Top Down proteomics: Facts and perspectives

Biochemical and Biophysical Research Communications

Volumn 445, Issue 4, 2014, Pages 683-693

  Catherman, Adam D ^a   Skinner, Owen S ^a   Kelleher, Neil L ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE; PROTEIN;

ANALYTIC METHOD; ANALYZER; CAPILLARY ELECTROPHORESIS; CAPILLARY ZONE ELECTROPHORESIS; CHEMICAL STRUCTURE; FOURIER TRANSFORM MASS SPECTROMETRY; GEL ELECTROPHORESIS; HUMAN; HYDROPHOBIC INTERACTION CHROMATOGRAPHY; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; ION EXCHANGE; ISOELECTRIC FOCUSING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETER; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; REVERSED PHASE LIQUID CHROMATOGRAPHY; REVIEW; TOP DOWN PROTEOMICS; TUBE GEL ELECTROPHORESIS;

AMINO ACID SEQUENCE; ANIMALS; CHROMATOGRAPHY, LIQUID; ELECTROPHORESIS; EQUIPMENT DESIGN; HUMANS; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PROTEINS; PROTEOMICS;

EID: 84897140688     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2014.02.041     Document Type: Review

References (140)

1. J. Cox, and M. Mann Is proteomics the new genomics? Cell 130 2007 395 398
2. R. Aebersold, and M. Mann Mass spectrometry-based proteomics Nature 422 2003 198 207
3. N.L. Kelleher Top-down proteomics Anal. Chem. 76 2004 196A 203A
4. B.T. Chait Mass spectrometry: Bottom-up or top-down? Science 314 2006 65 66
5. L.M. Smith, and N.L. Kelleher Proteoform: a single term describing protein complexity Nat. Methods 10 2013 186 187
6. N. Siuti, M.J. Roth, C.A. Mizzen, N.L. Kelleher, and J.J. Pesavento Gene-specific characterization of human histone H2B by electron capture dissociation J. Proteome Res. 5 2006 233 239
7. M. Li, L. Jiang, and N.L. Kelleher Global histone profiling by LC-FTMS after inhibition and knockdown of deacetylases in human cells J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 877 2009 3885 3892
8. A. Resemann, D. Wunderlich, U. Rothbauer, B. Warscheid, H. Leonhardt, J. Fuchser, K. Kuhlmann, and D. Suckau Top-down de Novo protein sequencing of a 13.6 kDa camelid single heavy chain antibody by matrix-assisted laser desorption ionization-time-of-flight/time-of-flight mass spectrometry Anal. Chem. 82 2010 3283 3292
9. J. Zhang, M.J. Guy, H.S. Norman, Y.-C. Chen, Q. Xu, X. Dong, H. Guner, S. Wang, T. Kohmoto, K.H. Young, R.L. Moss, and Y. Ge Top-down quantitative proteomics identified phosphorylation of cardiac troponin I as a candidate biomarker for chronic heart failure J. Proteome Res. 10 2011 4054 4065
10. N.P. Barrera, S.C. Isaacson, M. Zhou, V.N. Bavro, A. Welch, T.A. Schaedler, M.A. Seeger, R.N. Miguel, V.M. Korkhov, H.W. van Veen, H. Venter, A.R. Walmsley, C.G. Tate, and C.V. Robinson Mass spectrometry of membrane transporters reveals subunit stoichiometry and interactions Nat. Methods 6 2009 585 587
11. J. Erales, B. Gontero, J. Whitelegge, and F. Halgand Mapping of a copper-binding site on the small CP12 chloroplastic protein of Chlamydomonas reinhardtii using top-down mass spectrometry and site-directed mutagenesis Biochem. J. 419 2009 75 82
12. J.F. Kellie, J.C. Tran, J.E. Lee, D.R. Ahlf, H.M. Thomas, I. Ntai, A.D. Catherman, K.R. Durbin, L. Zamdborg, A. Vellaichamy, P.M. Thomas, and N.L. Kelleher The emerging process of Top Down mass spectrometry for protein analysis: biomarkers, protein-therapeutics, and achieving high throughput Mol. Biosyst. 6 2010 1532 1539
13. A.L. Capriotti, C. Cavaliere, P. Foglia, R. Samperi, and A. Lagana Intact protein separation by chromatographic and/or electrophoretic techniques for top-down proteomics J. Chromatogr. A 1218 2011 8760 8776
14. C.M. Whitehouse, R.N. Dreyer, M. Yamashita, and J.B. Fenn Electrospray interface for liquid chromatographs and mass spectrometers Anal. Chem. 57 1985 675 679
