MetaUniDec: High-Throughput Deconvolution of Native Mass Spectra

  • Deseree J. Reid
  • Jessica M. Diesing
  • Matthew A. Miller
  • Scott M. Perry
  • Jessica A. Wales
  • William R. Montfort
  • Michael T. Marty
Focus: Honoring Carol V. Robinson's Election to the National Academy of Sciences: Research Article

Abstract

The expansion of native mass spectrometry (MS) methods for both academic and industrial applications has created a substantial need for analysis of large native MS datasets. Existing software tools are poorly suited for high-throughput deconvolution of native electrospray mass spectra from intact proteins and protein complexes. The UniDec Bayesian deconvolution algorithm is uniquely well suited for high-throughput analysis due to its speed and robustness but was previously tailored towards individual spectra. Here, we optimized UniDec for deconvolution, analysis, and visualization of large data sets. This new module, MetaUniDec, centers around a hierarchical data format 5 (HDF5) format for storing datasets that significantly improves speed, portability, and file size. It also includes code optimizations to improve speed and a new graphical user interface for visualization, interaction, and analysis of data. To demonstrate the utility of MetaUniDec, we applied the software to analyze automated collision voltage ramps with a small bacterial heme protein and large lipoprotein nanodiscs. Upon increasing collisional activation, bacterial heme-nitric oxide/oxygen binding (H-NOX) protein shows a discrete loss of bound heme, and nanodiscs show a continuous loss of lipids and charge. By using MetaUniDec to track changes in peak area or mass as a function of collision voltage, we explore the energetic profile of collisional activation in an ultra-high mass range Orbitrap mass spectrometer.

Graphical abstract

Keywords

Native mass spectrometry Deconvolution Nanodiscs Heme proteins Collision-induced dissociation 

Notes

Acknowledgements

The authors thank Maria Reinhardt-Szyba and Alexander Makarov at Thermo Fisher Scientific for helpful discussions and support on the UHMR modification of the Q-Exactive HF instrument. The pMSP1D1 plasmid was a gift from Stephen Sligar (Addgene plasmid no. 20061). This work was funded by an American Cancer Society Institutional Research Grant (IRG-16-124-37-IRG) and the Bisgrove Scholar Award from Science Foundation Arizona to M.T.M.; by National Institutes of Health grants R01 GM117357 and P30 CA023074 to W.R.M. and T32 GM008804 to J.W.; and American Heart Association grant 16PRE31090034 to J.W.

Supplementary material

13361_2018_1951_MOESM1_ESM.pdf (270 kb)
ESM 1 (PDF 270 kb)

