Skip to main content

Hands on Native Mass Spectrometry Analysis of Multi-protein Complexes

  • Protocol
  • First Online:
Multiprotein Complexes

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2247))

Abstract

By maintaining intact multi-protein complexes in the gas-phase, native mass spectrometry provides their molecular weight with very good accuracy compared to other methods (typically native PAGE or SEC-MALS) (Marcoux and Robinson, Structure 21:1541–1550, 2013). Besides, heterogeneous samples, in terms of both oligomeric states and ligand-bound species can be fully characterized. Here we thoroughly describe the analysis of several oligomeric protein complexes ranging from a 16 = kDa dimer to a 801-kDa tetradecameric complex on different instrumental setups.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 149.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Ganem B (1991) Detection of noncovalent receptor-ligand complexes by mass spectrometry. J Am Chem Soc 113:6294–6296

    Article  CAS  Google Scholar 

  2. Ganem B (1991) Observation of noncovalent enzyme-substrate and enzyme-product complexes by ion-spray mass spectrometry. J Am Chem Soc 113:7818–7819

    Article  CAS  Google Scholar 

  3. Katta V, Chait B (1991) Observation of the hemoglobin complex in native myoglobin by electrospray-ionization mass spectrometry. J Am Chem Soc 113:8534–8535

    Article  CAS  Google Scholar 

  4. Nettleton EJ, Sunde M, Lai Z, Kelly JW, Dobson CM, Robinson CV (1998) Protein subunit interactions and structural integrity of amyloidogenic transthyretins: evidence from electrospray mass spectrometry. J Mol Biol 281(3):553–564

    Article  CAS  Google Scholar 

  5. Pinkse MWH, Heck AJR, Rumpel K, Pullen F (2004) Probing noncovalent protein-ligand interactions of the cGMP-dependent protein kinase using electrospray ionization time of flight mass spectrometry. J Am Soc Mass Spectrom 15(10):1392–1399

    Article  CAS  Google Scholar 

  6. Sobott F, Hernández H, McCammon MG, Tito MA, Robinson CV (2002) A tandem mass spectrometer for improved transmission and analysis of large macromolecular assemblies. Anal Chem 74(6):1402–1407

    Article  CAS  Google Scholar 

  7. Rose RJ, Damoc E, Denisov E, Makarov A, Heck AJ (2012) High-sensitivity Orbitrap mass analysis of intact macromolecular assemblies. Nat Methods 9(11):1084–1086

    Article  CAS  Google Scholar 

  8. Andersson FI, Tryggvesson A, Sharon M, Diemand AV, Classen M, Best C, Schmidt R, Schelin J, Stanne TM, Bukau B, Robinson CV, Witt S, Mogk A, Clarke AK (2009) Structure and function of a novel type of ATP-dependent Clp protease. J Biol Chem 284(20):13519–13532

    Article  CAS  Google Scholar 

  9. Sharon M, Mao H, Boeri Erba E, Stephens E, Zheng N, Robinson CV (2009) Symmetrical modularity of the COP9 signalosome complex suggests its multifunctionality. Structure 17(1):31–40

    Article  CAS  Google Scholar 

  10. Martinez-Zapien D, Saliou JM, Han X, Atmanene C, Proux F, Cianférani S, Dock-Bregeon AC (2015) Intermolecular recognition of the non-coding RNA 7SK and HEXIM protein in perspective. Biochimie 117:63–71

    Article  CAS  Google Scholar 

  11. Saliou JM, Manival X, Tillault AS, Atmanene C, Bobo C, Branlant C, Van Dorsselaer A, Charpentier B, Cianférani S (2015) Combining native MS approaches to decipher archaeal box H/ACA ribonucleoprotein particle structure and activity. Proteomics 15(16):2851–2861

    Article  CAS  Google Scholar 

  12. Barrera NP, Di Bartolo N, Booth PJ, Robinson CV (2008) Micelles protect membrane complexes from solution to vacuum. Science 321(5886):243–246

    Article  CAS  Google Scholar 

  13. Chorev DS, Baker LA, Wu D, Beilsten-Edmands V, Rouse SL, Zeev-Ben-Mordehai T, Jiko C, Samsudin F, Gerle C, Khalid S, Stewart AG, Matthews SJ, Grünewald K, Robinson CV (2018) Protein assemblies ejected directly from native membranes yield complexes for mass spectrometry. Science 362(6416):829–834

    Article  CAS  Google Scholar 

  14. Marcoux J, Robinson CV (2013) Twenty years of gas phase structural biology. Structure 21(9):1541–1550

    Article  CAS  Google Scholar 

  15. Gan J, Ben-Nissan G, Arkind G, Tarnavsky M, Trudeau D, Noda Garcia L, Tawfik DS, Sharon M (2017) Native mass spectrometry of recombinant proteins from crude cell lysates. Anal Chem 89(8):4398–4404

    Article  CAS  Google Scholar 

  16. van de Waterbeemd M, Tamara S, Fort KL, Damoc E, Franc V, Bieri P, Itten M, Makarov A, Ban N, Heck AJR (2018) Dissecting ribosomal particles throughout the kingdoms of life using advanced hybrid mass spectrometry methods. Nat Commun 9(1):2493