15. J.R. Johnson, F.Y. Meng, A.J. Forbes, B.J. Cargile, and N.L. Kelleher Fourier-transform mass spectrometry for automated fragmentation and identification of 5-20 kDa proteins in mixtures Electrophoresis 23 2002 3217 3223
16. F.Y. Meng, B.J. Cargile, S.M. Patrie, J.R. Johnson, S.M. McLoughlin, and N.L. Kelleher Processing complex mixtures of intact proteins for direct analysis by mass spectrometry Anal. Chem. 74 2002 2923 2929
17. B.E. Chong, F. Yan, D.M. Lubman, and F.R. Miller Chromatofocusing nonporous reversed-phase high-performance liquid chromatography/electrospray ionization time-of-flight mass spectrometry of proteins from human breast cancer whole cell lysates: a novel two-dimensional liquid chromatography/mass spectrometry method Rapid Commun. Mass Spectrom. 15 2001 291 296
18. D.B. Wall, M.T. Kachman, S.Y. Gong, R. Hinderer, S. Parus, D.E. Misek, S.M. Hanash, and D.M. Lubman Isoelectric focusing nonporous RP HPLC: a two-dimensional liquid-phase separation method for mapping of cellular proteins with identification using MALDI-TOF mass spectrometry Anal. Chem. 72 2000 1099 1111
19. D.B. Wall, M.T. Kachman, S.Y.S. Gong, S.J. Parus, M.W. Long, and D.M. Lubman Isoelectric focusing nonporous silica reversed-phase high-performance liquid chromatography/electrospray ionization time-of-flight mass spectrometry: a three-dimensional liquid-phase protein separation method as applied to the human erythroleukemia cell-line Rapid Commun. Mass Spectrom. 15 2001 1649 1661
20. D.B. Wall, S.J. Parus, and D.M. Lubman Comparison of the capabilities of liquid isoelectric focusing-one-dimensional nonporous silica reversed-phase liquid chromatography-electrospray ionization time-of-flight mass spectrometry and liquid isoelectric focusing-one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis mass mapping for the analysis of intact protein molecular masses J. Chromatogr. B 763 2001 139 148
21. M.J. Roth, D.A. Plymire, A.N. Chang, J. Kim, E.M. Maresh, S.E. Larson, and S.M. Patrie Sensitive and reproducible intact mass analysis of complex protein mixtures with superficially porous capillary reversed-phase liquid chromatography mass spectrometry Anal. Chem. 83 2011 9586 9592
22. C.D. Wenger, M.T. Boyne II, J.T. Ferguson, D.E. Robinson, and N.L. Kelleher Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra Anal. Chem. 80 2008 8055 8063
23. J.E. Lee, J.F. Kellie, J.C. Tran, J.D. Tipton, A.D. Catherman, H.M. Thomas, D.R. Ahlf, K.R. Durbin, A. Vellaichamy, I. Ntai, A.G. Marshall, and N.L. Kelleher A robust two-dimensional separation for top-down tandem mass spectrometry of the low-mass proteome J. Am. Soc. Mass Spectrom. 20 2009 2183 2191
24. A. Vellaichamy, J.C. Tran, A.D. Catherman, J.E. Lee, J.F. Kellie, S.M.M. Sweet, L. Zamdborg, P.M. Thomas, D.R. Ahlf, K.R. Durbin, G.A. Valaskovic, and N.L. Kelleher Size-sorting combined with improved nanocapillary liquid chromatography-mass spectrometry for identification of intact proteins up to 80 kDa Anal. Chem. 82 2010 1234 1244
25. S.W. Lee, S.J. Berger, S. Martinovic, L. Pasa-Tolic, G.A. Anderson, Y.F. Shen, R. Zhao, and R.D. Smith Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR Proc. Natl. Acad. Sci. U.S.A. 99 2002 5942 5947
26. A.J. Alpert, and P.C. Andrews Cation-exchange chromatography of peptides on poly(2-sulfoethyl aspartamide)-silica J. Chromatogr. 443 1988 85 96
27. A.J. Alpert Hydrophobic interaction chromatography of peptides as an alternative to reversed-phase chromatography J. Chromatogr. 444 1988 269 274
28. J. Carroll, I.M. Fearnley, and J.E. Walker Definition of the mitochondrial proteome by measurement of molecular masses of membrane proteins Proc. Natl. Acad. Sci. U.S.A. 103 2006 16170 16175
29. J. Carroll, M.C. Altman, I.M. Fearnley, and J.E. Walker Identification of membrane proteins by tandem mass spectrometry of protein ions Proc. Natl. Acad. Sci. U.S.A. 104 2007 14330 14335
