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Analysis of Golgi Protein Acetylation Using In Vitro Assays and Parallel Reaction Monitoring Mass Spectrometry

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Golgi

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2557))

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Abstract

Acetylation is one of the most abundant post-translational protein modifications that regulates all cellular compartments ranging from chromatin to cytoskeleton and Golgi. The dynamic acetylation of the Golgi stacking protein GRASP55 was shown to regulate Golgi reassembly after mitosis. Here we provide a detailed protocol for the analysis of Golgi acetylation including in vitro assays to detect protein acetylation and mass spectrometry analysis to identify specific acetylation sites and their relative abundance.

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References

  1. Berndsen CE, Denu JM (2008) Catalysis and substrate selection by histone/protein lysine acetyltransferases. Curr Opin Struct Biol 18(6):682–689. https://doi.org/10.1016/j.sbi.2008.11.004

    Article  CAS  Google Scholar 

  2. Baldensperger T, Glomb MA (2021) Pathways of non-enzymatic lysine acylation. Front Cell Dev Biol 9:664553. https://doi.org/10.3389/fcell.2021.664553

    Article  Google Scholar 

  3. Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M (2009) Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science (New York, NY) 325(5942):834–840. https://doi.org/10.1126/science.1175371

    Article  CAS  Google Scholar 

  4. Choudhary C, Weinert BT, Nishida Y, Verdin E, Mann M (2014) The growing landscape of lysine acetylation links metabolism and cell signalling. Nat Rev Mol Cell Biol 15(8):536–550. https://doi.org/10.1038/nrm3841

    Article  CAS  Google Scholar 

  5. Hansen BK, Gupta R, Baldus L, Lyon D, Narita T, Lammers M, Choudhary C, Weinert BT (2019) Analysis of human acetylation stoichiometry defines mechanistic constraints on protein regulation. Nat Commun 10(1):1055. https://doi.org/10.1038/s41467-019-09024-0

    Article  CAS  Google Scholar 

  6. Zhang X, Brachner A, Kukolj E, Slade D, Wang Y (2019) SIRT2 deacetylates GRASP55 to facilitate post-mitotic Golgi assembly. J Cell Sci 132(21). https://doi.org/10.1242/jcs.232389

  7. Joshi G, Bekier ME 2nd, Wang Y (2015) Golgi fragmentation in Alzheimer’s disease. Front Neurosci 9:340. https://doi.org/10.3389/fnins.2015.00340

    Article  Google Scholar 

  8. Rendon WO, Martinez-Alonso E, Tomas M, Martinez-Martinez N, Martinez-Menarguez JA (2013) Golgi fragmentation is Rab and SNARE dependent in cellular models of Parkinson’s disease. Histochem Cell Biol 139(5):671–684. https://doi.org/10.1007/s00418-012-1059-4

    Article  CAS  Google Scholar 

  9. Wang R, Sun H, Wang G, Ren H (2020) Imbalance of lysine acetylation contributes to the pathogenesis of Parkinson’s disease. Int J Mol Sci 21(19). https://doi.org/10.3390/ijms21197182

  10. Drazic A, Myklebust LM, Ree R, Arnesen T (2016) The world of protein acetylation. Biochim Biophys Acta 1864(10):1372–1401. https://doi.org/10.1016/j.bbapap.2016.06.007

    Article  CAS  Google Scholar 

  11. Bourmaud A, Gallien S, Domon B (2016) Parallel reaction monitoring using quadrupole-Orbitrap mass spectrometer: principle and applications. Proteomics 16(15–16):2146–2159. https://doi.org/10.1002/pmic.201500543

    Article  CAS  Google Scholar 

  12. Kaufmann T, Kukolj E, Brachner A, Beltzung E, Bruno M, Kostrhon S, Opravil S, Hudecz O, Mechtler K, Warren G, Slade D (2016) SIRT2 regulates nuclear envelope reassembly through ANKLE2 deacetylation. J Cell Sci 129(24):4607–4621. https://doi.org/10.1242/jcs.192633

