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Review

Top-down mass spectrometry of integral membrane proteins

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Pages 585-596 | Published online: 09 Jan 2014

References

  • Nedelkov D. Population proteomics: addressing protein diversity in humans. Expert Rev. Proteomics2(3), 315–324 (2005).
  • Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. Identification of post-translational modifications by blind search of mass spectra. Nat. Biotechnol.23(12), 1562–1567 (2005).
  • Savitski MM, Nielsen ML, Zubarev. RA. ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures. Mol. Cell Proteomics5(5), 935–948 (2006).
  • Fischle W, Wang Y, Allis CD. Binary switches and modification cassettes in histone biology and beyond. Nature425(6957), 475–479 (2003).
  • Gómez SM, Nishio JN, Faull KF, Whitelegge JP. The chloroplast grana proteome defined by intact mass measurements from LC-MS. Mol. Cell Proteomics1(1), 46–59 (2002).
  • Wu CC, MacCoss MJ, Howell KE, Yates JR 3rd. A method for the comprehensive proteomic analysis of membrane proteins. Nat. Biotechnol.21(5), 532–538 (2003).
  • Blonder J, Conrads TP, Yu LR et al. A detergent- and cyanogen bromide-free method for integral membrane proteomics: application to halobacterium purple membranes and the human epidermal membrane proteome. Proteomics4(1), 31–45 (2004).
  • Schey KL, Papac DI, Knapp DR, Crouch RK. Matrix-assisted laser desorption mass spectrometry of rhodopsin and bacteriorhodopsin. Biophys. J.63(5), 1240–1243 (1992).
  • le Maire M, Deschamps S, Moller JV, Le Caer JP, Rossier J. Electrospray ionization mass spectrometry on hydrophobic peptides electroeluted from sodium dodecyl sulfate–polyacrylamide gel electrophoresis application to the topology of the sarcoplasmic reticulum Ca2+ ATPase. Anal. Biochem.214(1), 50–57 (1993).
  • Schindler PA, Van Dorsselaer A, Falick AM. Analysis of hydrophobic proteins and peptides by electrospray ionization mass spectrometry. Anal. Biochem.213(2), 256–263 (1993).
  • Whitelegge JP, Gundersen C, Faull KF. Electrospray-ionization mass spectrometry of intact intrinsic membrane proteins. Protein Sci.7(6), 1423–1430 (1998).
  • Mørtz E, O’Connor PB, Roepstorff P et al. Sequence tag identification of intact proteins by matching tandem mass spectral data against sequence databases. Proc. Natl Acad. Sci. USA93(16), 8264–8267 (1996).
  • Fearnley IM, Walker JE. Analysis of hydrophobic proteins and peptides by electrospray ionization MS. Biochem. Soc. Trans.24(3), 912–917 (1996).
  • Kelleher NL, Lin HY, Valaskovic GA, Aaserud DJ, Fridriksson EK, McLafferty FW. Top down versus bottom up protein characterization by tandem high-resolution mass spectrometry. J. Am. Chem. Soc.121(4), 806–812 (1999).
  • Whitelegge JP. HPLC and mass spectrometry of intrinsic membrane proteins. Methods Mol. Biol.251, 323–340 (2004).
  • Tarr GE, Crabb JW. Reverse-phase high-performance liquid chromatography of hydrophobic proteins and fragments thereof. Anal. Biochem.131(1), 99–107 (1983).
  • Whitelegge JP. Tandem mass spectrometry of integral membrane proteins for top-down proteomics. Trends Anal. Chem.24, 576–582 (2005).
  • Whitelegge JP, le Coutre J, Lee JC et al. Towards the bilayer proteome, electrospray-ionization mass spectrometry of large intact transmembrane protein. Proc. Natl Acad. Sci. USA96(19), 10695–10698 (1999).
  • Turk E, Kim O, le Coutre J et al. Molecular characterization of Vibrio parahaemolyticus vSGLT: a model for sodium-coupled sugar cotransporters. J. Biol. Chem.275(33), 25711–25716 (2000).
  • Whitelegge JP, Aguilera R, Zhang H, Taylor R, Cramer WA. Full subunit coverage liquid chromatography electrospray-ionization mass spectrometry (LCMS+) of an oligomeric membrane protein: cytochrome b6f complex from spinach and the cyanobacterium, M. laminosus. Mol. Cell Proteomics1(10), 816–827 (2002).
