Multidimensional Separation of Proteins with Online Electrospray Time-of-Flight Mass Spectrometric Detection

Multidimensional Liquid Chromatography: Theory and Applications in Industrial Chemistry and the Life Sciences

Volumn , Issue , 2008, Pages 291-317

  Cohen, Steven A ^a   Berger, Scott J ^a  

^a WATERS CORPORATION   (United States)

Author keywords

Cellular extract, tissue homogenate, or biological fluid; Electrospray time of flight mass spectrometry; Ion exchange (IEX) separations

Indexed keywords

EID: 72749120448     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470276266.ch13     Document Type: Chapter

References (50)

1. Anderson, N.L., Anderson, N.G. (2001). The human plasma proteome: history, character, and diagnostic prospectss. Mol. Cell. Proteomics 1, 845-867.
2. Apffel, A. (2004). Multidimensional chromatography of intact proteins. In: Simpson, R.J., editor, Purifying Proteins for Proteomics: A Laboratory Manual. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, New York pp.75-100.
3. Apffel, A., Fischer, S., Goldberg, G., Goodley, P.C., Kuhlmann, F.E. (1995). Enhanced sensitivity for peptide mapping with electrospray liquid chromatography-mass spectrometry in the presence of signal suppression due to trifluoroacetic acid-containing mobile phases. J. Chromatogr. A 712, 177-190.
4. Benesch, J.L., Robinson, C.V. (2006). Mass spectrometry of macromolecular assemblies: preservation and dissociation. Curr. Opin. Struct. Biol. 6, 245-251.
5. Brunet, S., Thibault, P., Gagnon, E., Kearney, P., Bergeron, J.J., Desjardins, M. (2003). Organelle proteomics: looking at less to see more. Trends. Cell. Biol. 13, 629-638.
6. Bushey, M.M., Jorgenson, J.W. (1990). Automated instrumentation for comprehensive twodimensional liquid chromatography of proteins. Anal. Chem. 62, 161-167.
7. Chong, B.E., Yan, F., Lubman, D.M., Miller, F.R. (2001). Chromatofocusing nonporous reversed-phase high-performance liquid chromatography/electrospray ionization timeof-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, 291-296.
8. Coon, J.J., Ueberheide, B., Syka, J.E.P., Dryhurst, D.D., Ausio, J., Shabanowitz, J., Hunt, D.F. (2005). Protein identification using sequential ion/ion reactions and tandem mass spectrometry. Proc. Nat. Acad. Sci. USA 102, 9463-9468.
9. Drager, R.R., Regnier, F.E. (1986). Application of the stoichiometric displacement model of retention to anion-exchange chromatography of nucleic acids. J. Chromatogr. 359, 147-155.
10. Ducret, A., Van Oostveen, I., Eng, J.K., Yates, J.R., 3rd, Aebersold, R. (1998). High throughput protein characterization by automated reverse-phase chromatography/electrospray tandem mass spectrometry. Protein Sci. 7, 706-719.
11. Evans, C.R., Jorgenson, J.W. (2004). Multidimensional LC-LC and LC-CE for high-resolution separations of biological molecules. Anal. Bioanal. Chem. 378, 1952-1961.
12. Fenn, J.B., Mann, M., Meng, C.K., Wong, S.F., Whitehouse, C.M. (1989). Electrospray ionization for mass spectrometry of large biomolecules. Science 246, 64-71.
13. Ferrige, A.G., Seddon, M.J., Green, B.N., Jarvis, S.A., Skilling, J. (1992a). Disentangling electrospray spectra with maximum entropy. Rapid Commun. Mass Spectrom. 6, 707-711.
14. Ferrige, A.G., Seddon, M.J., Skilling, J., Ordsmith, N. (1992b). The application of MaxEnt to high resolution mass spectrometry. Rapid Commun. Mass Spectrom. 6, 765-770.
15. Geng, X., Regnier, F.E. (1984). Retention model for proteins in reversed-phase liquid chromatography. J. Chromatogr. 296, 15-30.
