Advertisement

Standard Proteoforms and Their Complexes for Native Mass Spectrometry

  • Luis F. Schachner
  • Ashley N. Ives
  • John P. McGee
  • Rafael D. Melani
  • Jared O. Kafader
  • Philip D. Compton
  • Steven M. Patrie
  • Neil L. KelleherEmail author
Research Article

Abstract

Native mass spectrometry (nMS) is a technique growing at the interface of analytical chemistry, structural biology, and proteomics that enables the detection and partial characterization of non-covalent protein assemblies. Currently, the standardization and dissemination of nMS is hampered by technical challenges associated with instrument operation, benchmarking, and optimization over time. Here, we provide a standard operating procedure for acquiring high-quality native mass spectra of 30–300 kDa proteins using an Orbitrap mass spectrometer. By describing reproducible sample preparation, loading, ionization, and nMS analysis, we forward two proteoforms and three complexes as possible standards to advance training and longitudinal assessment of instrument performance. Spectral data for five standards can guide assessment of instrument parameters, data production, and data analysis. By introducing this set of standards and protocols, we aim to help normalize native mass spectrometry practices across labs and provide benchmarks for reproducibility and high-quality data production in the years ahead.

Graphical abstract

Keywords

Native mass spectrometry Native top-down mass spectrometry Proteoforms Multi-proteoform complexes Standards Rigor and reproducibility 

Notes

Acknowledgements

This work was supported by the National Institute of General Medical Sciences P41 GM108569 for the National Resource for Translational and Developmental Proteomics at Northwestern University. Research in this publication is also supported by a fellowship associated with the Chemistry of Life Processes Predoctoral Training Grant T32GM105538 at Northwestern University. LFS is a Gilliam Fellow of the Howard Hughes Medical Institute.

Supplementary material

13361_2019_2191_MOESM1_ESM.docx (14.1 mb)
ESM 1 (DOCX 14436 kb)

