Resin-assisted enrichment of thiols as a general strategy for proteomic profiling of cysteine-based reversible modifications

Nature Protocols - Tập 9 Số 1 - Trang 64-75 - 2014
Jia Guo1, Matthew Gaffrey1, Dian Su1,2, Tao Liu1, Kristin Burnum-Johnson1, Richard Smith1, Weijun Qian1
1Biological Sciences Division, Pacific Northwest National Laboratory, Richland, USA
2Genentech, Inc., South San Francisco, USA

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Giron, P., Dayon, L. & Sanchez, J.C. Cysteine tagging for MS-based proteomics. Mass Spectrom. Rev. 30, 366–395 (2011).

Held, J.M. & Gibson, B.W. Regulatory control or oxidative damage? Proteomic approaches to interrogate the role of cysteine oxidation status in biological processes. Mol. Cell Proteomics 11, R111.013037 (2012).

Antelmann, H. & Helmann, J.D. Thiol-based redox switches and gene regulation. Antioxid. Redox Signal. 14, 1049–1063 (2011).

Bachi, A., Dalle-Donne, I. & Scaloni, A. Redox proteomics: chemical principles, methodological approaches and biological/biomedical promises. Chem. Rev. 113, 596–698 (2013).

Sato, Y. & Inaba, K. Disulfide bond formation network in the three biological kingdoms, bacteria, fungi and mammals. FEBS J. 279, 2262–2271 (2012).

Derakhshan, B., Wille, P.C. & Gross, S.S. Unbiased identification of cysteine S-nitrosylation sites on proteins. Nat. Protoc. 2, 1685–1691 (2007).

Greco, T.M. et al. Identification of S-nitrosylation motifs by site-specific mapping of the S-nitrosocysteine proteome in human vascular smooth muscle cells. Proc. Natl. Acad. Sci. USA 103, 7420–7425 (2006).

Hess, D.T., Matsumoto, A., Kim, S.O., Marshall, H.E. & Stamler, J.S. Protein S-nitrosylation: purview and parameters. Nat. Rev. Mol. Cell. Biol. 6, 150–166 (2005).

Paulsen, C.E. et al. Peroxide-dependent sulfenylation of the EGFR catalytic site enhances kinase activity. Nat. Chem. Biol. 8, 57–64 (2012).

Wan, J., Roth, A.F., Bailey, A.O. & Davis, N.G. Palmitoylated proteins: purification and identification. Nat. Protoc. 2, 1573–1584 (2007).

Roth, A.F. et al. Global analysis of protein palmitoylation in yeast. Cell 125, 1003–1013 (2006).

Brandes, N., Schmitt, S. & Jakob, U. Thiol-based redox switches in eukaryotic proteins. Antioxid. Redox Signal. 11, 997–1014 (2009).

Jortzik, E., Wang, L. & Becker, K. Thiol-based posttranslational modifications in parasites. Antioxid. Redox Signal. 17, 657–673 (2012).

Jaffrey, S.R., Erdjument-Bromage, H., Ferris, C.D., Tempst, P. & Snyder, S.H. Protein S-nitrosylation: a physiological signal for neuronal nitric oxide. Nat. Cell. Biol. 3, 193–197 (2001).

Jaffrey, S.R. & Snyder, S.H. The biotin switch method for the detection of S-nitrosylated proteins. Sci. STKE 2001, pl1 (2001).

Lind, C. et al. Identification of S-glutathionylated cellular proteins during oxidative stress and constitutive metabolism by affinity purification and proteomic analysis. Arch. Biochem. Biophys. 406, 229–240 (2002).

Reynaert, N.L. et al. In situ detection of S-glutathionylated proteins following glutaredoxin-1 catalyzed cysteine derivatization. Biochim. Biophys. Acta 1760, 380–387 (2006).

Leichert, L.I. et al. Quantifying changes in the thiol redox proteome upon oxidative stress in vivo. Proc. Natl. Acad. Sci. USA 105, 8197–8202 (2008).

Hao, G., Derakhshan, B., Shi, L., Campagne, F. & Gross, S.S. SNOSID, a proteomic method for identification of cysteine S-nitrosylation sites in complex protein mixtures. Proc. Natl. Acad. Sci. USA 103, 1012–1017 (2006).

Liu, T. et al. Improved proteome coverage using high-efficiency cysteinyl peptide enrichment: the mammary epithelial cell proteome. Proteomics 5, 1263–1273 (2005).