    Article  CAS  Google Scholar 

  13. Xiang Y, Wang Y (2010) GRASP55 and GRASP65 play complementary and essential roles in Golgi cisternal stacking. J Cell Biol 188(2):237–251. https://doi.org/10.1083/jcb.200907132

    Article  CAS  Google Scholar 

  14. Dephoure N, Gould KL, Gygi SP, Kellogg DR (2013) Mapping and analysis of phosphorylation sites: a quick guide for cell biologists. Mol Biol Cell 24(5):535–542. https://doi.org/10.1091/mbc.E12-09-0677

    Article  CAS  Google Scholar 

  15. Dekker LJM, Zeneyedpour L, Snoeijers S, Joore J, Leenstra S, Luider TM (2018) Determination of site-specific phosphorylation ratios in proteins with targeted mass spectrometry. J Proteome Res 17(4):1654–1663. https://doi.org/10.1021/acs.jproteome.7b00911

    Article  CAS  Google Scholar 

  16. Shevchenko A, Tomas H, Havli J, Olsen JV, Mann M (2006) In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc 1(6):2856–2860. https://doi.org/10.1038/nprot.2006.468

    Article  CAS  Google Scholar 

  17. Tyanova S, Temu T, Cox J (2016) The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat Protoc 11(12):2301–2319. https://doi.org/10.1038/nprot.2016.136

    Article  CAS  Google Scholar 

  18. Kong AT, Leprevost FV, Avtonomov DM, Mellacheruvu D, Nesvizhskii AI (2017) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics. Nat Methods 14(5):513–520. https://doi.org/10.1038/nmeth.4256

    Article  CAS  Google Scholar 

  19. Solntsev SK, Shortreed MR, Frey BL, Smith LM (2018) Enhanced global post-translational modification discovery with MetaMorpheus. J Proteome Res 17(5):1844–1851. https://doi.org/10.1021/acs.jproteome.7b00873

    Article  CAS  Google Scholar 

  20. Vaudel M, Barsnes H, Berven FS, Sickmann A, Martens L (2011) SearchGUI: an open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics 11(5):996–999. https://doi.org/10.1002/pmic.201000595

    Article  CAS  Google Scholar 

  21. Hjernø K, Højrup P (2015) Interpretation of tandem mass spectrometry (MSMS) spectra for peptide analysis. Methods Mol Biol 1348:83–102. https://doi.org/10.1007/978-1-4939-2999-3_10

    Article  CAS  Google Scholar 

  22. Kim MS, Zhong J, Pandey A (2016) Common errors in mass spectrometry-based analysis of post-translational modifications. Proteomics 16(5):700–714. https://doi.org/10.1002/pmic.201500355

    Article  CAS  Google Scholar 

  23. Gessulat S, Schmidt T, Zolg DP, Samaras P, Schnatbaum K, Zerweck J, Knaute T, Rechenberger J, Delanghe B, Huhmer A, Reimer U, Ehrlich HC, Aiche S, Kuster B, Wilhelm M (2019) Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning. Nat Methods 16(6):509–518. https://doi.org/10.1038/s41592-019-0426-7

    Article  CAS  Google Scholar 

  24. MacLean B, Tomazela DM, Shulman N, Chambers M, Finney GL, Frewen B, Kern R, Tabb DL, Liebler DC, MacCoss MJ (2010) Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26(7):966–968. https://doi.org/10.1093/bioinformatics/btq054

    Article  CAS  Google Scholar 

  25. Rauniyar N (2015) Parallel reaction monitoring: a targeted experiment performed using high resolution and high mass accuracy mass spectrometry. Int J Mol Sci 16(12):28566–28581. https://doi.org/10.3390/ijms161226120

    Article  CAS  Google Scholar 

  26. Chiva C, Sabidó E (2017) Peptide selection for targeted protein quantitation. J Proteome Res 16(3):1376–1380. https://doi.org/10.1021/acs.jproteome.6b00115

