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Top-Down Proteomics

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Manual of Cardiovascular Proteomics

Abstract

The field of proteomics, particularly top-down mass spectrometry (MS), holds great promise for cardiovascular research and diagnosis. Top-down MS provides a “bird’s eye view” of the entire protein. This is in contrast to bottom-up MS, which analyzes peptides. By studying intact proteins, more information can be gleaned. In particular, top-down proteomics provides valuable insights into what modifications are present on a protein of interest, including PTMs and sequence variations, even when a priori knowledge is lacking. PTMs, such as phosphorylation, have increasingly been linked to numerous cardiovascular diseases. Furthermore, changes in the expression levels of certain proteins have also been linked to disease. Top-down MS is able to quantify these changes, even when doing so necessitates distinguishing between various biologically relevant isoforms and proteoforms, which have proven difficult to differentiate using other methods. This chapter will explore how to prepare samples for top-down MS, the instrumentation required, data analysis, current applications, and future directions of this valuable technique.

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References

  1. Gregorich ZR, Chang YH, Ge Y. Proteomics in heart failure: top-down or bottom-up? Eur J Physiol. 2014;466(6):1199–209. doi:10.1007/s00424-014-1471-9.

    Article  CAS  Google Scholar 

  2. Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature. 2003;422(6928):198–207. doi:10.1038/nature01511.

    Article  CAS  PubMed  Google Scholar 

  3. Arrell DK, Neverova I, Van Eyk JE. Cardiovascular proteomics: evolution and potential. Circ Res. 2001;88(8):763–73.

    Article  CAS  PubMed  Google Scholar 

  4. Steen H, Mann M. The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol. 2004;5(9):699–711. doi:10.1038/nrm1468.

    Article  CAS  PubMed  Google Scholar 

  5. Zhang H, Ge Y. Comprehensive analysis of protein modifications by top-down mass spectrometry. Circ Cardiovasc Genet. 2011;4(6):711. doi:10.1161/CIRCGENETICS.110.957829.

    Article  PubMed  PubMed Central  Google Scholar 

  6. Smith LM, Kelleher NL, Consortium for Top Down P. Proteoform: a single term describing protein complexity. Nat Methods. 2013;10(3):186–7. doi:10.1038/nmeth.2369.

    Article  Google Scholar 

  7. Jin W, Brown AT, Murphy AM. Cardiac myofilaments: from proteome to pathophysiology. Proteomics Clin Appl. 2008;2(6):800–10. doi:10.1002/prca.200780075.

    Article  CAS  PubMed  Google Scholar 

  8. Siuti N, Kelleher NL. Decoding protein modifications using top-down mass spectrometry. Nat Methods. 2007;4(10):817–21. doi:10.1038/nmeth1097.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Zhang J, Dong X, Hacker TA, Ge Y. Deciphering modifications in swine cardiac troponin I by top-down high-resolution tandem mass spectrometry. J Am Soc Mass Spectrom. 2010;21(6):940–8. doi:10.1016/j.jasms.2010.02.005.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Zhang J, Guy MJ, Norman HS, Chen YC, Xu Q, Dong X, Guner H, Wang S, Kohmoto T, Young KH, Moss RL, Ge Y. Top-down quantitative proteomics identified phosphorylation of cardiac troponin I as a candidate biomarker for chronic heart failure. J Proteome Res. 2011;10(9):4054–65. doi:10.1021/pr200258m.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Peng Y, Gregorich ZR, Valeja SG, Zhang H, Cai W, Chen YC, Guner H, Chen AJ, Schwahn DJ, Hacker TA, Liu X, Ge Y. Top-down proteomics reveals concerted reductions in myofilament and Z-disc protein phosphorylation after acute myocardial infarction. Mol Cell Proteom. 2014;13(10):2752–64. doi:10.1074/mcp.M114.040675.

    Article  CAS  Google Scholar 

  12. Dong X, Sumandea CA, Chen YC, Garcia-Cazarin ML, Zhang J, Balke CW, Sumandea MP, Ge Y. Augmented phosphorylation of cardiac troponin I in hypertensive heart failure. J Biol Chem. 2012;287(2):848–57. doi:10.1074/jbc.M111.293258.

