Mass spectrometric identification and microcharacterization of proteins from electrophoretic gels: Strategies and applications

Proteins: Structure, Function and Genetics

Volumn 33, Issue SUPPL. 2, 1998, Pages 74-89

  Jensen, Ole Nørregaard ^a   Larsen, Martin R ^a   Roepstorff, Peter ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

Database searching; Electrospray; Gel electrophoresis; Mass spectrometry; Matrix assisted laser desorption ionization

Indexed keywords

GLYCOPROTEIN; DIFFERENTIATION ANTIGEN; GALECTIN 3; PEPTIDE; PHOSPHOPROTEIN; PROTEIN;

AMINO ACID SEQUENCE; ANALYTIC METHOD; ANIMAL CELL; ARTICLE; DATA BASE; DNA SEQUENCE; GEL ELECTROPHORESIS; GENOME; MASS SPECTROMETRY; NONHUMAN; NUCLEOTIDE SEQUENCE; PEPTIDE MAPPING; PRIORITY JOURNAL; RAT; ANIMAL; CHEMISTRY; FACTUAL DATABASE; HUMAN; METHODOLOGY; MOLECULAR GENETICS; POLYACRYLAMIDE GEL ELECTROPHORESIS;

ANIMALIA; EUKARYOTA; PROKARYOTA;

AMINO ACID SEQUENCE; ANIMALS; ANTIGENS, DIFFERENTIATION; DATABASES, FACTUAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; GALECTIN 3; GLYCOPROTEINS; HUMANS; MOLECULAR SEQUENCE DATA; PEPTIDE MAPPING; PEPTIDES; PHOSPHOPROTEINS; PROTEINS; RATS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 0032253972     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(sici)1097-0134(1998)33:2+<74::aid-prot9>3.0.co;2-b     Document Type: Article

References (80)