30. B.A. Garcia, J.J. Pesavento, C.A. Mizzen, and N.L. Kelleher Pervasive combinatorial modification of histone H3 in human cells Nat. Methods 4 2007 487 489
31. J.J. Pesavento, B.A. Garcia, J.A. Streeky, N.L. Kelleher, and C.A. Mizzen Mild performic acid oxidation enhances chromatographic and top down mass spectrometric analyses of histones Mol. Cell. Proteomics 6 2007 1510 1526
32. J.J. Pesavento, C.R. Bullock, R.D. Leduc, C.A. Mizzen, and N.L. Kelleher Combinatorial modification of human histone H4 quantitated by two-dimensional liquid chromatography coupled with top down mass spectrometry J. Biol. Chem. 283 2008 14927 14937
33. G.J. Opiteck, K.C. Lewis, J.W. Jorgenson, and R.J. Anderegg Comprehensive on-line LC/LC/MS of proteins Anal. Chem. 69 1997 1518 1524
34. K.M. Millea, I.S. Krull, S.A. Cohen, J.C. Gebler, and S.J. Berger Integration of multidimensional chromatographic protein separations with a combined "Top-Down" and "Bottom-Up" proteomic strategy J. Proteome Res. 5 2005 135 146
35. S. Sharma, D.C. Simpson, N. Tolić, N. Jaitly, A.M. Mayampurath, R.D. Smith, and L. Paša-Tolić Proteomic profiling of intact proteins using WAX-RPLC 2-D separations and FTICR mass spectrometry J. Proteome Res. 6 2006 602 610
36. B.A. Parks, L. Jiang, P.M. Thomas, C.D. Wenger, M.J. Roth, M.T. Boyne, P.V. Burke, K.E. Kwast, and N.L. Kelleher Top-down proteomics on a chromatographic time scale using linear ion trap Fourier transform hybrid mass spectrometers Anal. Chem. 79 2007 7984 7991
37. M.J. Roth, B.A. Parks, J.T. Ferguson, M.T. Boyne, and N.L. Kelleher "Proteotyping": population proteomics of human leukocytes using top down mass spectrometry Anal. Chem. 80 2008 2857 2866
38. S.M. Patrie, J.T. Ferguson, D.E. Robinson, D. Whipple, M. Rother, W.W. Metcalf, and N.L. Kelleher Top down mass spectrometry of <60-kDa proteins from Methanosarcina acetivorans using quadrupole FTMS with automated octopole collisionally activated dissociation Mol. Cell. Proteomics 5 2006 14 25
39. T. Rabilloud Two-dimensional gel electrophoresis in proteomics: Old, old fashioned, but it still climbs up the mountains Proteomics 2 2002 3 10
40. U.K. Laemmli Cleavage of structural proteins during assembly of head of bacteriophage T4 Nature 227 1970 680 685
41. A. Shevchenko, M. Wilm, O. Vorm, and M. Mann Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels Anal. Chem. 68 1996 850 858
42. M. Wilm, A. Shevchenko, T. Houthaeve, S. Breit, L. Schweigerer, T. Fotsis, and M. Mann Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry Nature 379 1996 466 469
43. S.P. Gygi, G.L. Corthals, Y. Zhang, Y. Rochon, and R. Aebersold Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology Proc. Natl. Acad. Sci. U.S.A. 97 2000 9390 9395
44. P. Davidsson, and C.L. Nilsson Peptide mapping of proteins in cerebrospinal fluid utilizing a rapid preparative two-dimensional electrophoretic procedure and matrix-assisted laser desorption/ionization mass spectrometry Biochim. Biophys. Acta 1473 1999 391 399
45. Y. Du, F.Y. Meng, S.M. Patrie, L.M. Miller, and N.L. Kelleher Improved molecular weight-based processing of intact proteins for interrogation by quadrupole-enhanced FT MS/MS J. Proteome Res. 3 2004 801 806
46. J.C. Tran, and A.A. Doucette Gel-eluted liquid fraction entrapment electrophoresis: an electrophoretic method for broad molecular weight range proteome separation Anal. Chem. 80 2008 1568 1573
47. D. Wessel, and U.I. Flugge A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids Anal. Biochem. 138 1984 141 143
48. H. Schagger, and G. Vonjagow Tricine-sodium dodecyl sulfate- polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa Anal. Biochem. 166 1987 368 379