16. Geng, M., Zhang, X., Bina, M., Regnier, F. (2001). Proteomics of glycoproteins based on affinity selection of glycopeptides from tryptic digests. J. Chromatogr. B 752, 293-306.
17. Gianazza, E., Righetti, P.G. (1980). Size and charge distribution of macromolecules in living systems. J. Chromatog. A 193, 1-198.
18. Giddings, J.C. (1984). Two-dimensional separations: concept and promise. Anal. Chem. 56, 1258A-1264A.
19. Giddings, J.C. (1987). Concepts and comparisons in multidimensional separation. J. High Resolut. Chromatogr. Chromatogr. Commun. 10, 319-323.
20. Gygi, S.P., Corthals, G.L., Zhang, Y., Rochon, Y., Aebersold, R. (2000). Evaluation of twodimensional gel electrophoresis-based proteome analysis technology. Proc. Natl. Acad. Sci. USA 97, 9390-9395.
21. Hamler, R.L., Zhu, K., Buchanan, N.S., Kreunin, P., Kachman, M.T., Miller, F.R., Lubman, D.M. (2004). A two-dimensional liquid-phase separation method coupled with mass spectrometry for proteomic studies of breast cancer and biomarker identification. Proteomics 4, 562-577.
22. Han, X., Jin, M., Breuker, K., McLafferty, F.W. (2006). Extending top-down mass spectrometry to proteins with masses greater than 200 kilodaltons. Science 314, 109-112.
23. Henzel, W.J., Billeci, T.M., Stults, J.T., Wong, S.C., Grimley, C., Watanabe, C. (1993). Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. USA 90, 5011-5015.
24. Huber, C.G., Premstaller, A. (1999). Evaluation of volatile eluents and electrolytes for highperformance liquid chromatography-electrospray ionization mass spectrometry and capillary electrophoresis-electrospray ionization mass spectrometry of proteins. I. Liquid chromatography. J. Chromatogr. A 849, 161-173.
25. Jensen, O.N. (2004). Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry. Curr. Opin. Chem. Biol. 8, 33-41.
26. Kelleher, N.L. (2004). Top-down proteomics. Anal. Chem. 76, 197A-203A.
27. LeDuc, R.D., Taylor, G.K., Kim, Y.B., Januszyk, T.E., Bynum, L.H., Sola, J.V., Garavelli, J.S., Kelleher, N.L. (2004). ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry. Nucleic Acids Res. 32, W340-W345.
28. Lee, S.W., Berger, S.J., Martinovic, S., Pasa-Tolic, L., Anderson, G.A., Shen, Y., Zhao, R., Smith, R.D. (2002). Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR. Proc. Natl. Acad. Sci. USA 99, 5942-5947.
29. Liu, H., Berger, S.J., Chakraborty, A.B., Plumb, R.S., Cohen, S.A. (2002). Multidimensional chromatography coupled to electrospray ionization time-of-flight mass spectrometry as an alternative to two-dimensional gels for the identification and analysis of complex mixtures of intact proteins. J. Chromatogr. B 782, 267-289.
30. Liu, Z., Patterson Jr., D.G., Lee, M.L. (1995). Geometric approach to factor analysis for the estimation of orthogonality and practical peak capacity in comprehensive two-dimensional separations. Anal. Chem. 67, 3840-3845.
31. Mann, M., Hojrup, P., Roepstorff, P. (1993). Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol. Mass Spectrom. 22, 338-345.
32. Masuda, J., Maynard, D.M., Nishimura, M., Ueda, T., Kowalak, J.A., Markey, S.P. (2005). Fully automated micro-and nanoscale one-or two-dimensional high-performance liquid chromatography system for liquid chromatography-mass spectrometry compatible with non-volatile salts for ion exchange chromatography. J. Chromatogr. A 1063, 57-69.
33. Meng, F., Forbes, A.J., Miller, L.M., Kelleher, N.L. (2005). Detection and localization of protein modifications by high resolutiont and emmassspectrometry.Mass Spectrom. Rev.24,126-134.