1. Wilkins, M.R., Pasquali, C., Appel, R.D., et al. From proteins to proteomes: Large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Bio/Technology 14:61-65, 1996.
2. O'Farrell, P.H. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250:4007-4021, 1975.
3. Klose, J. Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 26:231, 1975.
4. Celis, J.E., Ratz, G.P., Madsen, P., et al. Comprehensive, human cellular protein databases and their implication for the study of genome organization and function. FEBS Lett. 244:247-254, 1989.
5. Henzel, W.J., Billeci, T.M., Stults, J.T., Wong, S.C. Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. U.S.A. 90:5011-5015, 1993.
6. Mann, M., Højrup, P., Roepstorff, P. Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol. Mass Spectrom. 22:338-345, 1993.
7. Pappin, D.J.C., Højrup, P., Bleasby, A.J. Protein identification by peptide mass fingerprinting. Curr. Biol. 3:327-332, 1993.
8. James, P., Quadroni, M., Carafoli, E., Gonnet, G. Protein identification by mass profile fingerprinting. Biochem. Biophys. Res. Commun. 195:58-64, 1993.
9. Yates, J.R., Speicher, S., Griffin, P.R., Hunkapiller, T. Peptide mass maps: A highly informative approach to protein identification. Anal. Biochem. 214:397-408, 1993.
10. Eng, J.K., McCormack, A.L., Yates, J.R. I. An approach to correlate tandem mass spectra of peptides with amino acid sequences in protein databases. J. Am. Soc. Mass Spectrom. 5:976-989, 1994.
11. Mann, M., Wilm, M.S. Error tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 66:4390-4399, 1994.
12. Patterson, S.D., Aebersold, R. Mass spectrometric approaches for the identification of gel-separated proteins. Electrophoresis 16:1791-1814, 1995.
13. Shevchenko, A., Jensen, O.N., Podtelejnikov, A.V., et al. Linking genome and proteome by mass spectrometry: Large scale identification of yeast proteins from two dimensional gels. Proc. Natl. Acad. Sci. U.S.A. 93:14440-14445, 1996.
14. Dongre, A., Eng, J., Yates, J.R. Emerging tandem-mass-spectrometry techniques for the rapid identification of proteins. Trends Biotechnol. 15:418-425, 1997.
15. Mann, M. A shortcut to interesting human genes: Peptide sequence tags, ESTs and computers. Trends Biol. Sci. 21:494-495, 1996.
16. Center for Proteome Analysis in the Life Sciences, Science Park Odense, DK-5230 Odense M, Denmark.
17. Fey, S., Nawrocki, A., Larsen, M., et al. Proteome analysis of Saccharomyces cerevisiae: A methodological outline. Electrophoresis 18:1361-1372, 1997.
18. Rosenfeld, J., Capdevielle, J., Guillemot, J.C., Ferrara, P. In-gel digestion of proteins for internal sequence analysis after one-or two-dimensional gel electrophoresis. Anal. Biochem. 203:173-179, 1992.
19. Shevchenko, A., Wilm, M., Vorm, O., Mann, M. Mass spectrometric sequencing of proteins from silver stained polyacrylamide gels. Anal. Chem. 68:850-858, 1996.
20. Nawrocki, A., Larsen, M.R., Podtelejnikov, A.V., et al. Correlation of acidic and basic, ampholyte and immobilised pH gradient 2D gel patterns based on mass spectrometric identification. Electrophoresis 19:1024-1035, 1998.
21. Annan, R., McNulty, D., Carr, S. High sensitivity identification of proteins from SDS-PAGE using in-gel digestion and MALDI-PSD. Proceedings of the 44th ASMS Conference on Mass Spectrometry and Allied Topics, Portland, OR, 1996:702.
22. Gobom, J., Nordhoff, E., Ekman, R., Roepstorff, P. Rapid micro-scale proteolysis of proteins for MALDI-MS peptide mapping using immobilized trypsin. Int. J. Mass Spectrom. Ion Proc. 169/170:153-163, 1997.
23. Gobom, J., Nordhoff, E., Ekman, R., Roepstorff, P. Sample desalting for MALDI MS. Anal. Chem. (in press).
24. Vorm, O., Roepstorff, P., Mann, M. Matrix surfaces made by fast evaporation yield improved resolution and very high sensitivity in MALDI TOF. Anal. Chem. 66:3281-3287, 1994.
25. Jensen, O.N., Podtelejnikov, A., Mann, M. Delayed extraction improves specificity in database searches by MALDI peptide maps. Rapid Commun. Mass Spectrom. 10:1371-1378, 1996.
26. Kussmann, M., Nordhoff, E., Nielsen, H., et al. Sample preparation in MALDI-MS designed for various peptide and protein analytes. J. Mass Spectrom. 32:593, 1997.
27. Jensen, O.N., Mortensen, P., Vorm, O., Mann, M. Automation of MALDI mass spectrometry using fuzzy logic feedback control. Anal. Chem. 69:1706-1714, 1997.
28. Wilm, M., Mann, M. Analytical properties of the nanoelectrospray ion source. Anal. Chem. 66:1-8, 1996.