Liu, T. et al. High-throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology. Anal. Chem. 76, 5345–5353 (2004).

Forrester, M.T. et al. Proteomic analysis of S-nitrosylation and denitrosylation by resin-assisted capture. Nat. Biotechnol. 27, 557–559 (2009).

Su, D. et al. Quantitative site-specific reactivity profiling of S-nitrosylation in mouse skeletal muscle using cysteinyl peptide enrichment coupled with mass spectrometry. Free Radic. Biol. Med. 57, 68–78 (2013).

Liu, M. et al. Site-specific proteomics approach for study protein s-nitrosylation. Anal. Chem. 82, 7160–7168 (2010).

Forrester, M.T. et al. Site-specific analysis of protein S-acylation by resin-assisted capture. J. Lipid Res. 52, 393–398 (2011).

Paulech, J. et al. Large-scale capture of peptides containing reversibly oxidized cysteines by thiol-disulfide exchange applied to the myocardial redox proteome. Anal. Chem. 85, 3774–3780 (2013).

Ross, P.L. et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3, 1154–1169 (2004).

Dayon, L. et al. Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags. Anal. Chem. 80, 2921–2931 (2008).

Shelton, M.D., Chock, P.B. & Mieyal, J.J. Glutaredoxin: role in reversible protein s-glutathionylation and regulation of redox signal transduction and protein translocation. Antioxid. Redox Signal. 7, 348–366 (2005).

Zhang, C., Rodriguez, C., Circu, M.L., Aw, T.Y. & Feng, J. S-Glutathionyl quantification in the attomole range using glutaredoxin-3-catalyzed cysteine derivatization and capillary gel electrophoresis with laser-induced fluorescence detection. Anal. Bioanal. Chem. 401, 2165–2175 (2011).

Mustafa, A.K. et al. H2S signals through protein S-sulfhydration. Sci. Signal. 2, ra72 (2009).

Pan, J. & Carroll, K.S. Persulfide reactivity in the detection of protein S-sulfhydration. ACS Chem. Biol. 2013, 1110–1116 (2013).

Forrester, M.T., Foster, M.W. & Stamler, J.S. Assessment and application of the biotin switch technique for examining protein S-nitrosylation under conditions of pharmacologically induced oxidative stress. J. Biol. Chem. 282, 13977–13983 (2007).

Forrester, M.T., Foster, M.W., Benhar, M. & Stamler, J.S. Detection of protein S-nitrosylation with the biotin-switch technique. Free Radic. Biol. Med. 46, 119–126 (2009).

Ong, S.E. et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell Proteomics 1, 376–386 (2002).

Murray, C.I., Uhrigshardt, H., O'Meally, R.N., Cole, R.N. & Van Eyk, J.E. Identification and quantification of S-nitrosylation by cysteine reactive tandem mass tag switch assay. Mol. Cell Proteomics 11, M111 013441 (2012).

Foster, M.W. Methodologies for the characterization, identification and quantification of S-nitrosylated proteins. Biochim. Biophys. Acta 1820, 675–683 (2012).

Zhang, Y., Ficarro, S.B., Li, S. & Marto, J.A. Optimized orbitrap HCD for quantitative analysis of phosphopeptides. J. Am. Soc. Mass Spectrom. 20, 1425–1434 (2009).

Kelly, R.T. et al. Chemically etched open tubular and monolithic emitters for nanoelectrospray ionization mass spectrometry. Anal. Chem. 78, 7796–7801 (2006).

Livesay, E.A. et al. Fully automated four-column capillary LC-MS system for maximizing throughput in proteomic analyses. Anal. Chem. 80, 294–302 (2008).

Eng, J.K., Mccormack, A.L. & Yates, J.R. An approach to correlate tandem mass-spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976–989 (1994).

Elias, J.E. & Gygi, S.P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207–214 (2007).

Qian, W.J. et al. Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome. J. Proteome Res. 4, 53–62 (2005).

Kim, S., Gupta, N. & Pevzner, P.A. Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J. Proteome Res. 7, 3354–3363 (2008).

Viner, R.I., Williams, T.D. & Schoneich, C. Peroxynitrite modification of protein thiols: oxidation, nitrosylation, and S-glutathiolation of functionally important cysteine residue(s) in the sarcoplasmic reticulum Ca-ATPase. Biochemistry 38, 12408–12415 (1999).

Knoefler, D. et al. Quantitative in vivo redox sensors uncover oxidative stress as an early event in life. Mol. Cell 47, 767–776 (2012).