  • Kurisu G, Zhang H, Smith JL, Cramer WA. Structure of the cytochrome b(6)f complex of oxygenic photosynthesis: tuning the cavity. Science302(5647), 1009–1014 (2003).
  • Stroebel D, Choquet Y, Popot JL, Picot D. An atypical heme in the cytochrome b(6)f complex. Nature426(6965), 413–418 (2003).
  • Whitelegge JP, Gómez SM, Faull KF. Proteomics of membrane proteins. Adv. Protein Chem.65, 271–307 (2003).
  • Schagger H, Cramer WA, von Jagow G. Analysis of molecular masses and oligomeric states of protein complexes by blue native electrophoresis and isolation of membrane protein complexes by two-dimensional native electrophoresis. Anal. Biochem.217(2), 220–230 (1994).
  • Wessel D, Flugge UI. A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal. Biochem.138(1), 141–143 (1984).
  • Kelleher NL. Top-down proteomics. Anal. Chem.76(11), 197A–203A (2004).
  • Bogdanov B, Smith RD. Proteomics by FTICR mass spectrometry: top down and bottom up. Mass Spectrom. Rev.24(2), 168–200 (2005).
  • Cooper HJ, Hakansson K, Marshall AG. The role of electron-capture dissociation in biomolecular analysis. Mass Spectrom. Rev.24(2), 201–222 (2005).
  • Reid GE, McLuckey SA. ‘Top down’ protein characterization via tandem mass spectrometry. J. Mass Spectrom.37(7), 63–75, (2002).
  • Breuker K, Oh H, Lin C, Carpenter BK, McLafferty FW. Nonergodic and conformational control of the electron capture dissociation of protein cations. Proc. Natl Acad. Sci. USA101(39), 14011–14016 (2004).
  • Whitelegge JP. Thylakoid membrane proteomics. Photosyn. Res.78(3), 265–277 (2003).
  • Whitelegge JP, Laganowsky A, Nishio J, Souda P, Zhang H, Cramer WA. Sequencing covalent modifications of membrane proteins. J. Exp. Bot.57(7), 1515–1522 (2006).
  • Whitelegge JP. Tandem mass spectrometry of integral membrane proteins for top-down proteomics. Trends Anal. Chem.24, 576–582 (2005).
  • Carroll J, Fearnley IM, Skehel JM, Shannon RJ, Hirst J, Walker JE. Bovine complex I is a complex of forty-five different subunits. J. Biol. Chem. (2006) (In Press).
  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J. Mol. Biol.215(3), 403–410 (1990).
  • Taylor GK, Kim YB, Forbes AJ, Meng F, McCarthy R, Kelleher NL. Web and database software for identification of intact proteins using ‘top down’ mass spectrometry. Anal. Chem.75(16), 4081–4086 (2003).
  • Horn DM, Zubarev RA, McLafferty FW. Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J. Am. Soc. Mass Spectrom.11(4), 320–332 (2000).
  • Chen L, Sze SK, Yang H. Automated intensity descent algorithm for interpretation of complex high-resolution mass spectra. Anal. Chem.78(14), 5006–5018 (2006).
  • Pesavento JJ, Kim YB, Taylor GK, Kelleher NL. Shotgun annotation of histone modifications: a new approach for streamlined characterization of proteins by top down mass spectrometry. J. Am. Soc. Mass Spectrom.126(11), 3386–7 (2004).
  • Gauthier JW, Trautman TR, Jacobsen DB. Sustained off-resonance irradiation for collision-activated dissociation involving Fourier transform mass spectrometry. Collision-activated dissociation technique that emulates infrared multiphoton dissociation. Anal. Chim. Acta246, 211–225 (1991).
  • Zubarev RA, Kelleher NL, McLafferty FW. Electron capture dissociation of multiply charged protein cations. A nonergodic process. J. Am. Chem. Soc.120(13), 3265–3266 (1998).
  • Silivra OA, Kjeldsen F, Ivonin IA, Zubarev RA. Electron capture dissociation of polypeptides in a three-dimensional quadrupole ion trap: implementation and first results. J. Am. Soc. Mass Spectrom.16(1), 22–7, (2005).
  • Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl Acad. Sci. USA101(26), 9528–9533 (2004).
  • Mirgorodskaya E, Roepstorff P, Zubarev R. Localization of O-glycosylation sites in peptides by electron capture dissociation in a Fourier transform mass spectrometer. Anal. Chem.71(20), 4431–4436 (1999).