29. Figeys, D., Ning, Y., Aebersold, R. A microfabricated device for rapid protein identification by microelectrospray ion trap mass spectrometry. Anal. Chem. 69:3153-3160, 1997.
30. Morris, H.R., Paxton, T., Dell, A., et al. High sensitivity collisionally activated decomposition tandem mass spectrometry on a novel quadropole/orthogonal acceleration TOF mass spectrometer. Rapid Commun. Mass Spectrom. 10:889-896, 1996.
31. Shevchenko, A., Chernuchevich, I., Ens, W., et al. Rapid de novo peptide sequencing by a combination of nanoelectrospray, isotope labeling and a quadrupole/time-of-flight mass spectrometer. Rapid Commun. Mass Spectrom. 11: 1015-1024, 1997.
32. Hunt, D.F., Henderson, R.A., Shabanowitz, J., et al. Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry. Science 255: 1261-1263, 1992.
33. Davis, M.T., Lee, T.D. Rapid protein identification using a microscale electrospray LC/MS system on an ion trap mass spectrometer. J. Am. Soc. Mass Spectrom. 9:194-201, 1998.
34. 18O labeling. Rapid Commun. Mass Spectrom. 12:209-216, 1998.
35. Ducret, A., Van Oostveen, I., Eng, J., Yates, J.R., Aebersold, R. High throughput protein characterization by automated reverse-phase chromatography/electrospray tandem mass spectrometry. Protein Sci. 7:706-719, 1998.
36. Andersen, H.U., Fey, S.J., Larsen, P.M., et al. Interleukin-1beta induced changes in the protein expression of rat islets: a computerized database. Electrophoresis 18(11): 2091-2103, 1997.
37. Jensen, O., Podtelejnikov, A., Mann, M. Identification of the components of simple protein mixtures by high accuracy peptide mass mapping. Anal. Chem. 69:4741-4750, 1997.
38. Brown, R.S., Lennon, J.J. Mass resolution improvement by incorporation of pulsed ion extraction/ionization linear time-of-flight mass spectrometry. Anal. Chem. 67:1998-2003, 1995.
39. Whittal, R.M., Li, L. High resolution matrix-assisted laser desorption/ionization in a linear time-of-flight mass spectrometer. Anal. Chem. 67:1950-1954, 1995.
40. Vestal, M.L., Juhasz, P., Martin, S.A. Delayed extraction matrix-assisted laser desorption time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 9:1044-1050, 1995.
41. Jensen, O.N., Vorm, O., Mann, M. Sequence patterns produced by incomplete enzymatic digestion or one-step Edman degradation of peptide mixtures as probes for protein database searches. Electrophoresis 17:938-944, 1996.
42. Roepstorff, P., Fohlmann, J. Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed. Mass Spectrom. 11:601, 1984.
43. Biemann, K. Contributions of mass spectrometry to peptide and protein structure. Biomed. Environ. Mass Spectrom. 16:99-111, 1988.
44. Mørtz, E., O'Connor, P.B., Roepstorff, P., et al. Sequence tag identification of intact proteins by matching tandem mass spectral data against sequence data bases. Proc. Natl. Acad. Sci. U.S.A. 93:8264-8267, 1996.
45. Muzio, M., Chinnaiyan, A.M., Kischkel, F.C., et al. FLICE, a novel FADD-homologous ICE/CED-3-like protease, is recruited to the CD95 (Fas/APO-1) death-inducing signaling complex. Cell 85:817-827, 1996.
46. Deissler, H.W.M., Genc, B., Schmitz, B., et al. Rapid protein sequencing by tandem mass spectrometry and cDNA cloning of p20-CGGBP. A novel protein that binds to the unstable triplet repeat 5′-d(CGG)n-3′ in the human FMR1 gene. J. Biol. Chem. 272:16761-16768, 1997.
47. Neubauer, G., King, A., Rappsilber, J., et al. Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex. Nat Genet. 20(1):46-50, 1998.
48. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215:403-410, 1990.
49. Wilm, M., Shevchenko, A., Houthaeve, T., et al. Femtomole sequencing of proteins from polyacrylamide gels by nanoelectrospray mass spectrometry. Nature 379:466-469, 1996.
50. Shevchenko, A., Wilm, M., Mann, M. Peptide sequencing by mass spectrometry for homology searches and cloning of genes. J. Protein Chem. 16:481-490, 1997.
51. Hunt, D.F., Yates, J.R., Shabanowitz, J., Winston, S., Hauer, C.R. Peptide sequencing by tandem mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 83:6233-6237, 1986.
52. Alberts, B. The cell as a collection of protein machines: Preparing the next generation of molecular biologists. Cell 92:291-294, 1998.
53. Mann, M., Lamond, A. Cell biology and the genome projects - A concerted strategy for characterizing multi-protein complexes using mass spectrometry. Trends Cell Biol. 7:139-142, 1997.
54. Winter, D., Podtelejnikov, A., Mann, M., Li, R. The complex containing actin-related proteins Arp2 and Arp3 is required for the motility and integrity of yeast actin patches. Curr. Biol. 7:519-529, 1997.