49. J.F. Kellie, A.D. Catherman, K.R. Durbin, J.C. Tran, J.D. Tipton, J.L. Norris, C.E. Witkowski, P.M. Thomas, and N.L. Kelleher Robust analysis of the yeast proteome under 50 kDa by molecular-mass-based fractionation and top-down mass spectrometry Anal. Chem. 84 2012 209 215
50. J.C. Tran, L. Zamdborg, D.R. Ahlf, J.E. Lee, A.D. Catherman, K.R. Durbin, J.D. Tipton, A. Vellaichamy, J.F. Kellie, M. Li, C. Wu, S.M.M. Sweet, B.P. Early, N. Siuti, R.D. LeDuc, P.D. Compton, P.M. Thomas, and N.L. Kelleher Mapping intact protein isoforms in discovery mode using top-down proteomics Nature 480 2011 254-U141
51. D.R. Ahlf, P.D. Compton, J.C. Tran, B.P. Early, P.M. Thomas, and N.L. Kelleher Evaluation of the compact high-field Orbitrap for top-down proteomics of human cells J. Proteome Res. 11 2012 4308 4314
52. A.D. Catherman, M. Li, J.C. Tran, K.R. Durbin, P.D. Compton, B.P. Early, P.M. Thomas, and N.L. Kelleher Top down proteomics of human membrane proteins from enriched mitochondrial fractions Anal. Chem. 85 2013 1880 1888
53. A. Ayala, J. Parrado, and A. Machado Use of Rotofor preparative isoelectrofocusing cell in protein purification procedure Appl. Biochem. Biotechnol. 69 1998 11 16
54. J.C. Tran, and A.A. Doucette Rapid and effective focusing in a carrier ampholyte solution isoelectric focusing system: a proteome prefractionation tool J. Proteome Res. 7 2008 1761 1766
55. J.C. Tran, and A.A. Doucette Multiplexed size separation of intact proteins in solution phase for mass spectrometry Anal. Chem. 81 2009 6201 6209
56. S. Hjerten Free zone electrophoresis Chromatogr. Rev. 9 1967 122 219
57. J.W. Jorgenson, and K.D. Lukacs Zone electrophoresis in open-tubular glass capillaries Anal. Chem. 53 1981 1298 1302
58. J.W. Jorgenson, and K.D. Lukacs High-resolution separations based on electrophoresis and electroosmosis J. Chromatogr. 218 1981 209 216
59. R. Haselberg, G.J. de Jong, and G.W. Somsen Capillary electrophoresis-mass spectrometry for the analysis of intact proteins J. Chromatogr. A 1159 2007 81 109
60. S.A. Hofstadler, J.C. Severs, R.D. Smith, F.D. Swanek, and A.G. Ewing High performance Fourier transform ion cyclotron resonance mass spectrometric detection for capillary electrophoresis J. High Resolut. Chromatogr. 19 1996 617 621
61. E. Balaguer, and C. Neususs Glycoprotein characterization combining intact protein and glycan analysis by capillary electrophoresis-electrospray ionization-mass spectrometry Anal. Chem. 78 2006 5384 5393
62. M. Moini, and H.L. Huang Application of capillary electrophoresis/ electrospray ionization-mass spectrometry to subcellular proteomics of Escherichia coli ribosomal proteins Electrophoresis 25 2004 1981 1987
63. S. Hjerten, and M.D. Zhu Adaptation of the equipment for high-performance electrophoresis to isoelectric-focusing J. Chromatogr. 346 1985 265 270
64. F. Kilar, and S. Hjerten Fast and high resolution analysis of human serum transferrin by high performance isoelectric focusing in capillaries Electrophoresis 10 1989 23 29
65. L.Y. Yang, C.S. Lee, S.A. Hofstadler, L. Pasa-Tolić, and R.D. Smith Capillary isoelectric focusing-electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for protein characterization Anal. Chem. 70 1998 3235 3241
66. P.K. Jensen, L. Pasa-Tolic, G.A. Anderson, J.A. Horner, M.S. Lipton, J.E. Bruce, and R.D. Smith Probing proteomes using capillary isoelectric focusing-electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry Anal. Chem. 71 1999 2076 2084
67. P.K. Jensen, L. Pasa-Tolic, K.K. Peden, S. Martinovic, M.S. Lipton, G.A. Anderson, N. Tolic, K.K. Wong, and R.D. Smith Mass spectrometic detection for capillary isoelectric focusing separations of complex protein mixtures Electrophoresis 21 2000 1372 1380
68. F. Zhou, and M.V. Johnston Protein characterization by on-line capillary isoelectric focusing, reversed-phase liquid chromatography, and mass spectrometry Anal. Chem. 76 2004 2734 2740