References

  1. 1.
    Loo, J.A.: Studying noncovalent protein complexes by electrospray ionization mass spectrometry. Mass Spectrom. Rev. 16, 1–23 (1997)CrossRefGoogle Scholar
  2. 2.
    Heck, A.J.R., van den Heuvel, R.H.H.: Investigation of intact protein complexes by mass spectrometry. Mass Spectrom. Rev. 23, 368–389 (2004)CrossRefGoogle Scholar
  3. 3.
    Hilton, G.R., Benesch, J.L.P.: Two decades of studying non-covalent biomolecular assemblies by means of electrospray ionization mass spectrometry. J. R. Soc. Interface. 9, 801–816 (2012)Google Scholar
  4. 4.
    Fernandez de la Mora, J.: Electrospray ionization of large multiply charged species proceeds via Dole’s charged residue mechanism. Anal. Chim. Acta. 2000, 93–104 (1999)Google Scholar
  5. 5.
    Leney, A.C., Heck, A.J.: Native mass spectrometry: what is in the name? J. Am. Soc. Mass Spectrom. 28, 5–13 (2017)CrossRefGoogle Scholar
  6. 6.
    Benesch, J.L.P., Ruotolo, B.T., Simmons, D.A., Robinson, C.V.: Protein complexes in the gas phase: technology for structural genomics and proteomics. Chem. Rev. 107, 3544–3567 (2007)CrossRefGoogle Scholar
  7. 7.
    Sharon, M., Robinson, C.V.: The role of mass spectrometry in structure elucidation of dynamic protein complexes. Annu. Rev. Biochem. 76, 167–193 (2007)CrossRefGoogle Scholar
  8. 8.
    Belov, M.E., Damoc, E., Denisov, E., Compton, P.D., Horning, S., Makarov, A.A., Kelleher, N.L.: From protein complexes to subunit backbone fragments: a multi-stage approach to native mass spectrometry. Anal. Chem. 85, 11163–11173 (2013)CrossRefGoogle Scholar
  9. 9.
    Li, H., Nguyen, H.H., Ogorzalek Loo, R.R., Campuzano, I.D.G., Loo, J.A.: An integrated native mass spectrometry and top-down proteomics method that connects sequence to structure and function of macromolecular complexes. Nat. Chem. 10, 139–178 (2018)Google Scholar
  10. 10.
    Zhang, H., Cui, W., Wen, J., Blankenship, R.E., Gross, M.L.: Native electrospray and electron-capture dissociation in FTICR mass spectrometry provide top-down sequencing of a protein component in an intact protein assembly. J. Am. Soc. Mass Spectrom. 21, 1966–1968 (2010)CrossRefGoogle Scholar
  11. 11.
    Kenney, G.E., Dassama, L.M.K., Pandelia, M.-E., Gizzi, A.S., Martinie, R.J., Gao, P., DeHart, C.J., Schachner, L.F., Skinner, O.S., Ro, S.Y., Zhu, X., Sadek, M., Thomas, P.M., Almo, S.C., Bollinger, J.M., Krebs, C., Kelleher, N.L., Rosenzweig, A.C.: The biosynthesis of methanobactin. Science. 359, 1411–1416 (2018)CrossRefGoogle Scholar
  12. 12.
    Skinner, O.S., Haverland, N.A., Fornelli, L., Melani, R.D., Do Vale, L.H.F., Seckler, H.S., Doubleday, P.F., Schachner, L.F., Srzentic, K., Kelleher, N.L., Compton, P.D.: Top-down characterization of endogenous protein complexes with native proteomics. Nat. Chem. Biol. 14, 36–41 (2018)Google Scholar
  13. 13.
    Park, Y.J., Kenney, G.E., Schachner, L.F., Kelleher, N.L., Rosenzweig, A.C.: Repurposed HisC aminotransferases complete the biosynthesis of some methanobactins. Biochemistry. 57, 3515–3523 (2018)CrossRefGoogle Scholar
  14. 14.
    Sahasrabuddhe, A., Hsia, Y., Busch, F., Sheffler, W., King, N.P., Baker, D., Wysocki, V.H.: Confirmation of intersubunit connectivity and topology of designed protein complexes by native MS. Proc. Natl. Acad. Sci. 115, 1268–1273 (2018)Google Scholar
  15. 15.
    Smith, L.M., Kelleher, N.L.: Consortium for TOP DOWN, P.: Proteoform: a single term describing protein complexity. Nat. Methods. 10, 186–187 (2013)CrossRefGoogle Scholar
  16. 16.