    Article  CAS  PubMed  Google Scholar 

  13. Wilm M, Mann M. Analytical properties of the nanoelectrospray ion source. Anal Chem. 1996;68(1):1–8.

    Article  CAS  PubMed  Google Scholar 

  14. Gregorich ZR, Ge Y. Top-down proteomics in health and disease: challenges and opportunities. Proteomics. 2014;14(10):1195–210. doi:10.1002/pmic.201300432.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Xiu L, Valeja SG, Alpert AJ, Jin S, Ge Y. Effective protein separation by coupling hydrophobic interaction and reverse phase chromatography for top-down proteomics. Anal Chem. 2014;86(15):7899–906. doi:10.1021/ac501836k.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Chang YH, Gregorich ZR, Chen AJ, Hwang L, Guner H, Yu D, Zhang J, Ge Y. New mass-spectrometry-compatible degradable surfactant for tissue proteomics. J Proteome Res. 2015;14(3):1587–99. doi:10.1021/pr5012679.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Chen EI, McClatchy D, Park SK, Yates 3rd JR. Comparisons of mass spectrometry compatible surfactants for global analysis of the mammalian brain proteome. Anal Chem. 2008;80(22):8694–701. doi:10.1021/ac800606w.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Meng F, Cargile BJ, Patrie SM, Johnson JR, McLoughlin SM, Kelleher NL. Processing complex mixtures of intact proteins for direct analysis by mass spectrometry. Anal Chem. 2002;74(13):2923–9.

    Article  CAS  PubMed  Google Scholar 

  19. Whitelegge J, Halgand F, Souda P, Zabrouskov V. Top-down mass spectrometry of integral membrane proteins. Expert Rev Proteomics. 2006;3(6):585–96. doi:10.1586/14789450.3.6.585.

    Article  CAS  PubMed  Google Scholar 

  20. Carroll J, Fearnley IM, Walker JE. Definition of the mitochondrial proteome by measurement of molecular masses of membrane proteins. Proc Natl Acad Sci U S A. 2006;103(44):16170–5. doi:10.1073/pnas.0607719103.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Laganowsky A, Reading E, Hopper JT, Robinson CV. Mass spectrometry of intact membrane protein complexes. Nat Protoc. 2013;8(4):639–51. doi:10.1038/nprot.2013.024.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Valeja SG, Xiu L, Gregorich ZR, Guner H, Jin S, Ge Y. Three dimensional liquid chromatography coupling ion exchange chromatography/hydrophobic interaction chromatography/reverse phase chromatography for effective protein separation in top-down proteomics. Anal Chem. 2015;87(10):5363–71. doi:10.1021/acs.analchem.5b00657.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Fridriksson EK, Baird B, McLafferty FW. Electrospray mass spectra from protein electroeluted from sodium dodecylsulfate polyacrylamide gel electrophoresis gels. J Am Soc Mass Spectrom. 1999;10(5):453–5. doi:10.1016/S1044-0305(99)00012-4.

    Article  CAS  PubMed  Google Scholar 

  24. Neverova I, Van Eyk JE. Role of chromatographic techniques in proteomic analysis. J Chromatogr B Analyt Technol Biomed Life Sci. 2005;815(1–2):51–63. doi:10.1016/j.jchromb.2004.11.009.

    Article  CAS  PubMed  Google Scholar 

  25. Hage DS. Affinity chromatography: a review of clinical applications. Clin Chem. 1999;45(5):593–615.

    CAS  PubMed  Google Scholar 

  26. Ayaz-Guner S, Zhang J, Li L, Walker JW, Ge Y. In vivo phosphorylation site mapping in mouse cardiac troponin I by high resolution top-down electron capture dissociation mass spectrometry: Ser22/23 are the only sites basally phosphorylated. Biochemistry. 2009;48(34):8161–70. doi:10.1021/bi900739f.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Doucette AA, Tran JC, Wall MJ, Fitzsimmons S. Intact proteome fractionation strategies compatible with mass spectrometry. Expert Rev Proteomics. 2011;8(6):787–800. doi:10.1586/epr.11.67.

    Article  CAS  PubMed  Google Scholar 

  28. Chen X, Ge Y. Ultrahigh pressure fast size exclusion chromatography for top-down proteomics. Proteomics. 2013;13(17):2563–6. doi:10.1002/pmic.201200594.