69. F. Zhou, T.E. Hanson, and M.V. Johnston Intact protein profiling of Chlorobium tepidum by capillary isoelectric focusing, reversed-phase liquid chromatography, and mass spectrometry Anal. Chem. 79 2007 7145 7153
70. J.D. Tipton, J.C. Tran, A.D. Catherman, D.R. Ahlf, K.R. Durbin, and N.L. Kelleher Analysis of intact protein isoforms by mass spectrometry J. Biol. Chem. 286 2011 25451 25458
71. P.D. Compton, L. Zamdborg, P.M. Thomas, and N.L. Kelleher On the scalability and requirements of whole protein mass spectrometry Anal. Chem. 83 2011 6868 6874
72. M. Karas, and F. Hillenkamp Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons Anal. Chem. 60 1988 2299 2301
73. K. Tanaka, H. Waki, Y. Ido, S. Akita, Y. Yoshida, T. Yoshida, and T. Matsuo Protein and polymer analyses up to m/z 100 000 by laser ionization time-of-flight mass spectrometry Rapid Commun. Mass Spectrom. 2 1988 151 153
74. J.B. Fenn, M. Mann, C.K. Meng, S.F. Wong, and C.M. Whitehouse Electrospray ionization for mass-spectrometry of large biomolecules Science 246 1989 64 71
75. M. Yamashita, and J.B. Fenn Electrospray ion source. Another variation on the free-jet theme J. Phys. Chem. 88 1984 4451 4459
76. E.H. Seeley, and R.M. Caprioli MALDI imaging mass spectrometry of human tissue: method challenges and clinical perspectives Trends Biotechnol. 29 2011 136 143
77. M.B. Comisarow, and A.G. Marshall Fourier transform ion cyclotron resonance spectroscopy Chem. Phys. Lett. 25 1974 282 283
78. M.B. Comisarow, and A.G. Marshall Frequency-sweep fourier transform ion cyclotron resonance spectroscopy Chem. Phys. Lett. 26 1974 489 490
79. A.G. Marshall, C.L. Hendrickson, and G.S. Jackson Fourier transform ion cyclotron resonance mass spectrometry: a primer Mass Spectrom. Rev. 17 1998 1 35
80. K.D. Henry, E.R. Williams, B.H. Wang, F.W. McLafferty, J. Shabanowitz, and D.F. Hunt Fourier-transform mass spectrometry of large molecules by electrospray ionization Proc. Natl. Acad. Sci. U.S.A. 86 1989 9075 9078
81. K.D. Henry, and F.W. McLafferty Electrospray ionization with Fourier-transform mass spectrometry. Charge state assignment from resolved isotopic peaks Org. Mass Spectrom. 25 1990 490 492
82. K.D. Henry, J.P. Quinn, and F.W. McLafferty High-resolution electrospray mass spectra of large molecules J. Am. Chem. Soc. 113 1991 5447 5449
83. J.A. Loo, J.P. Quinn, S.I. Ryu, K.D. Henry, M.W. Senko, and F.W. McLafferty High-resolution tandem mass spectrometry of large biomolecules Proc. Natl. Acad. Sci. U.S.A. 89 1992 286 289
84. J.J. Coon Collisions or electrons? Protein sequence analysis in the 21st century Anal. Chem. 81 2009 3208 3215
85. R.A. Zubarev, N.L. Kelleher, and F.W. McLafferty Electron capture dissociation of multiply charged protein cations. A nonergodic process J. Am. Chem. Soc. 120 1998 3265 3266
86. R.A. Zubarev, K.F. Haselmann, B. Budnik, F. Kjeldsen, and F. Jensen Towards an understanding of the mechanism of electron-capture dissociation: a historical perspective and modern ideas Eur. J. Mass Spectrom. 8 2002 337 350
87. L. Sleno, and D.A. Volmer Ion activation methods for tandem mass spectrometry J. Mass Spectrom. 39 2004 1091 1112
88. S.C. Beu, M.W. Senko, J.P. Quinn, and F.W. McLafferty Improved Fourier-transform ion-cyclotron-resonance mass spectrometry of large biomolecules J. Am. Soc. Mass Spectrom. 4 1993 190 192
89. M.W. Senko, C.L. Hendrickson, L. Paša-Tolić, J.A. Marto, F.M. White, S. Guan, and A.G. Marshall Electrospray ionization Fourier transform ion cyclotron resonance at 9.4 T Rapid Commun. Mass Spectrom. 10 1996 1824 1828
90. M.E. Belov, E.N. Nikolaev, G.A. Anderson, K.J. Auberry, R. Harkewicz, and R.D. Smith Electrospray ionization-fourier transform ion cyclotron mass spectrometry using ion preselection and external accumulation for ultrahigh sensitivity J. Am. Soc. Mass Spectrom. 12 2001 38 48