    Article  Google Scholar 

  17. Opalka N, Brown J, Lane WJ, Twist KA, Landick R, Asturias FJ, Darst SA (2010) Complete structural model of Escherichia coli RNA polymerase from a hybrid approach. PLoS Biol 8(9):e1000483

    Article  Google Scholar 

  18. Twist KA, Husnain SI, Franke JD, Jain D, Campbell EA, Nickels BE, Thomas MS, Darst SA, Westblade LF (2011) A novel method for the production of in vivo-assembled, recombinant Escherichia coli RNA polymerase lacking the α C-terminal domain. Protein Sci 20(6):986–995

    Article  CAS  Google Scholar 

  19. Marty MT, Baldwin AJ, Marklund EG, Hochberg GK, Benesch JL, Robinson CV (2015) Bayesian deconvolution of mass and ion mobility spectra: from binary interactions to polydisperse ensembles. Anal Chem 87(8):4370–4376

    Article  CAS  Google Scholar 

  20. Reid DJ, Diesing JM, Miller MA, Perry SM, Wales JA, Montfort WR, Marty MT (2019) MetaUniDec: high-throughput deconvolution of native mass spectra. J Am Soc Mass Spectrom 30(1):118–127

    Article  CAS  Google Scholar 

  21. Radu L, Schönwetter E, Braun C, Marcoux J, Kölmel W, Schmitt DR, Kuper J, Cianferani S, Egly JM, Poterszman A, Kisker C (2017) The intricate network between the p34 and p44 subunits is central to the activity of the transcription/DNA repair factor TFIIH. Nucleic Acids Res 45(18):10872–10883

    Article  CAS  Google Scholar 

  22. Kolesnikova O, Radu L, Poterszman A (2019) TFIIH: a multi-subunit complex at the cross-roads of transcription and DNA repair. Adv Protein Chem Struct Biol 115:21–67

    Article  CAS  Google Scholar 

  23. Fouillen L, Abdulrhaman W, Moras D, van Dorsselaer A, Poterszman A, Sanglier-Cianférani S (2010) Analysis of recombinant phosphoprotein complexes with complementary mass spectrometry approaches. Anal Biochem 407(1):34–43

    Article  CAS  Google Scholar 

  24. Mohideen-Abdul K, Tazibt K, Bourguet M, Hazemann I, Lebars I, Takacs M, Cianférani S, Klaholz BP, Moras D, Billas IML (2017) Importance of the sequence-directed DNA shape for specific binding site recognition by the estrogen-related receptor. Front Endocrinol (Lausanne) 8:140

    Article  Google Scholar 

  25. Horwich AL, Fenton WA, Chapman E, Farr GW (2007) Two families of chaperonin: physiology and mechanism. Annu Rev Cell Dev Biol 23:115

    Article  CAS  Google Scholar 

  26. Vitorino M, Coin F, Zlobinskaya O, Atkinson A, Moras D, Egly JM, Poterszman A, Kieffer B (2007) Solution structure and self-association properties of the p8 TFIIH subunit responsible for Trichothiodystrophy. J Mol Biol 368(2):473–480

    Article  CAS  Google Scholar 

  27. Raj SB, Ramaswamy S, Plapp BV (2014) Yeast alcohol dehydrogenase structure and catalysis. Biochemistry 53(36):5791–5803

    Article  CAS  Google Scholar 

  28. Gervais V, Muller I, Mari PO, Mourcet A, Movellan K, Ramos P, Marcoux J, Guillet V, Javaid S, Burlet-Schiltz O, Czaplicki G, Milon A, Giglia-Mari G (2018) Small molecule-based targeting of TTD-A dimerization to control TFIIH transcriptional activity represents a potential strategy for anticancer therapy. J Biol Chem 293(39):14974–14988

    Article  CAS  Google Scholar 

  29. Marcoux J, Wang S, Politis A, Reading E, Ma J, Biggins P, Zhou M, Tao H, Zhang Q, Chang G, Morgner N, Robinson CV (2013) Mass spectrometry reveals synergistic binding of nucleotides, lipids and drugs to a multidrug resistance efflux pump. Proc Natl Acad Sci 110(24):9704–9709

    Article  CAS  Google Scholar 

  30. Laganowsky A, Reading E, Hopper JT, Robinson CV (2013) Mass spectrometry of intact membrane protein complexes. Nat Protoc 8(4):639–651

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The authors would like to thank Arnaud Poterszman (CAK complex), Albert Weixlbaumer (E. coli RNA polymerase), and Isabelle Billas Massobrio (ERR complexes) from the IGBMC (Strasbourg, France) and Virginie Gervais and Alain Milon (p8 protein) from IPBS (Toulouse, France) for kindly providing samples. This work was supported by the French Ministry of Research (Investissements d’Avenir Program, Proteomics French Infrastructure, ANR-10-INBS-08) and the FEDER (Fonds Européens de Développement Régional), Toulouse Métropole, and the Région Midi-Pyrénées.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Sarah Cianférani or Julien Marcoux .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Erb, S., Cianférani, S., Marcoux, J. (2021). Hands on Native Mass Spectrometry Analysis of Multi-protein Complexes. In: Poterszman, A. (eds) Multiprotein Complexes. Methods in Molecular Biology, vol 2247. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1126-5_10

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-1126-5_10

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1125-8

  • Online ISBN: 978-1-0716-1126-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics