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Gas-Phase Enrichment of Multiply Charged Peptide Ions by Differential Ion Mobility Extend the Comprehensiveness of SUMO Proteome Analyses

  • Sibylle Pfammatter
  • Eric Bonneil
  • Francis P. McManus
  • Pierre Thibault
Focus: Mass Spectrometry in Glycobiology and Related Fields: Research Article

Abstract

The small ubiquitin-like modifier (SUMO) is a member of the family of ubiquitin-like modifiers (UBLs) and is involved in important cellular processes, including DNA damage response, meiosis and cellular trafficking. The large-scale identification of SUMO peptides in a site-specific manner is challenging not only because of the low abundance and dynamic nature of this modification, but also due to the branched structure of the corresponding peptides that further complicate their identification using conventional search engines. Here, we exploited the unusual structure of SUMO peptides to facilitate their separation by high-field asymmetric waveform ion mobility spectrometry (FAIMS) and increase the coverage of SUMO proteome analysis. Upon trypsin digestion, branched peptides contain a SUMO remnant side chain and predominantly form triply protonated ions that facilitate their gas-phase separation using FAIMS. We evaluated the mobility characteristics of synthetic SUMO peptides and further demonstrated the application of FAIMS to profile the changes in protein SUMOylation of HEK293 cells following heat shock, a condition known to affect this modification. FAIMS typically provided a 10-fold improvement of detection limit of SUMO peptides, and enabled a 36% increase in SUMO proteome coverage compared to the same LC-MS/MS analyses performed without FAIMS.

Graphical Abstract

Keywords

High-field asymmetric waveform ion mobility spectrometry (FAIMS) Proteomics SUMOylation Heat shock 

Notes

Acknowledgements

The authors thank Jean-Jacques Dunyach, Michael Belford and Satendra Prasad (Thermo Fisher Scientific) for valuable help and assistance with the FAIMS interface. The Institute for Research in Immunology and Cancer (IRIC) receives infrastructure support from IRICoR, the Canadian Foundation for Innovation, and the Fonds de Recherche du Québec-Santé (FRQS). IRIC proteomics facility is a Genomics Technology platform funded in part by the Canadian Government through Genome Canada.

Funding

This work was carried out with financial support from the Natural Sciences and Engineering Research Council (NSERC 311598) and the Genomic Applications Partnership Program (GAPP) of Genome Canada. The Institute for Research in Immunology and Cancer (IRIC) receives infrastructure support from IRICoR, the Canadian Foundation for Innovation, and the Fonds de Recherche du Québec - Santé (FRQS). IRIC proteomics facility is a Genomics Technology platform funded in part by the Canadian Government through Genome Canada.

Supplementary material

13361_2018_1917_MOESM1_ESM.docx (1.7 mb)
ESM 1 (DOCX 1.69 mb)
13361_2018_1917_MOESM2_ESM.xlsx (613 kb)
ESM 2 (XLSX 612 kb)

References

  1. 1.
    Streich Jr., F.C., Lima, C.D.: Structural and functional insights to ubiquitin-like protein conjugation. Annu. Rev. Biophys. 43, 357–379 (2014)Google Scholar
  2. 2.
    van der Veen, A.G., Ploegh, H.L.: Ubiquitin-like proteins. Annu. Rev. Biochem. 81, 323–357 (2012)CrossRefGoogle Scholar
  3. 3.
    Dou, H., Huang, C., Van Nguyen, T., Lu, L.S., Yeh, E.T.: SUMOylation and de-SUMOylation in response to DNA damage. FEBS Lett. 585, 2891–2896 (2011)CrossRefGoogle Scholar
  4. 4.
    Niskanen, E.A., Malinen, M., Sutinen, P., Toropainen, S., Paakinaho, V., Vihervaara, A., Joutsen, J., Kaikkonen, M.U., Sistonen, L., Palvimo, J.J.: Global SUMOylation on active chromatin is an acute heat stress response restricting transcription. Genome Biol. 16, 153–172 (2015)CrossRefGoogle Scholar
  5. 5.
    Tatham, M.H., Matic, I., Mann, M., Hay, R.T.: Comparative proteomic analysis identifies a role for SUMO in protein quality control. Sci. Signal. 4(1), (2011)Google Scholar
  6. 6.
    Eiffer, K., Vertegaal, A.C.O.: Mapping the sumoylated laadscape. FEBS J. 282, 3669–3680 (2015)CrossRefGoogle Scholar
  7. 7.
    Hay, R.T.: Decoding the SUMO signal. Biochem. Soc. Trans. 41, 463–473 (2013)CrossRefGoogle Scholar
  8. 8.
    Hay, R.T.: SUMO: a history of modification. Mol. Cell. 18, 1–12 (2005)CrossRefGoogle Scholar
  9. 9.
    Tatham, M.H., Jaffray, E.G., Vaughan, O.A., desterro, J.M., Bottino, C.H., Naismith, J.H., Hay, R.T.: Polymeric chains of SUMO-2 and SUMO-3 are conjugated to protein substrates by SAE1/SAE2 and Ubc9. J. Biol. Chem. 276, 35368–35374 (2001)CrossRefGoogle Scholar
  10. 10.
    Hendricks, I.A., Lyon, D., Young, C., Jensen, L.J., Vertegaal, A.C., Nielsen, M.L.: Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation. Nat. Struct. Mol. Biol. 24, 325–336 (2017)CrossRefGoogle Scholar
  11. 11.
    Hendricks, I.A., Vertegaal, A.C.: A comprehensive compilation of SUMO proteomics. Nat. Rev. 17, 581–595 (2016)CrossRefGoogle Scholar
  12. 12.
    Hendriks, I.A., D’Souza, R.C., Yang, B., Verlaan-de Vries, M., Mann, M., Vertegaal, A.C.: Uncovering global SUMOylation signaling networks in a site-specific manner. Nat. Struct. Mol. Biol. 21, 927–936 (2014)Google Scholar
  13. 13.
    Galisson, F., Mahrouche, L., Courcelles, M., Bonneil, E., Meloche, S., Chelbi-Alix, M.K., Thibault, P.: A novel proteomics approach to identify SUMOylated proteins and their modification sites in human cells. Mol. Cell. Proteomics. 10, (2011)Google Scholar
  14. 14.
    Lamoliatte, F., Caron, D., Durette, C., Mahrouche, L., Maroui, M.A., Caron-Lizotte, O., Bonneil, E., Chelbi-Alix, M.K., Thibault, P.: Large-scale analysis of lysine SUMOylation by SUMO remnant immunoaffinity profiling. Nat. Commun. 5, 5409–5420 (2014)CrossRefGoogle Scholar
  15. 15.
    Lamoliatte, F., McManus, F.P., Maarifi, G., Chelbi-Alix, M.K., Thibault, P.: Uncovering the SUMOylation and Ubiquitylation crosstalk in Human Cells Using Sequential Peptide Immunopurification. Nat. Commun., (2017)Google Scholar
  16. 16.
    Tammsalu, T., Matic, I., Jaffray, E.G., Ibrahim, A.F., Tatham, M.H., Hay, R.T.: Proteome-wide identification of SUMO2 modification sites. Sci. Signal. 7, (2014)Google Scholar
  17. 17.
    Hendriks, I.A., D’Souza, R.C., Chang, J.-G., Mann, M., Vertegaal, A.C.O.: System-wide identification of wild-type SUMO-2 conjugation sites. Nat. Commun. 6, 7289–7305 (2015)CrossRefGoogle Scholar
  18. 18.
    Lamoliatte, F., Bonneil, E., Durette, C., Caron-Lizotte, O., Wildemann, D., Zerweck, J., Wenshuck, H., Thibault, P.: Targeted identification of SUMOylation sites in human proteins using affinity enrichment and paralog-specific reporter ions. Mol. Cell. Proteomics. 12, 2536–2550 (2013)CrossRefGoogle Scholar
  19. 19.
    Dumont, Q., Donaldson, D.L., Griffith, W.P.: Screening method for isopeptides from small ubiquitin-related modifier-conjugated proteins by ion mobility mass spectrometry. Anal. Chem. 83, 9638–9642 (2011)CrossRefGoogle Scholar
  20. 20.
    Barnett, D.A., Ding, L., Ells, B., Purves, R.W., Guevremont, R.: Tandem mass spectra of tryptic peptides at signal-to-background ratios approaching unity using electrospray ionization high-field asymmetric waveform ion mobility spectrometry/hybrid quadrupole time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 16, 676–680 (2002)CrossRefGoogle Scholar
  21. 21.
    Barnett, D.A., Ells, B., Guevremont, R., Purves, R.W.: Application of ESI-FAIMS-MS to the analysis of tryptic peptides. J. Am. Soc. Mass Spectrom. 13, 1282–1291 (2002)CrossRefGoogle Scholar
  22. 22.
    Purves, R.W., Guevremont, R.: Electrospray ionization high-field asymmetric waveform ion mobility spectrometry-mass spectrometry. Anal. Chem. 71, 2346–2357 (1999)CrossRefGoogle Scholar
  23. 23.
    Guevremont, R.: High-field asymmetric waveform ion mobility spectrometry: a new tool for mass spectrometry. J. Chromatogr. A. 1058, 3–19 (2004)CrossRefGoogle Scholar
  24. 24.
    Creese, A.J., Shimwell, N.J., Larkins, K.P.B., Heath, J.K., Cooper, H.J.: Probing the complementarity of FAIMS and strong cation exchange chromatography in shotgun proteomics. J. Am. Soc. Mass Spectrom. 24, 431–443 (2013)CrossRefGoogle Scholar
  25. 25.
    Saba, J., Bonneil, E., Pomiès, C., Eng, K., Thibault, P.: Enhanced sensitivity in proteomics experiments using FAIMS coupled with a hybrid linear ion trap/orbitrap mass analyzer. J. Proteome Res. 8, 3355–3366 (2009)CrossRefGoogle Scholar
  26. 26.
    Swearingen, K.E., Hoopmann, M.R., Johnson, R.S., Saleem, R.A., Aitchinson, J.D., Moritz, R.L.: Nanospray FAIMS fractionation provides significant increases in proteome coverage of unfractionated complex protein digests. Mol. Cellular Proteomics. (2012)Google Scholar
  27. 27.
    Xuan, Y., Creese, A.J., Horner, J.A., Cooper, H.J.: High-field asymmetric waveform ion mobility spectrometry (FAIMS) coupled with high-resolution electron transfer dissociation mass spectrometry for the analysis of isobaric phosphopeptides. Rapid Commun. Mass Spectrom. 23, 1963–1969 (2009)CrossRefGoogle Scholar
  28. 28.
    Bridon, G., Bonneil, E., Muratore-Schroeder, T., Caron-Lizotte, O., Thibault, P.: Improvement of phosphoproteome analyses using FAIMS and decision tree fragmentation. Application to the insulin signaling pathway in Drosophila melanogaster S2 cells. J. Proteome Res. 11, 927–940 (2012)CrossRefGoogle Scholar
  29. 29.
    Creese, A.J., Smart, J., Cooper, H.J.: Large-scale analysis of peptide sequence variants: the case for high-field asymmetric waveform ion mobility spectrometry. Anal. Chem. 85, 4836–4843 (2013)CrossRefGoogle Scholar
  30. 30.
    Zhao, H., Cunningham, D.L., Creese, A.J., Heath, J.K., Cooper, H.J.: FAIMS and phosphoproteomics of fibroblast growth factor signaling: enhanced identification of multiply phosphorylated peptides. J. Proteome Res. 14, 5077–5087 (2015)CrossRefGoogle Scholar
  31. 31.
    Pfammatter, S., Bonneil, E., Thibault, P.: Improvement of quantitative measurements in multiplex proteomics using high-field asymmetric waveform spectrometry. J. Proteome Res. 15, 4653–4665 (2016)CrossRefGoogle Scholar
  32. 32.
    McManus, F.P., Lamoliatte, F., Thibault, P.: Identification of cross talk between SUMOylation and ubiquitylation using a sequential peptide immunopurification approach. Nat. Protoc. 12, 2342–2358 (2017)CrossRefGoogle Scholar
  33. 33.
    Prasad, S., Belford, M.W., Dunyach, J.J., Purves, R.W.: On an aerodynamic mechanism to enhance ion transmission and sensitivity of FAIMS for nano-electrospray mass spectrometry. J. Am. Soc. Mass Spectrom. 25, 2143–2153 (2014)CrossRefGoogle Scholar
  34. 34.
    Barnett, D.A., Ouellette, R.J.: Elimination of the helium requirement in high-field asymmetric waveform ion mobility spectrometry (FAIMS): beneficial effects of decreasing the analyzer gap width on peptide analysis. Rapid Commun. Mass Spectrom. 25, 1959–1971 (2011)CrossRefGoogle Scholar
  35. 35.
    Enserink, J.M.: Sumo and the cellular stress response. Cell Div. 10, 4 (2015)CrossRefGoogle Scholar
  36. 36.
    Golebiowski, F., Matic, I., Tatham, M.H., Cole, C., Yin, Y., Nakamura, A., Cox, J., Barton, G.J., Mann, M., Hay, R.T.: System-wide changes to SUMO modifications in response to heat shock. Sci. Signal. 2, ra24 (2009)CrossRefGoogle Scholar
  37. 37.
    Bonneil, E., Pfammatter, S., Thibault, P.: Enhancement of mass spectrometry performances for proteomics analyses using high-field asymmetric waveform spectrometry (FAIMS). J. Mass Spectrom. 50, 1181–1195 (2015)CrossRefGoogle Scholar
  38. 38.
    Tyanova, S., Temu, T., Cox, J.: The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat. Protocols. 11, 2301–2319 (2016)CrossRefGoogle Scholar
  39. 39.
    Gill, G.: Post-translational modification by the small ubiquitin-related modifier SUMO has big effects on transcription factor activity. Curr. Opin. Genet. Dev. 13, 108–113 (2003)CrossRefGoogle Scholar
  40. 40.
    Seo, J., Lee, K.J.: Post-translational modifications and their biological functions: proteomic analysis and systematic approaches. J. Biochem. Mol. Biol. 37, 35–44 (2004)Google Scholar
  41. 41.
    Filtz, T.M., Vogel, W.K., Leid, M.: Regulation of transcription factor activity by interconnected post-translational modifications. Trends Pharmacol. Sci. 35, 76–85 (2014)CrossRefGoogle Scholar
  42. 42.
    Rosonina, E., Akhter, A., Dou, Y., Babu, J., Sri Theivakadadcham, V.S.: Regulation of transcription factors by sumoylation. Transcription. e1311829 (2017)Google Scholar
  43. 43.
    Hong, Y., Rogers, R., Matunis, M.J., Mayhew, C.N., Goodson, M.L., Park-Sarge, O.K., Sarge, K.D.: Regulation of heat shock transcription factor 1 by stress-induced SUMO-1 modification. J. Biol. Chem. 276, 40263–40267 (2001)CrossRefGoogle Scholar
  44. 44.
    Fulda, S., Gorman, A.M., Hori, O., Samali, A.: Cellular stress responses: cell survival and cell death. International Journal of Cell Biology. 2010(23), (2010)Google Scholar
  45. 45.
    Roy, A.L.: Biochemistry and biology of the inducible multifunctional transcription factor TFII-I: 10 years later. Gene. 492, 32–41 (2012)CrossRefGoogle Scholar
  46. 46.
    Chu, Y., Yang, X.: SUMO E3 ligase activity of TRIM proteins. Oncogene. 30, 1108–1116 (2011)CrossRefGoogle Scholar
  47. 47.
    Guo, L., Giasson, B.I., Glavis-Bloom, A., Brewer, M.D., Shorter, J., Gitler, A.D., Yang, X.: A cellular system that degrades misfolded proteins and protects against neurodegeneration. Mol. Cell. 55, 15–30 (2014)CrossRefGoogle Scholar
  48. 48.
    Martin, N., Schwamborn, K., Schreiber, V., Werner, A., Guillier, C., Zhang, X.D., Bischof, O., Seeler, J.S., Dejean, A.: PARP-1 transcriptional activity is regulated by sumoylation upon heat shock. EMBO J. 28, 3534–3548 (2009)CrossRefGoogle Scholar
  49. 49.
    Luo, X., Kraus, W.L.: On PAR with PARP: cellular stress signaling through poly(ADP-ribose) and PARP-1. Genes Dev. 26, 417–432 (2012)CrossRefGoogle Scholar
  50. 50.
    Woodhouse, B.C., Dianov, G.L.: Poly ADP-ribose polymerase-1: an international molecule of mystery. DNA repair. 7, 1077–1086 (2008)CrossRefGoogle Scholar
  51. 51.
    Morris, J.R., Boutell, C., Keppler, M., Densham, R., Weekes, D., Alamshah, A., Butler, L., Galanty, Y., Pangon, L., Kiuchi, T., Ng, T., Solomon, E.: The SUMO modification pathway is involved in the BRCA1 response to genotoxic stress. Nature. 462, 886–890 (2009)CrossRefGoogle Scholar
  52. 52.
    Takahashi, A., Matsumoto, H., Nagayama, K., Kitano, M., Hirose, S., Tanaka, H., Mori, E., Yamakawa, N., Yasumoto, J., Yuki, K., Ohnishi, K., Ohnishi, T.: Evidence for the involvement of double-strand breaks in heat-induced cell killing. Cancer Res. 64, 8839–8845 (2004)CrossRefGoogle Scholar
  53. 53.
    Takahashi, A., Mori, E., Somakos, G.I., Ohnishi, K., Ohnishi, T.: Heat induces gammaH2AX foci formation in mammalian cells. Mutat. Res. 656, 88–92 (2008)CrossRefGoogle Scholar
  54. 54.
    Cheng, J., Wang, D., Wang, Z., Yeh, E.T.: SENP1 enhances androgen receptor-dependent transcription through desumoylation of histone deacetylase 1. Mol. Cell. Biol. 24, 6021–6028 (2004)CrossRefGoogle Scholar
  55. 55.
    David, G., Neptune, M.A., DePinho, R.A.: SUMO-1 modification of histone deacetylase 1 (HDAC1) modulates its biological activities. J. Biol. Chem. 277, 23658–23663 (2002)CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2018

Authors and Affiliations

  1. 1.Institute for Research in Immunology and CancerUniversité de MontréalMontréalCanada
  2. 2.Department of ChemistryUniversité de MontréalMontréalCanada

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