    Article  CAS  Google Scholar 

  27. Wu R, Haas W, Dephoure N, Huttlin EL, Zhai B, Sowa ME, Gygi SP (2011) A large-scale method to measure absolute protein phosphorylation stoichiometries. Nat Methods 8(8):677–683. https://doi.org/10.1038/nmeth.1636

    Article  CAS  Google Scholar 

  28. Prus G, Hoegl A, Weinert BT, Choudhary C (2019) Analysis and interpretation of protein post-translational modification site stoichiometry. Trends Biochem Sci 44(11):943–960. https://doi.org/10.1016/j.tibs.2019.06.003

    Article  CAS  Google Scholar 

  29. Johnson J, Harman VM, Franco C, Emmott E, Rockliffe N, Sun Y, Liu LN, Takemori A, Takemori N, Beynon RJ (2021) Construction of à la carte QconCAT protein standards for multiplexed quantification of user-specified target proteins. BMC Biol 19(1):195. https://doi.org/10.1186/s12915-021-01135-9

    Article  CAS  Google Scholar 

  30. Gallien S, Bourmaud A, Kim SY, Domon B (2014) Technical considerations for large-scale parallel reaction monitoring analysis. J Proteomics 100:147–159. https://doi.org/10.1016/j.jprot.2013.10.029

    Article  CAS  Google Scholar 

  31. Gallien S, Domon B (2015) Detection and quantification of proteins in clinical samples using high resolution mass spectrometry. Methods 81:15–23. https://doi.org/10.1016/j.ymeth.2015.03.015

    Article  CAS  Google Scholar 

  32. van Bentum M, Selbach M (2021) An introduction to advanced targeted acquisition methods. Mol Cell Proteom 20:100165. https://doi.org/10.1016/j.mcpro.2021.100165

    Article  CAS  Google Scholar 

  33. Escher C, Reiter L, MacLean B, Ossola R, Herzog F, Chilton J, MacCoss MJ, Rinner O (2012) Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics 12(8):1111–1121. https://doi.org/10.1002/pmic.201100463

    Article  CAS  Google Scholar 

  34. Oberg AL, Vitek O (2009) Statistical design of quantitative mass spectrometry-based proteomic experiments. J Proteome Res 8(5):2144–2156. https://doi.org/10.1021/pr8010099

    Article  CAS  Google Scholar 

  35. Burger B, Vaudel M, Barsnes H (2021) Importance of block randomization when designing proteomics experiments. J Proteome Res 20(1):122–128. https://doi.org/10.1021/acs.jproteome.0c00536

    Article  CAS  Google Scholar 

  36. Team RC (2021) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna

    Google Scholar 

  37. Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43(7):e47. https://doi.org/10.1093/nar/gkv007

    Article  CAS  Google Scholar 

  38. Trevisiol S, Ayoub D, Lesur A, Ancheva L, Gallien S, Domon B (2016) The use of proteases complementary to trypsin to probe isoforms and modifications. Proteomics 16(5):715–728. https://doi.org/10.1002/pmic.201500379

    Article  CAS  Google Scholar 

  39. Giansanti P, Tsiatsiani L, Low TY, Heck AJ (2016) Six alternative proteases for mass spectrometry-based proteomics beyond trypsin. Nat Protoc 11(5):993–1006. https://doi.org/10.1038/nprot.2016.057

    Article  CAS  Google Scholar 

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Correspondence to Dea Slade or Markus Hartl .

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Slade, D., Hartl, M. (2023). Analysis of Golgi Protein Acetylation Using In Vitro Assays and Parallel Reaction Monitoring Mass Spectrometry. In: Wang, Y., Lupashin, V.V., Graham, T.R. (eds) Golgi. Methods in Molecular Biology, vol 2557. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2639-9_43

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  • DOI: https://doi.org/10.1007/978-1-0716-2639-9_43

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2638-2

  • Online ISBN: 978-1-0716-2639-9

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