholar
  28. 28.
    Valkenborg, D., Jansen, I., Burzykowski, T.: A model-based method for the prediction of the isotopic distribution of peptides. J. Am. Soc. Mass Spectrom. 19, 703–712 (2008)CrossRefGoogle Scholar
  29. 29.
    Hall, M.P., Schneider, L.V.: Isotope-differentiated binding energy shift tags (IDBEST) for improved targeted biomarker discovery and validation. Expert Rev. Proteomics 1, 421–431 (2004)CrossRefGoogle Scholar
  30. 30.
    Hage, C., Falvo, F., Schäfer M., Sinz, A.: Novel concepts of MS-cleavable cross-linkers for improved peptide structure analysis. J. Am. Soc. Mass Spectrom. (2017). Doi:10.1007/s13361-017-1712-1
  31. 31.
    McLuckey, S.A., Goeringer, D.E.: Slow heating methods in tandem mass spectrometry. J. Mass Spectrom. 32, 461–474 (1997)CrossRefGoogle Scholar
  32. 32.
    Qi, Y., Volmer, D.A.: Structural analysis of small to medium-sized molecules by mass spectrometry after electron-ion fragmentation (ExD) reactions. Analyst 141, 794–806 (2016)CrossRefGoogle Scholar
  33. 33.
    Syka, J.E., Coon, J.J., Schroeder, M.J., Shabanowitz, J., Hunt, D.F.: Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 101, 9528–9533 (2004)CrossRefGoogle Scholar
  34. 34.
    Frese, C.K., Altelaar, A.F.M., van den Toorn, H., Nolting, D., Griep-Raming, J., Heck, A.J.R., Mohammed, S.: Toward full peptide sequence coverage by dual fragmentation combining electron-transfer and higher-energy collision dissociation tandem mass spectrometry. Anal. Chem. 84, 9668–9673 (2012)CrossRefGoogle Scholar
  35. 35.
    Giese, S.H., Belsom, A., Rappsilber, J.: Optimized fragmentation regime for diazirine photo-cross-linked peptides. Anal. Chem. 88, 8239–8247 (2016)CrossRefGoogle Scholar
  36. 36.
    Arlt, C., Götze, M., Ihling, C.H., Hage, C., Schäfer, M., Sinz, A.: Integrated workflow for structural proteomics studies based on cross-linking/mass spectrometry with an MS/MS cleavable cross-linker. Anal. Chem. 88, 7930–7937 (2016)CrossRefGoogle Scholar
  37. 37.
    Zubarev, R.A., Zubarev, A.R., Savitski, M.M.: Electron capture/transfer versus collisionally activated/induced dissociations: solo or duet? J. Am. Soc. Mass Spectrom. 19, 753–761 (2008)CrossRefGoogle Scholar
  38. 38.
    Chowdhury, S.M., Du, X.X., Tolic, N., Wu, S., Moore, R.J., Mayer, M.U., Smith, R.D., Adkins, J.N.: Identification of cross-linked peptides after click-based enrichment using sequential collision-induced dissociation and electron transfer dissociation tandem mass spectrometry. Anal. Chem. 81, 5524–5532 (2009)CrossRefGoogle Scholar
  39. 39.
    Liu, F., Rijkers, D.T., Post, H., Heck, A.J.: Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry. Nat. Methods 12, 1179–1184 (2015)CrossRefGoogle Scholar
  40. 40.
    Sinz, A.: Divide and conquer: cleavable cross-linkers to study protein conformation and protein–protein interactions. Anal. Bioanal. Chem. 409, 33–44 (2016)CrossRefGoogle Scholar
  41. 41.
    Sharon, M., Sinz, A.: Studying protein–protein interactions in the gas phase with mass spectrometry, Analyzing biomolecular interactions by mass spectrometry. In: Kool, J., Niessen, W. (eds.) Wiley-VCH, Germany (2015)Google Scholar
  42. 42.
    Soderblom, E.J., Goshe, M.B.: Collision-induced dissociative chemical cross-linking reagents and methodology: applications to protein structural characterization using tandem mass spectrometry analysis. Anal. Chem. 78, 8059–8068 (2006)CrossRefGoogle Scholar
  43. 43.