    Skinner, O.S., Havugimana, P.C., Haverland, N.A., Fornelli, L., Early, B.P., Greer, J.B., Fellers, R.T., Durbin, K.R., Do Vale, L.H.F., Melani, R.D., Seckler, H.S., Nelp, M.T., Belov, M.E., Horning, S.R., Makarov, A.A., LeDuc, R.D., Bandarian, V., Compton, P.D., Kelleher, N.L.: An informatic framework for decoding protein complexes by top-down mass spectrometry. Nat. Methods. 13, 237 (2016)CrossRefGoogle Scholar
  17. 17.
    Marty, M.T., Hoi, K.K., Gault, J., Robinson, C.V.: Probing the lipid annular belt by gas-phase dissociation of membrane proteins in nanodiscs. Angew. Chem. Int. Ed. 55, 550–554 (2016)CrossRefGoogle Scholar
  18. 18.
    Hopper, J.T.S., Yu, Y.T.-C., Li, D., Raymond, A., Bostock, M., Liko, I., Mikhailov, V., Laganowsky, A., Benesch, J.L.P., Caffrey, M., Nietlispach, D., Robinson, C.V.: Detergent-free mass spectrometry of membrane protein complexes. Nat. Methods. 10, 1206 (2013)CrossRefGoogle Scholar
  19. 19.
    Campuzano, I.D.G., Li, H., Bagal, D., Lippens, J.L., Svitel, J., Kurzeja, R.J.M., Xu, H., Schnier, P.D., Loo, J.A.: Native MS analysis of bacteriorhodopsin and an empty nanodisc by orthogonal acceleration time-of-flight, Orbitrap and ion cyclotron resonance. Anal. Chem. 88, 12427–12436 (2016)CrossRefGoogle Scholar
  20. 20.
    Konijnenberg, A., Bannwarth, L., Yilmaz, D., Koçer, A., Venien-Bryan, C., Sobott, F.: Top-down mass spectrometry of intact membrane protein complexes reveals oligomeric state and sequence information in a single experiment. Protein Sci. 24, 1292–1300 (2015)CrossRefGoogle Scholar
  21. 21.
    Haberger, M., Leiss, M., Heidenreich, A.-K., Pester, O., Hafenmair, G., Hook, M., Bonnington, L., Wegele, H., Haindl, M., Reusch, D., Bulau, P.: Rapid characterization of biotherapeutic proteins by size-exclusion chromatography coupled to native mass spectrometry. MAbs. 8, 331–339 (2016)CrossRefGoogle Scholar
  22. 22.
    Muneeruddin, K., Thomas, J.J., Salinas, P.A., Kaltashov, I.A.: Characterization of small protein aggregates and oligomers using size exclusion chromatography with online detection by native electrospray ionization mass spectrometry. Anal. Chem. 86, 10692–10699 (2014)CrossRefGoogle Scholar
  23. 23.
    Melani, R.D., Seckler, H.S., Skinner, O.S., Do Vale, L.H., Catherman, A.D., Havugimana, P.C., Valle de Sousa, M., Domont, G.B., Kelleher, N.L., Compton, P.D.: CN-GELFrEE - clear native gel-eluted liquid fraction entrapment electrophoresis. J. Vis. Exp. (108) 53597 (2016)Google Scholar
  24. 24.
    Debaene, F., Bœuf, A., Wagner-Rousset, E., Colas, O., Ayoub, D., Corvaïa, N., Van Dorsselaer, A., Beck, A., Cianférani, S.: Innovative native MS methodologies for antibody drug conjugate characterization: high resolution native MS and IM-MS for average DAR and DAR distribution assessment. Anal. Chem. 86, 10674–10683 (2014)CrossRefGoogle Scholar
  25. 25.
    Shen, X., Kou, Q., Guo, R., Yang, Z., Chen, D., Liu, X., Hong, H., Sun, L.: Native proteomics in discovery mode using size-exclusion chromatography–capillary zone electrophoresis–tandem mass spectrometry. Anal. Chem. 90, 10095–10099 (2018)Google Scholar
  26. 26.
    Cleary, S.P., Li, H., Bagal, D., Loo, J.A., Campuzano, I.D.G., Prell, J.S.: Extracting charge and mass information from highly congested mass spectra using Fourier-domain harmonics. J. Am. Soc. Mass Spectrom. 29, 2067–2080 (2018)Google Scholar
  27. 27.
    Marty, M.T., Baldwin, A.J., Marklund, E.G., Hochberg, G.K.A., Benesch, J.L.P., Robinson, C.V.: Bayesian deconvolution of mass and ion mobility spectra: from binary interactions to polydisperse ensembles. Anal. Chem. 87, 4370–4376 (2015)CrossRefGoogle Scholar
  28. 28.