References

  1. 1.
    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)CrossRefGoogle Scholar
  2. 2.
    Yang, Y., Liu, F., Franc, V., Halim, L.A., Schellekens, H., Heck, A.J.R.: Hybrid mass spectrometry approaches in glycoprotein analysis and their usage in scoring biosimilarity. Nat. Commun. 7, 13397 (2016)CrossRefGoogle Scholar
  3. 3.
    Gault, J., Donlan, J.A.C., Liko, I., Hopper, J.T.S., Gupta, K., Housden, N.G., Struwe, W.B., Marty, M.T., Mize, T., Bechara, C., Zhu, Y., Wu, B., Kleanthous, C., Belov, M., Damoc, E., Makarov, A., Robinson, C.V.: High-resolution mass spectrometry of small molecules bound to membrane proteins. Nat. Methods. 13, 333–336 (2016)CrossRefGoogle Scholar
  4. 4.
    Rose, R.J., Damoc, E., Denisov, E., Makarov, A., Heck, A.J.R.: High-sensitivity Orbitrap mass analysis of intact macromolecular assemblies. Nat. Methods. 9, 1084–1086 (2012)CrossRefGoogle Scholar
  5. 5.
    Rajabi, K., Ashcroft, A.E., Radford, S.E.: Mass spectrometric methods to analyze the structural organization of macromolecular complexes. Methods. 89, 13–21 (2015)CrossRefGoogle Scholar
  6. 6.
    Chait, B.T., Cadene, M., Olinares, P.D., Rout, M.P., Shi, Y.: Revealing higher order protein structure using mass spectrometry. J. Am. Soc. Mass Spectrom. 27, 952–965 (2016)CrossRefGoogle Scholar
  7. 7.
    Landreh, M., Marty, M.T., Gault, J., Robinson, C.V.: A sliding selectivity scale for lipid binding to membrane proteins. Curr. Opin. Struct. Biol. 39, 54–60 (2016)CrossRefGoogle Scholar
  8. 8.
    Liko, I., Allison, T.M., Hopper, J.T.S., Robinson, C.V.: Mass spectrometry guided structural biology. Curr. Opin. Struct. Biol. 40, 136–144 (2016)CrossRefGoogle Scholar
  9. 9.
    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
  10. 10.
    Eschweiler, J.D., Kerr, R., Rabuck-Gibbons, J., Ruotolo, B.T.: Sizing up protein-ligand complexes: the rise of structural mass spectrometry approaches in the pharmaceutical sciences. Annu. Rev. Anal. Chem. 10, 25–44 (2017)CrossRefGoogle Scholar
  11. 11.
    Terral, G., Beck, A., Cianferani, S.: Insights from native mass spectrometry and ion mobility-mass spectrometry for antibody and antibody-based product characterization. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 1032, 79–90 (2016)CrossRefGoogle Scholar
  12. 12.
    Eschweiler, J.D., Rabuck-Gibbons, J.N., Tian, Y., Ruotolo, B.T.: CIUSuite: a quantitative analysis package for collision induced unfolding measurements of gas-phase protein ions. Anal. Chem. 87, 11516–11522 (2015)CrossRefGoogle Scholar
  13. 13.
    Migas, L.G., France, A.P., Bellina, B., Barran, P.E.: ORIGAMI: a software suite for activated ion mobility mass spectrometry (aIM-MS) applied to multimeric protein assemblies. Int. J, Mass Spectrom. 427, 20–28 (2018)Google Scholar
  14. 14.
    Allison, T.M., Reading, E., Liko, I., Baldwin, A.J., Laganowsky, A., Robinson, C.V.: Quantifying the stabilizing effects of protein-ligand interactions in the gas phase. Nat. Commun. 6, 8551 (2015)CrossRefGoogle Scholar
  15. 15.
    Morgner, N., Robinson, C.V.: Massign: an assignment strategy for maximizing information from the mass spectra of heterogeneous protein assemblies. Anal. Chem. 84, 2939–2948 (2012)CrossRefGoogle Scholar
  16. 16.
    Sivalingam, G.N., Yan, J., Sahota, H., Thalassinos, K.: Amphitrite: a program for processing travelling wave ion mobility mass spectrometry data. Int. J. Mass Spectrom. 345–347, 54–62 (2013)CrossRefGoogle Scholar
  17. 17.
    Tseng, Y.-H., Uetrecht, C., Yang, S.-C., Barendregt, A., Heck, A.J.R., Peng, W.-P.: Game-theory-based search engine to automate the mass assignment in complex native electrospray mass spectra. Anal. Chem. 85, 11275–11283 (2013)CrossRefGoogle Scholar
  18. 18.
    Cleary, S.P., Thompson, A.M., Prell, J.S.: Fourier analysis method for analyzing highly congested mass spectra of ion populations with repeated subunits. Anal. Chem. 88, 6205–6213 (2016)CrossRefGoogle Scholar