  • Kelleher NL, Zubarev RA, Bush K et al. Localization of labile post-translational modifications by electron capture dissociation: the case of γ-carboxyglutamic acid. Anal. Chem.71(19), 4250–4253 (1999).
  • Schroeder MJ, Webb DJ, Shabanowitz J, Horwitz AF, Hunt DF. Methods for the detection of paxillin post-translational modifications and interacting proteins by mass spectrometry. J. Proteome Res.4(5), 1832–1841 (2005).
  • McLafferty FW, Horn DM, Breuker K et al. Electron-capture dissociation of gaseous multiply charged ions by Fourier-transform ion cyclotron resonance. J. Am. Soc. Mass Spectrom.12(3), 245–249 (2001).
  • Hakansson K, Chalmers MJ, Quinn JP, McFarland MA, Hendrickson CL, Marshall AG. Combined electron capture and infrared multiphoton dissociation for multistage MS/MS in a Fourier transform ion cyclotron resonance mass spectrometer. Anal. Chem.75(13), 3256–3262 (2003).
  • Makarov A. Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis. Anal. Chem.72(6), 1156–1162 (2000).
  • Hu Q, Noll RJ, Li H, Makarov A, Hardman M, Cooks G. The orbitrap: a new mass spectrometer. J. Mass Spectrom.40(4), 430–443 (2005).
  • Marshall AG, Hendrickson CL, Jackson GS. Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom. Rev.17(1), 1–35 (1998).
  • Macek B, Waanders LF, Olsen JV, Mann M. Top-down protein sequencing and MS3 on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer. Mol. Cell Proteomics5(5), 949–958 (2006).
  • Henry KD, Williams ER, Wang BH, McLafferty FW, Shabanowitz J, Hunt DF. Fourier-transform mass spectrometry of large molecules by electrospray ionization. Proc. Natl Acad. Sci. USA86(23), 9075–9078 (1989).
  • Loo JA, Udseth HR, Smith RD. Peptide and protein analysis by electrospray ionization-mass spectrometry and capillary electrophoresis–mass spectrometry. Anal. Biochem.179(2), 404–412 (1989).
  • Premstaller A, Oberacher H, Walcher W et al. High-performance liquid chromatography-electrospray ionization mass spectrometry using monolithic capillary columns for proteomic studies. Anal. Chem.73(11), 2390–2396 (2001).
  • Martosella J, Zolotarjova N, Liu H, Moyer SC, Perkins PD, Boyes BE. High recovery HPLC separation of lipid rafts for membrane proteome analysis. J. Proteome Res.5(6), 1301–1312 (2006).
  • Kjeldsen F, Haselmann KF, Budnik BA, Sorensen ES, Zubarev RA. Complete characterization of post-translational modification sites in the bovine milk protein PP3 by tandem mass spectrometry with electron capture dissociation as the last stage. Anal. Chem.75(10), 2355–2361 (2003).
  • Wu SL, Kim J, Hancock WS, Karger B. Extended range proteomic analysis (ERPA): a new and sensitive LC-MS platform for high sequence coverage of complex proteins with extensive post-translational modifications-comprehensive analysis of β-casein and epidermal growth factor receptor (EGFR). J. Proteome Res.4(4), 1155–1170 (2005).
  • Du Y, Parks BA, Sohn S, Kwast KE, Kelleher NL. Top-down approaches for measuring expression ratios of intact yeast proteins using Fourier transform mass spectrometry. Anal. Chem.78(3), 686–694 (2006).
  • Whitelegge JP, Katz JE, Pihakari KA et al. Subtle modification of isotope ratio proteomics; an integrated strategy for expression proteomics. Phytochemistry65(11), 1507–1515 (2004).
  • Senko MW, Hendrickson CL, Pasa-Tolic L et al. Electrospray ionization Fourier transform ion cyclotron resonance at 9.4 T. Rapid Commun. Mass Spectrom.10(14), 1824–1828 (1996).
  • Olsen JV, de Godoy LM, Li G et al. Parts per million mass accuracy on an orbitrap mass spectrometer via lock mass injection into a C-trap. Mol. Cell Proteomics4(12), 2010–2021 (2005).
  • Ruotolo BT, Giles K, Campuzano I, Sandercock AM, Bateman RH, Robinson CV. Evidence for macromolecular protein rings in the absence of bulk water. Science310(5754), 1658–1661 (2005).
  • Robinson EW, Leib RD, Williams ER. The role of conformation on electron capture dissociation of ubiquitin. J. Am. Soc. Mass Spectrom. (2006) (In Press).

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