91. M. Senko, C. Hendrickson, M. Emmett, S.H. Shi, and A. Marshall External accumulation of ions for enhanced electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry J. Am. Soc. Mass Spectrom. 8 1997 970 976
92. B. Wilcox, C. Hendrickson, and A. Marshall Improved ion extraction from a linear octopole ion trap: SIMION analysis and experimental demonstration J. Am. Soc. Mass Spectrom. 13 2002 1304 1312
93. S.M. Patrie, J.P. Charlebois, D. Whipple, N.L. Kelleher, C.L. Hendrickson, J.P. Quinn, A.G. Marshall, and B. Mukhopadhyay Construction of a hybrid quadrupole/Fourier transform ion cyclotron resonance mass spectrometer for versatile MS/MS above 10 kDa J. Am. Soc. Mass Spectrom. 15 2004 1099 1108
94. M.J. Roth, A.J. Forbes, M.T. Boyne, Y.B. Kim, D.E. Robinson, and N.L. Kelleher Precise and parallel characterization of coding polymorphisms, alternative splicing, and modifications in human proteins by mass spectrometry Mol. Cell. Proteomics 4 2005 1002 1008
95. J.E.P. Syka, J.A. Marto, D.L. Bai, S. Horning, M.W. Senko, J.C. Schwartz, B. Ueberheide, B. Garcia, S. Busby, T. Muratore, J. Shabanowitz, and D.F. Hunt Novel linear quadrupole ion trap/FT mass spectrometer: performance characterization and use in the comparative analysis of histone H3 post-translational modifications J. Proteome Res. 3 2004 621 626
96. C.M. Ryan, P. Souda, S. Bassilian, R. Ujwal, J. Zhang, J. Abramson, P.P. Ping, A. Durazo, J.U. Bowie, S.S. Hasan, D. Baniulis, W.A. Cramer, K.F. Faull, and J.P. Whitelegge Post-translational modifications of integral membrane proteins resolved by top-down Fourier transform mass spectrometry with collisionally activated dissociation Mol. Cell. Proteomics 9 2010 791 803
97. B. Thangaraj, C.M. Ryan, P. Souda, K. Krause, K.F. Faull, A.P.M. Weber, P. Fromme, and J.P. Whitelegge Data-directed top-down Fourier-transform mass spectrometry of a large integral membrane protein complex: photosystem II from Galdieria sulphuraria Proteomics 10 2010 3644 3656
98. J.T. Ferguson, C.D. Wenger, W.W. Metcalf, and N.L. Kelleher Top-down proteomics reveals novel protein forms expressed in Methanosarcina acetivorans J. Am. Soc. Mass Spectrom. 20 2009 1743 1750
99. T.M. Schaub, C.L. Hendrickson, S. Horning, J.P. Quinn, M.W. Senko, and A.G. Marshall High-performance mass spectrometry: Fourier transform ion cyclotron resonance at 14.5 tesla Anal. Chem. 80 2008 3985 3990
100. J.D. Tipton, J.C. Tran, A.D. Catherman, D.R. Ahlf, K.R. Durbin, J.E. Lee, J.F. Kellie, N.L. Kelleher, C.L. Hendrickson, and A.G. Marshall Nano-LC FTICR tandem mass spectrometry for top-down proteomics: routine baseline unit mass resolution of whole cell lysate proteins up to 72 kDa Anal. Chem. 84 2012 2111 2117
101. A. Makarov Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis Anal. Chem. 72 2000 1156 1162
102. A. Makarov, E. Denisov, A. Kholomeev, W. Baischun, O. Lange, K. Strupat, and S. Horning Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer Anal. Chem. 78 2006 2113 2120
103. B. Macek, L.F. Waanders, J.V. Olsen, and M. Mann Top-down protein sequencing and MS3 on a hybrid linear quadrupole ion trap-Orbitrap mass spectrometer Mol. Cell. Proteomics 5 2006 949 958
104. M.T. Mazur, H.L. Cardasis, D.S. Spellman, A. Liaw, N.A. Yates, and R.C. Hendrickson Quantitative analysis of intact apolipoproteins in human HDL by top-down differential mass spectrometry Proc. Natl. Acad. Sci. U.S.A. 107 2010 7728 7733
105. R. Théberge, G. Infusini, W. Tong, M.E. McComb, and C.E. Costello 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. 300 2011 130 142
106. P. Bondarenko, T. Second, V. Zabrouskov, A. Makarov, and Z. Zhang Mass measurement and top-down HPLC/MS analysis of intact monoclonal antibodies on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer J. Am. Soc. Mass Spectrom. 20 2009 1415 1424