    Huttlin, E.L., Ting, L., Bruckner, R.J., Gebreab, F., Gygi, M.P., Szpyt, J., Tam, S., Zarraga, G., Colby, G., Baltier, K., Dong, R., Guarani, V., Vaites, L.P., Ordureau, A., Rad, R., Erickson, B.K., Wühr, M., Chick, J., Zhai, B., Kolippakkam, D., Mintseris, J., Obar, R.A., Harris, T., Artavanis-Tsakonas, S., Sowa, M.E., De Camilli, P., Paulo, J.A., Harper, J.W., Gygi, S.P.: The BioPlex network: a systematic exploration of the human interactome. Cell. 162, 425–440 (2015)CrossRefGoogle Scholar
  29. 29.
    DeHart, C.J., Fellers, R.T., Fornelli, L., Kelleher, N.L., Thomas, P.M.: Bioinformatics Analysis of Top-Down Mass Spectrometry Data with ProSight Lite. In: Wu, C.H., Arighi, C.N., Ross, K.E. (eds.) Protein Bioinformatics. Methods in Molecular Biology, vol. 1558. Humana Press, New York, NY (2017)Google Scholar
  30. 30.
    Fellers, R.T., Greer, J.B., Early, B.P., Yu, X., LeDuc, R.D., Kelleher, N.L., Thomas, P.M.: ProSight lite: graphical software to analyze top-down mass spectrometry data. Proteomics. 15, 1235–1238 (2015)CrossRefGoogle Scholar
  31. 31.
    Marshall, A.G., Hendrickson, C.L.: High-resolution mass spectrometers. Annu. Rev. Anal. Chem. 1, 579–599 (2008)CrossRefGoogle Scholar
  32. 32.
    Ens, W., Standing, K.G.: Hybrid Quadrupole/Time-of-Flight Mass Spectrometers for Analysis of Biomolecules. Methods Enzymol. 402, 49–78 (2005)Google Scholar
  33. 33.
    Snijder, J., Heck, A.J.R.: Analytical approaches for size and mass analysis of large protein assemblies. Annu. Rev. Anal. Chem. 7, 43–64 (2014)CrossRefGoogle Scholar
  34. 34.
    Kozlovski, V.I., Donald, L.J., Collado, V.M., Spicer, V., Loboda, A.V., Chernushevich, I.V., Ens, W., Standing, K.G.: A TOF mass spectrometer for the study of noncovalent complexes. Int. J. Mass Spectrom. 308, 118–125 (2011)CrossRefGoogle Scholar
  35. 35.
    Sobott, F., Hernandez, H., McCammon, M.G., Tito, M.A., Robinson, C.V.: A tandem mass spectrometer for improved transmission and analysis of large macromolecular assemblies. Anal. Chem. 74, 1402–1407 (2002)CrossRefGoogle Scholar
  36. 36.
    van den Heuvel, R.H.H., van Duijn, E., Mazon, H., Synowsky, S.A., Lorenzen, K., Versluis, C., Brouns, S.J.J., Langridge, D., van der Oost, J., Hoyes, J., Heck, A.J.R.: Improving the performance of a quadrupole time-of-flight instrument for macromolecular mass spectrometry. Anal. Chem. 78, 7473–7483 (2006)CrossRefGoogle Scholar
  37. 37.
    Zubarev, R.A., Makarov, A.: Orbitrap mass spectrometry. Anal. Chem. 85, 5288–5296 (2013)CrossRefGoogle Scholar
  38. 38.
    Rose, R.J., Damoc, E., Denisov, E., Makarov, A., Heck, A.J.: High-sensitivity Orbitrap mass analysis of intact macromolecular assemblies. Nat. Methods. 9, 1084–1086 (2012)CrossRefGoogle Scholar
  39. 39.
    Jhingree, J.R., Bellina, B., Pacholarz, K.J., Barran, P.E.: Charge mediated compaction and rearrangement of gas-phase proteins: a case study considering two proteins at opposing ends of the structure-disorder continuum. J. Am. Soc. Mass Spectrom. 28, 1450–1461 (2017)CrossRefGoogle Scholar
  40. 40.
    Laszlo, K.J., Bush, M.F.: Effects of charge state, charge distribution, and structure on the ion mobility of protein ions in helium gas: results from trajectory method calculations. J. Phys. Chem. A. 121, 7768–7777 (2017)CrossRefGoogle Scholar
  41. 41.
    Ruotolo, B.T., Hyung, S.-J., Robinson, P.M., Giles, K., Bateman, R.H., Robinson, C.V.: Ion mobility–mass spectrometry reveals long-lived, unfolded intermediates in the dissociation of protein complexes. Angew. Chem. Int. Ed. 46, 8001–8004 (2007)CrossRefGoogle Scholar
  42. 42.
    Wongkongkathep, P., Han, J.Y., Choi, T.S., Yin, S., Kim, H.I., Loo, J.A.: Native top-down mass spectrometry and ion mobility MS for characterizing the cobalt and manganese metal binding of α-synuclein protein. J. Am. Soc. Mass Spectrom. 29, 1870–1880 (2018)Google Scholar