    Soderblom, E.J., Bobay, B.G., Cavanagh, J., Goshe, M.B.: Tandem mass spectrometry acquisition approaches to enhance identification of protein–protein interactions using low-energy collision-induced dissociative chemical cross-linking reagents. Rapid Commun. Mass Spectrom. 21, 3395–3408 (2007)CrossRefGoogle Scholar
  44. 44.
    Argo, A.S., Shi, C., Liu, F., Goshe, M.B.: Performing protein cross-linking using gas phase cleavable chemical cross-linkers and liquid chromatography-tandem mass spectrometry. Methods 89, 64–73 (2015)CrossRefGoogle Scholar
  45. 45.
    Müller, M.Q., Dreiocker, F., Ihling, C.H., Schäfer, M., Sinz, A.: Cleavable cross-linker for protein structure analysis: reliable identification of cross-linking products by tandem MS. Anal. Chem. 82, 6958–6968 (2010)CrossRefGoogle Scholar
  46. 46.
    Müller, M.Q., Dreiocker, F., Ihling, C.H., Schäfer, M., Sinz, A.: Fragmentation behavior of a thiourea-based reagent for protein structure analysis by collision-induced dissociative chemical cross-linking. J. Mass Spectrom. 45, 880–891 (2010)CrossRefGoogle Scholar
  47. 47.
    Müller, M.Q., Zeiser, J.J., Dreiocker, F., Pich, A., Schäfer, M., Sinz, A.: A universal matrix-assisted laser desorption/ionization cleavable cross-linker for protein structure analysis. Rapid Commun. Mass Spectrom. 25, 155–161 (2011)CrossRefGoogle Scholar
  48. 48.
    Kao, A.H., Chiu, C.L., Vellucci, D., Yang, Y.Y., Patel, V.R., Guan, S.H., Randall, A., Baldi, P., Rychnovsky, S.D., Huang, L.: Development of a novel cross-linking strategy for fast and accurate identification of cross-linked peptides of protein complexes. Mol. Cell. Proteomics 10, 1–17 (2011)CrossRefGoogle Scholar
  49. 49.
    Kandur, W.V., Kao, A., Vellucci, D., Huang, L., Rychnovsky, S.D.: Design of CID-cleavable protein cross-linkers: identical mass modifications for simpler sequence analysis. Org. Biomol. Chem. 13, 9793–9807 (2015)CrossRefGoogle Scholar
  50. 50.
    Burke, A.M., Kandur, W., Novitsky, E.J., Kaake, R.M., Yu, C., Kao, A., Vellucci, D., Huang, L., Rychnovsky, S.D.: Synthesis of two new enrichable and MS-cleavable cross-linkers to define protein–protein interactions by mass spectrometry. Org. Biomol. Chem. 13, 5030–5037 (2015)CrossRefGoogle Scholar
  51. 51.
    Gardner, M.W., Brodbelt, J.S.: Preferential cleavage of N-N hydrazone bonds for sequencing bis-arylhydrazone conjugated peptides by electron transfer dissociation. Anal. Chem. 82, 5751–5759 (2010)CrossRefGoogle Scholar
  52. 52.
    Trnka, M.J., Burlingame, A.L.: Topographic studies of the GroEL–GroES chaperonin complex by chemical cross-linking using diformyl ethynylbenzene: the power of high resolution electron transfer dissociation for determination of both peptide sequences and their attachment sites. Mol. Cell. Proteomics 9, 2306–2317 (2010)CrossRefGoogle Scholar
  53. 53.
    Gardner, M.W., Vasicek, L.A., Shabbir, S., Anslyn, E.V., Brodbelt, J.S.: Chromogenic cross-linker for the characterization of protein structure by infrared multiphoton dissociation mass spectrometry. Anal. Chem. 80, 4807–4819 (2008)CrossRefGoogle Scholar
  54. 54.
    Petrotchenko, E.V., Xiao, K., Cable, J., Chen, Y., Dokholyan, N.V., Borchers, C.H.: BiPS, a photocleavable, isotopically coded, fluorescent cross-linker for structural proteomics. Mol. Cell. Proteomics 8, 273–286 (2009)CrossRefGoogle Scholar
  55. 55.