  19. 19.
    Marty, M.T., Baldwin, A.J., Marklund, E.G., Hochberg, G.K., Benesch, J.L., 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
  20. 20.
    Lu, J., Trnka, M.J., Roh, S.-H., Robinson, P.J.J., Shiau, C., Fujimori, D.G., Chiu, W., Burlingame, A.L., Guan, S.: Improved peak detection and deconvolution of native electrospray mass spectra from large protein complexes. J. Am. Soc. Mass Spectrom. 26, 2141–2151 (2015)CrossRefGoogle Scholar
  21. 21.
    Cong, X., Liu, Y., Liu, W., Liang, X., Russell, D.H., Laganowsky, A.: Determining membrane protein–lipid binding thermodynamics using native mass spectrometry. J. Am. Chem. Soc. 138, 4346–4349 (2016)CrossRefGoogle Scholar
  22. 22.
    Hopper, J.T.S., Ambrose, S., Grant, O.C., Krumm, S.A., Allison, T.M., Degiacomi, M.T., Tully, M.D., Pritchard, L.K., Ozorowski, G., Ward, A.B., Crispin, M., Doores, K.J., Woods, R.J., Benesch, J.L.P., Robinson, C.V., Struwe, W.B.: The tetrameric plant lectin banlec neutralizes HIV through bidentate binding to specific viral glycans. Structure. 25, 773–782.e775 (2017)CrossRefGoogle Scholar
  23. 23.
    Yao, Y., Richards, M.R., Kitova, E.N., Klassen, J.S.: Influence of Sulfolane on ESI-MS measurements of protein–ligand affinities. J. Am. Soc. Mass Spectrom. 27, 498–506 (2015)CrossRefGoogle Scholar
  24. 24.
    Reading, E., Walton, T.A., Liko, I., Marty, M.T., Laganowsky, A., Rees, D.C., Robinson, C.V.: The effect of detergent, temperature, and lipid on the oligomeric state of MscL constructs: insights from mass spectrometry. Chem. Biol. 22, 593–603 (2015)CrossRefGoogle Scholar
  25. 25.
    Laganowsky, A., Reading, E., Allison, T.M., Ulmschneider, M.B., Degiacomi, M.T., Baldwin, A.J., Robinson, C.V.: Membrane proteins bind lipids selectively to modulate their structure and function. Nature. 510, 172–175 (2014)CrossRefGoogle Scholar
  26. 26.
    Benesch, J.L.P., Aquilina, J.A., Baldwin, A.J., Rekas, A., Stengel, F., Lindner, R.A., Basha, E., Devlin, G.L., Horwitz, J., Vierling, E., Carver, J.A., Robinson, C.V.: The quaternary organization and dynamics of the molecular chaperone HSP26 are thermally regulated. Chem. Biol. 17, 1008–1017 (2010)CrossRefGoogle Scholar
  27. 27.
    Stengel, F., Baldwin, A.J., Painter, A.J., Jaya, N., Basha, E., Kay, L.E., Vierling, E., Robinson, C.V., Benesch, J.L.: Quaternary dynamics and plasticity underlie small heat shock protein chaperone function. Proc. Natl. Acad. Sci. 107, 2007–2012 (2010)CrossRefGoogle Scholar
  28. 28.
    Baldwin, A.J., Lioe, H., Hilton, G.R., Baker, L.A., Rubinstein, J.L., Kay, L.E., Benesch, J.L.P.: The polydispersity of αB-crystallin is rationalized by an interconverting polyhedral architecture. Structure. 19, 1855–1863 (2011)CrossRefGoogle Scholar
  29. 29.
    Baldwin, A.J., Lioe, H., Robinson, C.V., Kay, L.E., Benesch, J.L.P.: αB-crystallin polydispersity is a consequence of unbiased quaternary dynamics. J. Mol. Biol. 413, 297–309 (2011)CrossRefGoogle Scholar
  30. 30.
    Belov, A.M., Viner, R., Santos, M.R., Horn, D.M., Bern, M., Karger, B.L., Ivanov, A.R.: Analysis of proteins, protein complexes, and organellar proteomes using sheathless capillary zone electrophoresis—native mass spectrometry. J. Am. Soc, Mass Spectrom. 28, 2614–2634 (2017)Google Scholar
  31. 31.
    Bungard, D., Copple, J.S., Yan, J., Chhun, J.J., Kumirov, V.K., Foy, S.G., Masel, J., Wysocki, V.H., Cordes, M.H.J.: Foldability of a natural de novo evolved protein. Structure. 25, 1687–1696 e1684 (2017)CrossRefGoogle Scholar
  32. 32.
    Cai, W., Guner, H., Gregorich, Z.R., Chen, A.J., Ayaz-Guner, S., Peng, Y., Valeja, S.G., Liu, X., Ge, Y.: MASH suite pro: a comprehensive software tool for top-down proteomics. Mol. Cell. Proteomics. 15, 703–714 (2016)CrossRefGoogle Scholar
  33. 33.