  43. 43.
    Caravatti, P., Allemann, M.: The ‘infinity cell’: a new trapped-ion cell with radiofrequency covered trapping electrodes for Fourier transform ion cyclotron resonance mass spectrometry. Org. Mass Spectrom. 26, 514–518 (1991)CrossRefGoogle Scholar
  44. 44.
    Li, H., Wolff, J.J., Van Orden, S.L., Loo, J.A.: Native top-down electrospray ionization-mass spectrometry of 158 kDa protein complex by high-resolution Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 86, 317–320 (2014)CrossRefGoogle Scholar
  45. 45.
    van de Waterbeemd, M., Fort, K.L., Boll, D., Reinhardt-Szyba, M., Routh, A., Makarov, A., Heck, A.J.: High-fidelity mass analysis unveils heterogeneity in intact ribosomal particles. Nat. Methods. 14, 283–286 (2017)Google Scholar
  46. 46.
    Snijder, J., Uetrecht, C., Rose, R.J., Sanchez-Eugenia, R., Marti, G.A., Agirre, J., Guérin, D.M.A., Wuite, G.J.L., Heck, A.J.R., Roos, W.H.: Probing the biophysical interplay between a viral genome and its capsid. Nat. Chem. 5, 502 (2013)CrossRefGoogle Scholar
  47. 47.
    van de Waterbeemd, M., Tamara, S., Fort, K.L., Damoc, E., Franc, V., Bieri, P., Itten, M., Makarov, A., Ban, N., Heck, A.J.R.: Dissecting ribosomal particles throughout the kingdoms of life using advanced hybrid mass spectrometry methods. Nat. Commun. 9, 2493 (2018)CrossRefGoogle Scholar
  48. 48.
    Haverland, N.A., Skinner, O.S., Fellers, R.T., Tariq, A.A., Early, B.P., LeDuc, R.D., Fornelli, L., Compton, P.D., Kelleher, N.L.: Defining gas-phase fragmentation propensities of intact proteins during native top-down mass spectrometry. J. Am. Soc. Mass Spectrom. 28, 1203–1215 (2017)CrossRefGoogle Scholar
  49. 49.
    Zhou, M., Wysocki, V.H.: Surface induced dissociation: dissecting noncovalent protein complexes in the gas phase. Acc. Chem. Res. 47, 1010–1018 (2014)CrossRefGoogle Scholar
  50. 50.
    Brodbelt, J.S.: Photodissociation mass spectrometry: new tools for characterization of biological molecules. Chem. Soc. Rev. 43, 2757–2783 (2014)CrossRefGoogle Scholar
  51. 51.
    Lermyte, F., Valkenborg, D., Loo, J.A., Sobott, F.: Radical solutions: principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure. Mass Spectrom. Rev. 37, 750–771 (2018)Google Scholar
  52. 52.
    Hewitt, J.A., Brown, L.L., Murphy, S.J., Grieder, F., Silberberg, S.D.: Accelerating biomedical discoveries through rigor and transparency. ILAR J. 58, 115–128 (2017)CrossRefGoogle Scholar
  53. 53.
    Landis, S.C., Amara, S.G., Asadullah, K., Austin, C.P., Blumenstein, R., Bradley, E.W., Crystal, R.G., Darnell, R.B., Ferrante, R.J., Fillit, H., Finkelstein, R., Fisher, M., Gendelman, H.E., Golub, R.M., Goudreau, J.L., Gross, R.A., Gubitz, A.K., Hesterlee, S.E., Howells, D.W., Huguenard, J., Kelner, K., Koroshetz, W., Krainc, D., Lazic, S.E., Levine, M.S., Macleod, M.R., McCall, J.M., Moxley, R.T., Narasimhan, K., Noble, L.J., Perrin, S., Porter, J.D., Steward, O., Unger, E., Utz, U., Silberberg, S.D.: A call for transparent reporting to optimize the predictive value of preclinical research. Nature. 490, 187–191 (2012)CrossRefGoogle Scholar
  54. 54.
    Hartshorne, J.K., Schachner, A.: Tracking replicability as a method of post-publication open evaluation. Front. Comput. Neurosci. 6, 8 (2012)CrossRefGoogle Scholar
  55. 55.
    Ioannidis, J.P.A., Khoury, M.J.: Improving validation practices in “omics” research. Science. 334, 1230–1232 (2011)CrossRefGoogle Scholar
  56. 56.
    Kirshenbaum, N., Michaelevski, I., Sharon, M.: Analyzing large protein complexes by structural mass spectrometry. J. Vis. Exp. (40) 1954 (2010)Google Scholar
  57. 57.