    Hodyss, R., Cox, H.A., Beauchamp, J.L.: Bioconjugates for tunable peptide fragmentation: free radical initiated peptide sequencing (FRIPS). J. Am. Soc. Mass Spectrom. 127, 12436–12437 (2005)Google Scholar
  56. 56.
    Oh, H.B., Moon, B.: Radical-driven peptide backbone dissociation tandem mass spectrometry. Mass Spectrom. Rev. 34, 116–132 (2015)CrossRefGoogle Scholar
  57. 57.
    Lee, M., Kang, M., Moon, B., Oh, H.B.: Gas phase peptide sequencing by TEMPO-mediated radical generation. Analyst 134, 1706–1712 (2009)CrossRefGoogle Scholar
  58. 58.
    Hage, C., Ihling, C.H., Götze, M., Schäfer, M., Sinz, A.: Dissociation behavior of a TEMPO-active ester cross-linker for peptide structure analysis by free radical initiated peptide sequencing (FRIPS) in negative ESI-MS. J. Am. Soc. Mass Spectrom. 28, 56–68 (2017)CrossRefGoogle Scholar
  59. 59.
    Ihling, C., Falvo, F., Kratochvil, I., Sinz, A., Schäfer, M.: Dissociation behavior of a bifunctional tempo-active ester reagent for peptide structure analysis by free radical initiated peptide sequencing (FRIPS) mass spectrometry. J. Mass Spectrom. 50, 396–406 (2015)CrossRefGoogle Scholar
  60. 60.
    Jang, I., Lee, S.Y., Hwangbo, S., Kang, D., Lee, H., Kim, H.I., Moon, B., Oh, H.B.: TEMPO-assisted free radical-initiated peptide sequencing mass spectrometry (FRIPS MS) in Q-TOF and Orbitrap mass spectrometers: single-step peptide backbone dissociations in positive ion mode. J. Am. Soc. Mass Spectrom. 28, 154–163 (2017)CrossRefGoogle Scholar
  61. 61.
    Falvo, F., Fiebig, L., Schäfer, M.: Presentation of a homobifunctional azo-reagent for protein structure analysis by collision-induced dissociative chemical cross-linking: proof-of-principle. Int. J. Mass Spectrom. 354, 26–32 (2013)CrossRefGoogle Scholar
  62. 62.
    Matyjaszewski, K.: Cationic polymerizations: mechanisms, synthesis, and applications. Marcel Dekker, New York (1996)Google Scholar
  63. 63.
    Koolen, H.H., Gomes, A.F., Schwab, N.V., Eberlin, M.N., Gozzo, F.C.: Imidate-based cross-linkers for structural proteomics: increased charge of protein and peptide ions and CID and ECD fragmentation studies. J. Am. Soc. Mass Spectrom. 25, 1181–1191 (2014)CrossRefGoogle Scholar
  64. 64.
    Götze, M., Pettelkau, J., Fritzsche, R., Ihling, C.H., Schäfer, M., Sinz, A.: Automated assignment of MS/MS cleavable cross-links in protein 3D-structure analysis. J. Am. Soc. Mass Spectrom. 26, 83–97 (2015)CrossRefGoogle Scholar
  65. 65.
    Wee, S., O'Hair, R.A., McFadyen, W.D.: Side-chain radical losses from radical cations allows distinction of leucine and isoleucine residues in the isomeric peptides Gly-XXX-Arg. Rapid Commun. Mass Spectrom. 16, 884–890 (2002)CrossRefGoogle Scholar
  66. 66.
    Schilling, B., Row, R.H., Gibson, B.W., Guo, X., Young, M.M.: MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides. J. Am. Soc. Mass Spectrom. 14, 834–850 (2003)CrossRefGoogle Scholar
  67. 67.
    Turecek, F., Julian, R.R.: Peptide radicals and cation radicals in the gas phase. Chem. Rev. 113, 6691–6733 (2013)CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2017

Authors and Affiliations

  1. 1.Institute of PharmacyMartin Luther University Halle-WittenbergHalle (Saale)Germany
  2. 2.Department of ChemistryInstitute of Organic Chemistry, University of CologneKӧlnGermany

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