107. J. Zhang, H. Liu, and V. Katta Structural characterization of intact antibodies by high-resolution LTQ Orbitrap mass spectrometry J. Mass Spectrom. 45 2010 112 120
108. J.V. Olsen, B. Macek, O. Lange, A. Makarov, S. Horning, and M. Mann Higher-energy C-trap dissociation for peptide modification analysis Nat. Methods 4 2007 709 712
109. T. Pekar Second, J.D. Blethrow, J.C. Schwartz, G.E. Merrihew, M.J. MacCoss, D.L. Swaney, J.D. Russell, J.J. Coon, and V. Zabrouskov Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures Anal. Chem. 81 2009 7757 7765
110. J.V. Olsen, J.C. Schwartz, J. Griep-Raming, M.L. Nielsen, E. Damoc, E. Denisov, O. Lange, P. Remes, D. Taylor, M. Splendore, E.R. Wouters, M. Senko, A. Makarov, M. Mann, and S. Horning A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed Mol. Cell. Proteomics 8 2009 2759 2769
111. R. Edwards, P. Griffiths, J. Bunch, and H. Cooper Top-down proteomics and direct surface sampling of neonatal dried blood spots: diagnosis of unknown hemoglobin variants J. Am. Soc. Mass Spectrom. 23 2012 1921 1930
112. S. Wu, R.N. Brown, S.H. Payne, D. Meng, R. Zhao, N. Tolić, L. Cao, A. Shukla, M.E. Monroe, R.J. Moore, M.S. Lipton, and L. Paša- Tolić Top-down characterization of the post-translationally modified intact periplasmic proteome from the bacterium Novosphingobium aromaticivorans Int. J. Proteomics 2013 2013 10
113. L. Fornelli, E. Damoc, P.M. Thomas, N.L. Kelleher, K. Aizikov, E. Denisov, A. Makarov, and Y.O. Tsybin Analysis of intact monoclonal antibody IgG1 by electron transfer dissociation Orbitrap FTMS Mol. Cell. Proteomics 11 2012 1758 1767
114. J.E.P. Syka, J.J. Coon, M.J. Schroeder, J. Shabanowitz, and D.F. Hunt Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry Proc. Natl. Acad. Sci. U.S.A. 101 2004 9528 9533
115. G.C. McAlister, D. Phanstiel, D.M. Good, W.T. Berggren, and J.J. Coon Implementation of electron-transfer dissociation on a hybrid linear ion trap-Orbitrap mass spectrometer Anal. Chem. 79 2007 3525 3534
116. G.C. McAlister, W.T. Berggren, J. Griep-Raming, S. Horning, A. Makarov, D. Phanstiel, G. Stafford, D.L. Swaney, J.E.P. Syka, V. Zabrouskov, and J.J. Coon A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer J. Proteome Res. 7 2008 3127 3136
117. A. Michalski, E. Damoc, O. Lange, E. Denisov, D. Nolting, M. Mueller, R. Viner, J. Schwartz, P. Remes, M. Belford, J.-J. Dunyach, J. Cox, S. Horning, M. Mann, and A. Makarov Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes Mol. Cell. Proteomics 11 2012 1 11
118. A.D. Catherman, K.R. Durbin, D.R. Ahlf, B.P. Early, R.T. Fellers, J.C. Tran, P.M. Thomas, and N.L. Kelleher Large-scale Top-down proteomics of the human proteome: membrane proteins, mitochondria, and senescence Mol Cell Proteomics 12 2013 3465 3473
119. G.K. Taylor, Y.-B. Kim, A.J. Forbes, F. Meng, R. McCarthy, and N.L. Kelleher Web and database software for identification of intact proteins using "top down" mass spectrometry Anal. Chem. 75 2003 4081 4086
120. R.D. LeDuc, G.K. Taylor, Y.B. Kim, T.E. Januszyk, L.H. Bynum, J.V. Sola, J.S. Garavelli, and N.L. Kelleher ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry Nucleic Acids Res. 32 2004 W340 W345
121. F.Y. Meng, B.J. Cargile, L.M. Miller, A.J. Forbes, J.R. Johnson, and N.L. Kelleher Informatics and multiplexing of intact protein identification in bacteria and the archaea Nat. Biotechnol. 19 2001 952 957
122. L. Zamdborg, R.D. LeDuc, K.J. Glowacz, Y.B. Kim, V. Viswanathan, I.T. Spaulding, B.P. Early, E.J. Bluhm, S. Babai, and N.L. Kelleher ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry Nucleic Acids Res. 35 2007 W701 W706
123. D.M. Horn, R.A. Zubarev, and F.W. McLafferty Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules J. Am. Soc. Mass Spectrom. 11 2000 320 332