    Article  CAS  PubMed  Google Scholar 

  29. Kellie JF, Tran JC, Lee JE, Ahlf DR, Thomas HM, Ntai I, Catherman AD, Durbin KR, Zamdborg L, Vellaichamy A, Thomas PM, Kelleher NL. The emerging process of Top down mass spectrometry for protein analysis: biomarkers, protein-therapeutics, and achieving high throughput. Mol Biosyst. 2010;6(9):1532–9. doi:10.1039/c000896f.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Sluyterman LAE. Chromatofocusing – a preparative protein separation method. Trends Biochem Sci. 1982;7(5):168–70. doi:10.1016/0968-0004(82)90129-3.

    Article  CAS  Google Scholar 

  31. Righetti PG. Isoelectric focusing: theory, methodology, and applications. Amsterdam: Elsevier; 1983.

    Google Scholar 

  32. Zhang J, Roth MJ, Chang AN, Plymire DA, Corbett JR, Greenberg BM, Patrie SM. Top-down mass spectrometry on tissue extracts and biofluids with isoelectric focusing and superficially porous silica liquid chromatography. Anal Chem. 2013;85(21):10377–84. doi:10.1021/ac402394w.

    Article  CAS  PubMed  Google Scholar 

  33. Tran JC, Doucette AA. Gel-eluted liquid fraction entrapment electrophoresis: an electrophoretic method for broad molecular weight range proteome separation. Anal Chem. 2008;80(5):1568–73. doi:10.1021/ac702197w.

    Article  CAS  PubMed  Google Scholar 

  34. Vellaichamy A, Tran JC, Catherman AD, Lee JE, Kellie JF, Sweet SM, Zamdborg L, Thomas PM, Ahlf DR, Durbin KR, Valaskovic GA, Kelleher NL. Size-sorting combined with improved nanocapillary liquid chromatography-mass spectrometry for identification of intact proteins up to 80 kDa. Anal Chem. 2010;82(4):1234–44. doi:10.1021/ac9021083.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Tran JC, Zamdborg L, Ahlf DR, Lee JE, Catherman AD, Durbin KR, Tipton JD, Vellaichamy A, Kellie JF, Li M, Wu C, Sweet SM, Early BP, Siuti N, LeDuc RD, Compton PD, Thomas PM, Kelleher NL. Mapping intact protein isoforms in discovery mode using top-down proteomics. Nature. 2011;480(7376):254–8. doi:10.1038/nature10575.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Catherman AD, Durbin KR, Ahlf DR, Early BP, Fellers RT, Tran JC, Thomas PM, Kelleher NL. Large-scale top-down proteomics of the human proteome: membrane proteins, mitochondria, and senescence. Mol Cell Proteom. 2013;12(12):3465–73. doi:10.1074/mcp.M113.030114.

    Article  CAS  Google Scholar 

  37. Ge Y, Lawhorn BG, ElNaggar M, Strauss E, Park JH, Begley TP, McLafferty FW. Top down characterization of larger proteins (45 kDa) by electron capture dissociation mass spectrometry. J Am Chem Soc. 2002;124(4):672–8.

    Article  CAS  PubMed  Google Scholar 

  38. Scherperel G, Reid GE. Emerging methods in proteomics: top-down protein characterization by multistage tandem mass spectrometry. Analyst. 2007;132(6):500–6. doi:10.1039/b618499p.

    Article  CAS  PubMed  Google Scholar 

  39. Zubarev RA, Kelleher NL, McLafferty FW. Electron capture dissociation of multiply charged protein cations. A nonergodic process. J Am Chem Soc. 1998;120(13):3265–6.

    Article  CAS  Google Scholar 

  40. 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 U S A. 2004;101(26):9528–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Iavarone AT, Paech K, Williams ER. Effects of charge state and cationizing agent on the electron capture dissociation of a peptide. Anal Chem. 2004;76(8):2231–8. doi:10.1021/ac035431p.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Marshall AG, Hendrickson CL, Jackson GS. Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom Rev. 1998;17(1):1–35. doi:10.1002/(SICI)1098-2787(1998)17:1<1::AID-MAS1>3.0.CO;2-K.

    Article  CAS  PubMed  Google Scholar 

  43. Mann M, Kelleher NL. Precision proteomics: the case for high resolution and high mass accuracy. Proc Natl Acad Sci U S A. 2008;105(47):18132–8. doi:10.1073/pnas.0800788105.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Makarov A. Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis. Anal Chem. 2000;72(6):1156–62.

    Article  CAS  PubMed  Google Scholar 

  45. Cotter RJ. Time-of-flight mass-spectrometry – preface. ACS Symp Ser. 1994;549:R9–R12.

    Google Scholar 

  46. Coelho Graca D, Lescuyer P, Clerici L, Tsybin YO, Hartmer R, Meyer M, Samii K, Hochstrasser D, Scherl A. Electron transfer dissociation mass spectrometry of hemoglobin on clinical samples. J Am Soc Mass Spectrom. 2012;23(10):1750–6.

    Article  CAS  PubMed  Google Scholar 

  47. Wells JM, McLuckey SA. Collision-induced dissociation (CID) of peptides and proteins. Methods Enzymol. 2005;402:148–85. doi:10.1016/S0076-6879(05)02005-7.

    Article  CAS  PubMed  Google Scholar 

  48. Olsen JV, Macek B, Lange O, Makarov A, Horning S, Mann M. Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods. 2007;4(9):709–12. doi:10.1038/nmeth1060.

    Article  CAS  PubMed  Google Scholar 

  49. Little DP, Speir JP, Senko MW, O'Connor PB, McLafferty FW. Infrared multiphoton dissociation of large multiply charged ions for biomolecule sequencing. Anal Chem. 1994;66(18):2809–15.

    Article  CAS  PubMed  Google Scholar 

  50. Chaurand P, Luetzenkirchen F, Spengler B. Peptide and protein identification by matrix-assisted laser desorption ionization (MALDI) and MALDI-post-source decay time-of-flight mass spectrometry. J Am Soc Mass Spectrom. 1999;10(2):91–103. doi:10.1016/S1044-0305(98)00145-7.

    Article  CAS  PubMed  Google Scholar 

  51. Shaw JB, Li W, Holden DD, Zhang Y, Griep-Raming J, Fellers RT, Early BP, Thomas PM, Kelleher NL, Brodbelt JS. Complete protein characterization using top-down mass spectrometry and ultraviolet photodissociation. J Am Chem Soc. 2013;135(34):12646–51. doi:10.1021/ja4029654.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Bakhtiar R, Guan Z. Electron capture dissociation mass spectrometry in characterization of post-translational modifications. Biochem Biophys Res Commun. 2005;334(1):1–8. doi:10.1016/j.bbrc.2005.05.138.

    Article  CAS  PubMed  Google Scholar 

  53. Ge Y, Rybakova IN, Xu Q, Moss RL. Top-down high-resolution mass spectrometry of cardiac myosin binding protein C revealed that truncation alters protein phosphorylation state. Proc Natl Acad Sci U S A. 2009;106(31):12658–63. doi:10.1073/pnas.0813369106.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Mao Y, Valeja SG, Rouse JC, Hendrickson CL, Marshall AG. Top-down structural analysis of an intact monoclonal antibody by electron capture dissociation-Fourier transform ion cyclotron resonance-mass spectrometry. Anal Chem. 2013;85(9):4239–46. doi:10.1021/ac303525n.

    Article  CAS  PubMed  Google Scholar 

  55. McAlister GC, Phanstiel D, Good DM, Berggren WT, Coon JJ. Implementation of electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer. Anal Chem. 2007;79(10):3525–34. doi:10.1021/ac070020k.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. McLafferty FW, Breuker K, Jin M, Han X, Infusini G, Jiang H, Kong X, Begley TP. Top-down MS, a powerful complement to the high capabilities of proteolysis proteomics. FEBS J. 2007;274(24):6256–68. doi:10.1111/j.1742-4658.2007.06147.x.

    Article  CAS  PubMed  Google Scholar 

  57. Han X, Jin M, Breuker K, McLafferty FW. Extending top-down mass spectrometry to proteins with masses greater than 200 kilodaltons. Science. 2006;314(5796):109–12. doi:10.1126/science.1128868.

    Article  CAS  PubMed  Google Scholar 

  58. Peng Y, Chen X, Zhang H, Xu Q, Hacker TA, Ge Y. Top-down targeted proteomics for deep sequencing of tropomyosin isoforms. J Proteome Res. 2013;12(1):187–98. doi:10.1021/pr301054n.

    Article  CAS  PubMed  Google Scholar 

  59. Compton PD, Zamdborg L, Thomas PM, Kelleher NL. On the scalability and requirements of whole protein mass spectrometry. Anal Chem. 2011;83(17):6868–74. doi:10.1021/ac2010795.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Valeja SG, Tipton JD, Emmett MR, Marshall AG. New reagents for enhanced liquid chromatographic separation and charging of intact protein ions for electrospray ionization mass spectrometry. Anal Chem. 2010;82(17):7515–9. doi:10.1021/ac1016858.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Miladinovic SM, Fornelli L, Lu Y, Piech KM, Girault HH, Tsybin YO. In-spray supercharging of peptides and proteins in electrospray ionization mass spectrometry. Anal Chem. 2012;84(11):4647–51. doi:10.1021/ac300845n.

    Article  CAS  PubMed  Google Scholar 

  62. Kou Q, Wu S, Liu X. A new scoring function for top-down spectral deconvolution. BMC Genomics. 2014;15:1140. doi:10.1186/1471-2164-15-1140.

    Article  PubMed  PubMed Central  Google Scholar 

  63. Horn DM, Zubarev RA, McLafferty FW. Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J Am Soc Mass Spectrom. 2000;11(4):320–32.

    Article  CAS  PubMed  Google Scholar 

  64. Jaitly N, Mayampurath A, Littlefield K, Adkins JN, Anderson GA, Smith RD. Decon2LS: an open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinformatics. 2009;10:87. doi:10.1186/1471-2105-10-87.

    Article  PubMed  PubMed Central  Google Scholar 

  65. Mayampurath AM, Jaitly N, Purvine SO, Monroe ME, Auberry KJ, Adkins JN, Smith RD. DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. Bioinformatics. 2008;24(7):1021–3. doi:10.1093/bioinformatics/btn063.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Guner H, Close PL, Cai W, Zhang H, Peng Y, Gregorich ZR, Ge Y. MASH Suite: a user-friendly and versatile software interface for high-resolution mass spectrometry data interpretation and visualization. J Am Soc Mass Spectrom. 2014;25(3):464–70. doi:10.1007/s13361-013-0789-4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Liu X, Inbar Y, Dorrestein PC, Wynne C, Edwards N, Souda P, Whitelegge JP, Bafna V, Pevzner PA. Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach. Mol Cell Proteom. 2010;9(12):2772–82. doi:10.1074/mcp.M110.002766.

    Article  CAS  Google Scholar 

  68. LeDuc RD, Taylor GK, Kim YB, Januszyk TE, Bynum LH, Sola JV, Garavelli JS, Kelleher NL. ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry. Nucleic Acids Res. 2004;32(Web server issue):W340–5. doi:10.1093/nar/gkh447.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Fellers RT, Greer JB, Early BP, Yu X, LeDuc RD, Kelleher NL, Thomas PM. ProSight Lite: graphical software to analyze top-down mass spectrometry data. Proteomics. 2015;15(7):1235–8. doi:10.1002/pmic.201570050.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Tsai YS, Scherl A, Shaw JL, MacKay CL, Shaffer SA, Langridge-Smith PR, Goodlett DR. Precursor ion independent algorithm for top-down shotgun proteomics. J Am Soc Mass Spectrom. 2009;20(11):2154–66. doi:10.1016/j.jasms.2009.07.024.

    Article  CAS  PubMed  Google Scholar 

  71. Karabacak NM, Li L, Tiwari A, Hayward LJ, Hong P, Easterling ML, Agar JN. Sensitive and specific identification of wild type and variant proteins from 8 to 669 kDa using top-down mass spectrometry. Mol Cell Proteom. 2009;8(4):846–56. doi:10.1074/mcp.M800099-MCP200.

    Article  CAS  Google Scholar 

  72. Frank AM, Pesavento JJ, Mizzen CA, Kelleher NL, Pevzner PA. Interpreting top-down mass spectra using spectral alignment. Anal Chem. 2008;80(7):2499–505. doi:10.1021/ac702324u.

    Article  CAS  PubMed  Google Scholar 

  73. Liu X, Sirotkin Y, Shen Y, Anderson G, Tsai YS, Ting YS, Goodlett DR, Smith RD, Bafna V, Pevzner PA. Protein identification using top-down. Mol Cell Proteom. 2012;11(6):M111 008524. doi:10.1074/mcp.M111.008524.

    Article  Google Scholar 

  74. Cai W, Guner H, Chen AJ, Ayaz-Guner S, Peng Y, Valeja SG, Liu Z, Gregorich Z, Ge Y. MASH Suite Pro: a comprehensive software tool for top-down proteomics. Mole Cell Proteomics. 2016;15(2):703–14. doi: 10.1074/mcp.O115.054387.

    Google Scholar 

  75. Edwards RL, Griffiths P, Bunch J, Cooper HJ. Top-down proteomics and direct surface sampling of neonatal dried blood spots: diagnosis of unknown hemoglobin variants. J Am Soc Mass Spectrom. 2012;23(11):1921–30. doi:10.1007/s13361-012-0477-9.

    Article  CAS  PubMed  Google Scholar 

  76. Theberge R, Infusini G, Tong W, McComb ME, Costello CE. Top-down analysis of small plasma proteins using an LTQ-orbitrap. Potential for mass spectrometry-based clinical assays for transthyretin and hemoglobin. Int J Mass Spectrom. 2011;300(2–3):130–42. doi:10.1016/j.ijms.2010.08.012.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Zabrouskov V, Ge Y, Schwartz J, Walker JW. Unraveling molecular complexity of phosphorylated human cardiac troponin I by top down electron capture dissociation/electron transfer dissociation mass spectrometry. Mol Cell Proteom. 2008;7(10):1838–49. doi:10.1074/mcp.M700524-MCP200.

    Article  CAS  Google Scholar 

  78. Peng Y, Yu D, Gregorich Z, Chen X, Beyer AM, Gutterman DD, Ge Y. In-depth proteomic analysis of human tropomyosin by top-down mass spectrometry. J Muscle Res Cell Motil. 2013;34(3–4):199–210. doi:10.1007/s10974-013-9352-y.

    Article  CAS  PubMed  Google Scholar 

  79. Hwang L, Ayaz-Guner S, Gregorich ZR, Cai W, Valeja SG, Jin S, Ge Y. Specific enrichment of phosphoproteins using functionalized multivalent nanoparticles. J Am Chem Soc. 2015;137(7):2432–5. doi:10.1021/ja511833y.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. McLuckey SA, Reid GE, Wells JM. Ion parking during ion/ion reactions in electrodynamic ion traps. Anal Chem. 2002;74(2):336–46.

    Article  CAS  PubMed  Google Scholar 

  81. Huang TY, McLuckey SA. Top-down protein characterization facilitated by ion/ion reactions on a quadrupole/time of flight platform. Proteomics. 2010;10(20):3577–88. doi:10.1002/pmic.201000187.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Copeland O, Nowak KJ, Laing NG, Ravenscroft G, Messer AE, Bayliss CR, Marston SB. Investigation of changes in skeletal muscle alpha-actin expression in normal and pathological human and mouse hearts. J Muscle Res Cell Motil. 2010;31(3):207–14. doi:10.1007/s10974-010-9224-7.

    Article  CAS  PubMed  Google Scholar 

  83. Chen YC, Ayaz-Guner S, Peng Y, Lane NM, Locher MR, Kohmoto T, Larsson L, Moss RL, Ge Y. Effective Top-down LC/MS+ method for assessing actin isoforms as a potential cardiac disease marker. Anal Chem. 2015;87(16):8399–406. doi:10.1021/acs.analchem.5b01745.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Sze SK, Ge Y, Oh H, McLafferty FW. Top-down mass spectrometry of a 29-kDa protein for characterization of any posttranslational modification to within one residue. Proc Natl Acad Sci U S A. 2002;99(4):1774–9. doi:10.1073/pnas.251691898.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Solaro RJ, van der Velden J. Why does troponin I have so many phosphorylation sites? Fact and fancy. J Mol Cell Cardiol. 2010;48(5):810–6. doi:10.1016/j.yjmcc.2010.02.014.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Huang L, Wolska BM, Montgomery DE, Burkart EM, Buttrick PM, Solaro RJ. Increased contractility and altered Ca(2+) transients of mouse heart myocytes conditionally expressing PKCbeta. Am J Physiol Cell Physiol. 2001;280(5):C1114–20.