    Calabrese, A.N., Jackson, S.M., Jones, L.N., Beckstein, O., Heinkel, F., Gsponer, J., Sharples, D., Sans, M., Kokkinidou, M., Pearson, A.R., Radford, S.E., Ashcroft, A.E., Henderson, P.J.F.: Topological dissection of the membrane transport protein mhp1 derived from cysteine accessibility and mass spectrometry. Anal. Chem. 89, 8844–8852 (2017)Google Scholar
  34. 34.
    Campuzano, I.D.G., Li, H.L., 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
  35. 35.
    Gupta, K., Donlan, J.A.C., Hopper, J.T.S., Uzdavinys, P., Landreh, M., Struwe, W.B., Drew, D., Baldwin, A.J., Stansfeld, P.J., Robinson, C.V.: The role of interfacial lipids in stabilizing membrane protein oligomers. Nature. 541, 421–424 (2017)CrossRefGoogle Scholar
  36. 36.
    Hendus-Altenburger, R., Pedraz-Cuesta, E., Olesen, C.W., Papaleo, E., Schnell, J.A., Hopper, J.T.S., Robinson, C.V., Pedersen, S.F., Kragelund, B.B.: The human Na+/H+ exchanger 1 is a membrane scaffold protein for extracellular signal-regulated kinase 2. BMC Biol. 14, 31 (2016)CrossRefGoogle Scholar
  37. 37.
    Hoi, K.K., Robinson, C.V., Marty, M.T.: Unraveling the composition and behavior of heterogeneous lipid nanodiscs by mass spectrometry. Anal. Chem. 88, 6199–6204 (2016)CrossRefGoogle Scholar
  38. 38.
    Iadanza, M.G., Higgins, A.J., Schiffrin, B., Calabrese, A.N., Brockwell, D.J., Ashcroft, A.E., Radford, S.E., Ranson, N.A.: Lateral opening in the intact beta-barrel assembly machinery captured by cryo-EM. Nat. Commun. 7, 12865 (2016)CrossRefGoogle Scholar
  39. 39.
    Larson, A.G., Elnatan, D., Keenen, M.M., Trnka, M.J., Johnston, J.B., Burlingame, A.L., Agard, D.A., Redding, S., Narlikar, G.J.: Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature. 547, 236 (2017)CrossRefGoogle Scholar
  40. 40.
    Li, J., Richards, M.R., Bagal, D., Campuzano, I.D.G., Kitova, E.N., Xiong, Z.J., Prive, G.G., Klassen, J.S.: Characterizing the size and composition of saposin A lipoprotein picodiscs. Anal. Chem. 88, 9524–9531 (2016)CrossRefGoogle Scholar
  41. 41.
    Liu, Y., Cong, X., Liu, W., Laganowsky, A.: Characterization of membrane protein-lipid interactions by mass spectrometry ion mobility mass spectrometry. J. Am. Soc. Mass Spectrom. 28, 579–586 (2017)CrossRefGoogle Scholar
  42. 42.
    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. Engl. 55, 550–554 (2016)CrossRefGoogle Scholar
  43. 43.
    Morgner, N., Schmidt, C., Beilsten-Edmands, V., Ebong, I.-O., Patel, N.A., Clerico, E.M., Kirschke, E., Daturpalli, S., Jackson, S.E., Agard, D., Robinson, C.V.: Hsp70 forms antiparallel dimers stabilized by post-translational modifications to position clients for transfer to Hsp90. Cell Rep. 11, 759–769 (2015)CrossRefGoogle Scholar
  44. 44.
    Root, K., Wittwer, Y., Barylyuk, K., Anders, U., Zenobi, R.: Insight into signal response of protein ions in native ESI-MS from the analysis of model mixtures of covalently linked protein oligomers. J. Am. Soc. Mass, Spectrom. 28, 1863–1875 (2017)Google Scholar
  45. 45.
    Rouse, S.L., Hawthorne, W.J., Berry, J.-L., Chorev, D.S., Ionescu, S.A., Lambert, S., Stylianou, F., Ewert, W., Mackie, U., Morgan, R.M.L., Otzen, D., Herbst, F.-A., Nielsen, P.H., Dueholm, M., Bayley, H., Robinson, C.V., Hare, S., Matthews, S.: A new class of hybrid secretion system is employed in Pseudomonas amyloid biogenesis. Nat. Commun. 8, 263 (2017)CrossRefGoogle Scholar
  46. 46.
    Schiffrin, B., Calabrese, A.N., Higgins, A.J., Humes, J.R., Ashcroft, A.E., Kalli, A.C., Brockwell, D.J., Radford, S.E.: Effects of periplasmic chaperones and membrane thickness on BamA-catalyzed outer membrane protein folding. J. Mol. Biol. 429, 3776–3792 (2017)Google Scholar
  47. 47.
    Smith, F.D., Esseltine, J.L., Nygren, P.J., Veesler, D., Byrne, D.P., Vonderach, M., Strashnov, I., Eyers, C.E., Eyers, P.A., Langeberg, L.K., Scott, J.D.: Local protein kinase A action proceeds through intact holoenzymes. Science. 356, 1288–1293 (2017)CrossRefGoogle Scholar