34. Millea, K.M., Kass, I.J., Cohen, S.A., Krull, I.S., Gebler, J.C., Berger, S.J. (2005). Evaluation of multidimensional (ion-exchange/reversed-phase) protein separations using linear and step gradients in the first dimension. J. Chromatogr. A 1079, 287-298.
35. Millea, K.M., Krull, I.S., Cohen, S.A., Gebler, J.C., Berger, S.J. (2006). Integration of multidimensional chromatographic protein separations with a combined "top-down'' and "bottomup'' proteomic strategy. J. Proteome. Res. 5, 135-146.
36. Murphy, R.E., Schure, M.R., Foley, J.P. (1998). Effect of sampling rate on resolution in comprehensive two-dimensional liquid chromatography. Anal. Chem. 70, 1585-1594.
37. Nemeth-Cawley, J.F., Tangarone, B.S., Rouse, J.C. (2003). "Top Down'' characterization is a complementary technique to peptide sequencing for identifying protein species in complex mixtures. J. Proteome Res. 2, 495-505.
38. Opiteck, G.J., Jorgenson, J.W., Anderegg, R.J. (1997). Two-dimensional SEC/RPLC coupled to mass spectrometry for the analysis of peptides. Anal. Chem. 69, 2283-2291.
39. Opiteck, G.J., Ramirez, S.M., Jorgenson, J.W., Moseley, M.A., III (1998). Comprehensive twodimensional high-performance liquid chromatography for the isolation of overexpressed proteins and proteome mapping. Anal. Biochem. 258, 349-361.
40. Peng, J., Gygi, S.P. (2001). Proteomics: the move to mixtures. J. Mass. Spec. 36, 1083-1091.
41. Slonecker, P.J., Li, X., Ridgway, T.H., Dorsey, J.G. (1996). Informational orthogonality of twodimensional chromatographic separations. Anal. Chem. 68, 682-689.
42. Threadgill, G.J., Conrad, R.C., Cannon, M., Craven, G.R. (1987). A rapid and preparative method for the separation of yeast ribosomal proteins by using high-performance liquid chromatography. Biochem. J. 244, 523-532.
43. Wall, D.B., Kachman, M.T., Gong, S., Hinderer, R., Parus, S., Misek, D.E., Hanash, S.M., Lubman, D.M (2000). Isoelectric focusing nonporous RP HPLC: a two-dimensional liquidphase separation method for mapping of cellular proteins with identification using MALDITOF mass spectrometry. Anal. Chem. 72, 1099-1111.
44. Wall, D.B., Kachman, M.T., Gong, S.S., Parus, S.J., Long, M.W., Lubman, D.M. (2001). 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, 1649-1661.
45. Wang, H., Hanash, S. (2005). Intact-protein based sample preparation strategies for proteome analysis in combination with mass spectrometry. Mass Spectrom. Rev. 24, 413-426.
46. Wang, H., Clouthier, S.G., Galchev, V., Misek, D.E., Duffner, U., Min, C.K., Zhao, R., Tra, J., Omenn, G.S., Ferrara, J.L., Hanash, S.M. (2005). Intact-protein-based high-resolution three-dimensional quantitative analysis system for proteome profiling of biological fluids. Mol. Cell. Proteomics 4, 618-625.
47. Wenzel, R.J., Matter, U., Schultheis, L., Zenobi, R. (2005). Analysis of megadalton ions using cryodetection MALDI time-of-flight mass spectrometry. Anal. Chem. 77, 4329-4337.
48. Whitelegge, J.P., Zhang, H., Aguilera, R., Taylor, R.M., Cramer, W.A. (2002). Full subunit coverage liquid chromatography electrospray ionization mass spectrometry (LCMS{thorn}) ofan oligomeric membrane protein: cytochrome b(6) f complex from spinach and the cyanobacterium Mastigocladus laminosus. Mol. Cell. Proteomics. 1, 816-827.
49. Williams, T.L., Leopold, P., Musser, S. (2002). Automated postprocessing of electrospray LC/MS data for profiling protein expression in bacteria. Anal. Chem. 74, 5807-5813.
50. Zuo, X., Speicher, D.W. (2004). Microscale solution isoelectricfocusing: a sample prefractionation method for comprehensive proteome analysis. Methods Mol. Biol. 244, 361-375.