124. K.R. Durbin, R.T. Fellers, I. Ntai, N.L. Kelleher, and P.D. Compton Autopilot: an online data acquisition control system for the enhanced high-throughput characterization of intact proteins Anal. Chem. 8 2014 846 856
125. N.M. Karabacak, L. Li, A. Tiwari, L.J. Hayward, P.Y. Hong, M.L. Easterling, and J.N. Agar Sensitive and specific identification of wild type and variant proteins from 8 to 669 kDa using top-down mass spectrometry Mol. Cell. Proteomics 8 2009 846 856
126. Y. Tsai, A. Scherl, J. Shaw, C.L. MacKay, S. Shaffer, P.R. Langridge-Smith, and D. Goodlett Precursor ion independent algorithm for top-down shotgun proteomics J. Am. Soc. Mass Spectrom. 20 2009 2154 2166
127. D.N. Perkins, D.J.C. Pappin, D.M. Creasy, and J.S. Cottrell Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 20 1999 3551 3567
128. H.J.C.T. Wessels, R.O. Vogel, R.N. Lightowlers, J.N. Spelbrink, R.J. Rodenburg, L.P. van den Heuvel, A.J. van Gool, J. Gloerich, J.A.M. Smeitink, and L.G. Nijtmans Analysis of 953 human proteins from a mitochondrial HEK293 fraction by complexome profiling PLoS One 8 2013 e68340
129. Pierre C. Havugimana, G.T. Hart, T. Nepusz, H. Yang, Andrei L. Turinsky, Z. Li, Peggy I. Wang, Daniel R. Boutz, V. Fong, S. Phanse, M. Babu, Stephanie A. Craig, P. Hu, C. Wan, J. Vlasblom, V.-U.N. Dar, A. Bezginov, Gregory W. Clark, Gabriel C. Wu, Shoshana J. Wodak, Elisabeth R.M. Tillier, A. Paccanaro, Edward M. Marcotte, and A. Emili A census of human soluble protein complexes Cell 150 2012 1068 1081
130. B. Ganem, Y.T. Li, and J.D. Henion Detection of noncovalent receptor-ligand complexes by mass spectrometry J. Am. Chem. Soc. 113 1991 6294 6296
131. Y.T. Li, Y.L. Hsieh, J.D. Henion, M.W. Senko, F.W. McLafferty, and B. Ganem Mass spectrometric studies on noncovalent dimers of leucine zipper peptides J. Am. Chem. Soc. 115 1993 8409 8413
132. J.C. Jurchen, and E.R. Williams Origin of asymmetric charge partitioning in the dissociation of gas-phase protein homodimers J. Am. Chem. Soc. 125 2003 2817 2826
133. M.E. Belov, E. Damoc, E. Denisov, P.D. Compton, S. Horning, A.A. Makarov, and N.L. Kelleher From protein complexes to subunit backbone fragments: a multi-stage approach to native mass spectrometry Anal. Chem. 85 2013 11163 11173
134. C.M. Jones, R.L. Beardsley, A.S. Galhena, S. Dagan, G. Cheng, and V.H. Wysocki Symmetrical gas-phase dissociation of noncovalent protein complexes via surface collisions J. Am. Chem. Soc. 128 2006 15044 15045
135. H. Zhang, W. Cui, J. Wen, R.E. Blankenship, and M.L. Gross Native electrospray and electron-capture dissociation FTICR mass spectrometry for top-down studies of protein assemblies Anal. Chem. 83 2011 5598 5606
136. C.J. Hogan, B.T. Ruotolo, C.V. Robinson, and J. Fernandez de la Mora Tandem differential mobility analysis-mass spectrometry reveals partial gas-phase collapse of the GroEL complex J. Phys. Chem. B 115 2011 3614 3621
137. A.J.R. Heck Native mass spectrometry: a bridge between interactomics and structural biology Nat. Methods 5 2008 927 933
138. C.S. Kaddis, S.H. Lomeli, S. Yin, B. Berhane, M.I. Apostol, V.A. Kickhoefer, L.H. Rome, and J.A. Loo Sizing large proteins and protein complexes by electrospray ionization mass spectrometry and ion mobility J. Am. Soc. Mass Spectrom. 18 2007 1206 1216
139. J.Z. Bereszczak, I.M. Barbu, M. Tan, M. Xia, X. Jiang, E. van Duijn, and A.J.R. Heck Structure, stability and dynamics of norovirus P domain derived protein complexes studied by native mass spectrometry J. Struct. Biol. 177 2012 273 282
140. L. Konermann, and D.J. Douglas Acid-induced unfolding of cytochrome c at different methanol concentrations: electrospray ionization mass spectrometry specifically monitors changes in the tertiary structure Biochemistry 36 1997 12296 12302