  48. 48.
    Uppal, S.S., Beasley, S.E., Scian, M., Guttman, M.: Gas-phase hydrogen/deuterium exchange for distinguishing isomeric carbohydrate ions. Anal. Chem. 89, 4737–4742 (2017)CrossRefGoogle Scholar
  49. 49.
    Xuan, W., Surman, A.J., Zheng, Q., Long, D.-L., Cronin, L.: Self-templating and in situ assembly of a cubic cluster-of-clusters architecture based on a {Mo24Fe12} inorganic macrocycle. Angew. Chem. Int. Ed. 55, 12703–12707 (2016)CrossRefGoogle Scholar
  50. 50.
    Yen, H.-Y., Liko, I., Allison, T.M., Robinson, C.V., Hopper, J.T.S., Liko, I., Zhu, Y., Wang, D., Wu, B., Wang, D., Wu, B., Stegmann, M., Mohammed, S.: Ligand binding to a G protein-coupled receptor captured in a mass spectrometer. Sci. Adv. 3, e1701016 (2017)CrossRefGoogle Scholar
  51. 51.
    Hierarchical Data Format, version 5. The HDF Group, (1997–2017)Google Scholar
  52. 52.
    Wales, J.A., Chen, C.Y., Breci, L., Weichsel, A., Bernier, S.G., Sheppeck 2nd, J.E., Solinga, R., Nakai, T., Renhowe, P.A., Jung, J., Montfort, W.R.: Discovery of stimulator binding to a conserved pocket in the heme domain of soluble guanylyl cyclase. J. Biol. Chem. 293, 1850–1864 (2018)CrossRefGoogle Scholar
  53. 53.
    Marty, M.T., Zhang, H., Cui, W., Blankenship, R.E., Gross, M.L., Sligar, S.G.: Native mass spectrometry characterization of intact nanodisc lipoprotein complexes. Anal. Chem. 84, 8957–8960 (2012)CrossRefGoogle Scholar
  54. 54.
    Denisov, I.G., Grinkova, Y.V., Lazarides, A.A., Sligar, S.G.: Directed self-assembly of monodisperse phospholipid bilayer nanodiscs with controlled size. J. Am. Chem. Soc. 126, 3477–3487 (2004)CrossRefGoogle Scholar
  55. 55.
    Ritchie, T.K., Grinkova, Y.V., Bayburt, T.H., Denisov, I.G., Zolnerciks, J.K., Atkins, W.M., Sligar, S.G.: Reconstitution of membrane proteins in phospholipid bilayer nanodiscs. In: Nejat, D. (ed.) Academic Press. San Diego, CA (2009)Google Scholar
  56. 56.
    Rogniaux, H., Van Dorsselaer, A., Barth, P., Biellmann, J.F., Barbanton, J., van Zandt, M., Chevrier, B., Howard, E., Mitschler, A., Potier, N., Urzhumtseva, L., Moras, D., Podjarny, A.: Binding of aldose reductase inhibitors: correlation of crystallographic and mass spectrometric studies. J. Am. Soc. Mass Spectrom. 10, 635–647 (1999)CrossRefGoogle Scholar
  57. 57.
    Marty, M.T., Zhang, H., Cui, W., Gross, M.L., Sligar, S.G.: Interpretation and deconvolution of nanodisc native mass spectra. J. Am. Soc. Mass Spectrom. 25, 269–277 (2014)CrossRefGoogle Scholar
  58. 58.
    Rosati, S., Rose, R.J., Thompson, N.J., van Duijn, E., Damoc, E., Denisov, E., Makarov, A., Heck, A.J.: Exploring an orbitrap analyzer for the characterization of intact antibodies by native mass spectrometry. Angew. Chem. Int. Ed. 51, 12992–12996 (2012)CrossRefGoogle Scholar
  59. 59.
    Mistarz, U.H., Brown, J.M., Haselmann, K.F., Rand, K.D.: Probing the binding interfaces of protein complexes using gas-phase H/D exchange mass spectrometry. Structure. 24, 310–318 (2016)CrossRefGoogle Scholar
  60. 60.
    Beeston, H.S., Ault, J.R., Pringle, S.D., Brown, J.M., Ashcroft, A.E.: Changes in protein structure monitored by use of gas-phase hydrogen/deuterium exchange. Proteomics. 15, 2842–2850 (2015)CrossRefGoogle Scholar
  61. 61.
    Hambly, D., Gross, M.: Laser flash photolysis of hydrogen peroxide to oxidize protein solvent-accessible residues on the microsecond timescale. J. Am. Soc. Mass Spectrom. 16, 2057–2063 (2005)CrossRefGoogle Scholar
  62. 62.
    Tang, Y., Tang, F., Yang, Y., Zhao, L., Zhou, H., Dong, J., Huang, W.: Real-time analysis on drug-antibody ratio of antibody-drug conjugates for synthesis, process optimization, and quality control. Sci. Rep. 7, 7763 (2017)CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2018

Authors and Affiliations

  1. 1.Department of Chemistry and BiochemistryUniversity of ArizonaTucsonUSA

Personalised recommendations