    Laganowsky, A., Reading, E., Hopper, J.T.S., Robinson, C.V.: Mass spectrometry of intact membrane protein complexes. Nat. Protoc. 8, 639 (2013)CrossRefGoogle Scholar
  58. 58.
    van Dyck, J.F., Konijnenberg, A., Sobott, F.: Native Mass Spectrometry for the Characterization of Structure and Interactions of Membrane Proteins. In: Lacapere, J.-J. (ed.) Membrane Protein Structure and Function Characterization. Methods Mol Biol, vol. 1635. Humana Press, New York, NY (2017)Google Scholar
  59. 59.
    Thompson, N.J., Rosati, S., Heck, A.J.: Performing native mass spectrometry analysis on therapeutic antibodies. Methods. 65, 11–17 (2014)CrossRefGoogle Scholar
  60. 60.
    Perry, R.H., Cooks, R.G., Noll, R.J.: Orbitrap mass spectrometry: instrumentation, ion motion and applications. Mass Spectrom. Rev. 27, 661–699 (2008)CrossRefGoogle Scholar
  61. 61.
    Konermann, L.: Addressing a common misconception: ammonium acetate as neutral pH “buffer” for native electrospray mass spectrometry. J. Am. Soc. Mass Spectrom. 28, 1827–1835 (2017)CrossRefGoogle Scholar
  62. 62.
    Liu, C.C., Zhang, J., Dovichi, N.J.: A sheath-flow nanospray interface for capillary electrophoresis/mass spectrometry. Rapid Commun. Mass Spectrom. 19, 187–192 (2005)CrossRefGoogle Scholar
  63. 63.
    Hao, Z., Zhang, T., Xuan, Y., Wang, H., Qian, J., Lin, S., Chen, J., Horn, D.M., Argoti, D., Beck, A., Cianférani, S., Bennett, P., Miller, K., Makarov, A.: Intact Antibody Characterization Using Orbitrap Mass Spectrometry. State-of-the-Art and Emerging Technologies for Therapeutic Monoclonal Antibody Characterization Volume 3. Defining the Next Generation of Analytical and Biophysical Techniques, American Chemical Society. 1202, 289–315 (2015)Google Scholar
  64. 64.
    Rosati, S., Yang, Y., Barendregt, A., Heck, A.J.: Detailed mass analysis of structural heterogeneity in monoclonal antibodies using native mass spectrometry. Nat. Protoc. 9, 967–976 (2014)CrossRefGoogle Scholar
  65. 65.
    Schachner, L., Han, G., Dillon, M., Zhou, J., McCarty, L., Ellerman, D., Yin, Y., Spiess, C., Lill, J.R., Carter, P.J., Sandoval, W.: Characterization of chain pairing variants of bispecific IgG expressed in a single host cell by high-resolution native and denaturing mass spectrometry. Anal. Chem. 88, 12122–12127 (2016)CrossRefGoogle Scholar
  66. 66.
    Zhang, H., Cui, W., Gross, M.L.: Mass spectrometry for the biophysical characterization of therapeutic monoclonal antibodies. FEBS Lett. 588, 308–317 (2014)CrossRefGoogle Scholar
  67. 67.
    Saito, R., Sato, T., Ikai, A., Tanaka, N.: Structure of bovine carbonic anhydrase II at 1.95 A resolution. Acta Crystallogr. D Biol. Crystallogr. 60, 792–795 (2004)CrossRefGoogle Scholar
  68. 68.
    Jörnvall, H.: The primary structure of yeast alcohol dehydrogenase. Eur. J. Biochem. 72, 425–442 (1977)CrossRefGoogle Scholar
  69. 69.
    Li, H., Wongkongkathep, P., Van Orden, S.L., Loo, R.R.O., Loo, J.A.: Revealing ligand binding sites and quantifying subunit variants of non-covalent protein complexes in a single native top-down FTICR MS experiment. J. Am. Soc. Mass Spectrom. 25, 2060–2068 (2014)CrossRefGoogle Scholar
  70. 70.
    Holland, M.J., Holland, J.P., Thill, G.P., Jackson, K.A.: The primary structures of two yeast enolase genes. Homology between the 5′ noncoding flanking regions of yeast enolase and glyceraldehyde-3-phosphate dehydrogenase genes. J. Biol. Chem. 256, 1385–1395 (1981)Google Scholar

Copyright information

© American Society for Mass Spectrometry 2019

Authors and Affiliations

  1. 1.Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of ExcellenceNorthwestern UniversityEvanstonUSA

Personalised recommendations