    CAS  PubMed  Google Scholar 

  87. Goldspink PH, Montgomery DE, Walker LA, Urboniene D, McKinney RD, Geenen DL, Solaro RJ, Buttrick PM. Protein kinase Cepsilon overexpression alters myofilament properties and composition during the progression of heart failure. Circ Res. 2004;95(4):424–32. doi:10.1161/01.RES.0000138299.85648.92.

    Article  CAS  PubMed  Google Scholar 

  88. de Tombe PP. Myosin binding protein C in the heart. Circ Res. 2006;98(10):1234–6. doi:10.1161/01.RES.0000225873.63162.c4.

    Article  PubMed  Google Scholar 

  89. Barefield D, Sadayappan S. Phosphorylation and function of cardiac myosin binding protein-C in health and disease. J Mol Cell Cardiol. 2010;48(5):866–75. doi:10.1016/j.yjmcc.2009.11.014.

    Article  CAS  PubMed  Google Scholar 

  90. Gautel M, Zuffardi O, Freiburg A, Labeit S. Phosphorylation switches specific for the cardiac isoform of myosin binding protein-C: a modulator of cardiac contraction? EMBO J. 1995;14(9):1952–60.

    CAS  PubMed  PubMed Central  Google Scholar 

  91. Borges CR, Oran PE, Buddi S, Jarvis JW, Schaab MR, Rehder DS, Rogers SP, Taylor T, Nelson RW. Building multidimensional biomarker views of type 2 diabetes on the basis of protein microheterogeneity. Clin Chem. 2011;57(5):719–28. doi:10.1373/clinchem.2010.156976.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Steen H, Jebanathirajah JA, Rush J, Morrice N, Kirschner MW. Phosphorylation analysis by mass spectrometry: myths, facts, and the consequences for qualitative and quantitative measurements. Mol Cellular Proteom. 2006;5(1):172–81. doi:10.1074/mcp.M500135-MCP200.

    Article  CAS  Google Scholar 

  93. Gregorich ZR, Peng Y, Lane NM, Wolff JJ, Wang S, Guo W, Guner H, Doop J, Hacker TA, Ge Y. Comprehensive assessment of chamber-specific and transmural heterogeneity in myofilament protein phosphorylation by top-down mass spectrometry. J Mol Cell Cardiol. 2015;87:102–12. doi:10.1016/j.yjmcc.2015.08.007.

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Cellular and Molecular Pathology Training Program, University of Wisconsin-Madison, Madison, WI, 53706, USA

    Nicole M. Lane BS, BA & Ying Ge PhD

  2. Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA

    Nicole M. Lane BS, BA & Zachery R. Gregorich BS

  3. Molecular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI, 53706, USA

    Zachery R. Gregorich BS

  4. Human Proteomics Program, University of Wisconsin-Madison, 1300 University Ave., SMI 130, Madison, WI, 53706, USA

    Ying Ge PhD

Authors
  1. Nicole M. Lane BS, BA
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  2. Zachery R. Gregorich BS
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  3. Ying Ge PhD
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Corresponding author

Correspondence to Ying Ge PhD .

Editor information

Editors and Affiliations

  1. Division of Cardiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Giulio Agnetti

  2. Dept. of Physiology & Biophysics, University Mississippi Medical Center, Jackson, Mississippi, USA

    Merry L. Lindsey

  3. Division of Cardiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    D. Brian Foster

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© 2016 Springer International Publishing Switzerland

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Lane, N.M., Gregorich, Z.R., Ge, Y. (2016). Top-Down Proteomics. In: Agnetti, G., Lindsey, M., Foster, D. (eds) Manual of Cardiovascular Proteomics. Springer, Cham. https://doi.org/10.1007/978-3-319-31828-8_8

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  • DOI: https://doi.org/10.1007/978-3-319-31828-8_8

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