55. Wigge, P., Jensen, O.N., Holmes, S., Soues, S., Mann, M., Kilmartin, J.V. Analysis of the Saccharomyces spindle pole by MALDI mass spectrometry. J. Cell Biol. 141:967-977, 1998.
56. Neubauer, G., Gottschalk, A., Fabrizio, P., Séraphin, B., Lührmann, R., Mann, M. Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 94:385-390, 1997.
57. Jensen, O.N., Houthaeve, T., Shevchenko, A., et al. Identification of the major membrane and core proteins of vaccinia virus by two-dimensional electrophoresis. J. Virol. 70:7485-7497, 1996.
58. Zachariae, W.S.A., Andrews, P.D., Ciosk, R., et al. Mass spectrometric analysis of the anaphase-promoting complex from yeast: Identification of a subunit related to cullins. Science 279:1216-1219, 1998.
59. Lindquist, J.A., Jensen, O.N., Mann, M., Hammerling, G.J. ER-60, a chaperone with thiol-dependent reductase activity involved in MHC class I assembly. EMBO J. 17:2186-2195, 1998.
60. Strupat, K., Karas, M., Hillenkamp, F., Eckerskorn, C., Lottspeich, F. Matrix-assisted laser desorption ionization mass spectrometry of proteins electroblotted after polyacrylamide gel electrophoresis. Anal. Chem. 66:464-470, 1994.
61. Ogorzalek-Loo, R., Mitchell, C., Stevenson, T., et al. Sensitivity and mass accuracy for proteins analyzed directly from polyacrylamide gels: Implications for proteome mapping. Electrophoresis 18:382-390, 1997.
62. Haebel, S.J.C., Andersen, S.O., Roepstorff, P. Isoforms of a cuticular protein from larvae of the meal beetle, Tenebrio molitor, studied by mass spectrometry in combination with Edman degradation and two-dimensional polyacrylamide gel electrophoresis. Protein Sci. 4:394-404, 1995.
63. Schuhmacher, M., Glocker, M.O., Wunderlin, M., Przybylski, M. Direct isolation of proteins from SDS-PAGE and analysis by ES MS. Electrophoresis 17:848-854, 1996.
64. Cohen, S., Chait, B. Mass spectrometry of whole proteins eluted from sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels. Anal. Biochem. 247:257-267, 1997.
65. Jensen, C., Haebel, S., Andersen, S.O., Roepstorff, P. Towards monitoring of protein purification by matrix-assisted laser desorption ionization mass spectrometry. Int. J. Mass Spectrom. Ion Proc. 160:339-356, 1997.
66. Yip, T., Hutchens, T. Mapping and sequence-specific identification of phosphopeptides in unfractionated protein digest mixtures by matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry. FEBS Lett. 308:149-153, 1992.
67. Liao, P.-C., Leykam, J., Andrews, P.C., Gage, D.A., Allison, J. An approach to locate phosphorylation sites in a phosphoprotein: Mass mapping by combining specific enzymatic degradation with matrix-assisted laser desorption/ionization mass spectrometry. Anal. Biochem. 219:9-20, 1994.
68. Zhang, W., Czernik, A.J., Yungwirth, T., Aebersold, R., Chait, B.T. Matrix-assisted laser desorption mass spectrometric peptide mapping of proteins separated by two-dimensional gel electrophoresis: Determination of phosphorylation in synapsin I. Protein Sci. 3:677-686, 1994.
69. 68a. Zhang, X., Herring, C.J., Romano, P.R., et al. Identification of phosphorylation sites in proteins separated by polyacrylamide gel electrophoresis. Anal. Chem. 70(10): 2050-2059, 1998.
70. Feng, L., Yoon, H., Donahue, T.F. Casein kinase II mediates multiple phosphorylation of Saccharomyces cerevisiae eIF-2 alpha (encoded by SUI2), which is required for optimal eIF-2 function in S. cerevisiae. Mol. Cell. Biol. 14:5139-5153, 1994.
71. Annan, R., Carr, S. Phosphopeptide analysis by matrix-assisted laser desorption time-of-flight mass spectrometry Anal. Chem. 68:3413-3421, 1996.
72. Wilm, M., Neubauer, G., Mann, M. Parent ion scans of unseparated peptide mixtures. Anal. Chem. 68:527-533, 1996.
73. Carr, S.A., Huddleston, M.J., Annan, R.S. Selective detection and sequencing of phosphopeptides at the femtomole level by mass spectrometry. Anal. Biochem. 239:180-192, 1996.
74. 72a. Neubauer, G., Mann, M. Mapping phosphorylation sites of gel-isolated proteins by nanoelectrospray: Potentials and limitations (in press).
75. 72b. Wong, H.N., Ward, M.A., Bell A.W., et al. Conserved in vivo phosphorylation of calnexin at casein kinase II sites as well as a protein kinase C/proline-directed kinase site. J. Biol. Chem. 273(27):17,227-17,235, 1998.
76. Roos, M., Su, K., Baker, J., Je, K. O-glycosylation of an Sp1-derived peptide blocks known Sp1 protein interactions. Mol. Cell. Biol. 17:6472-6480, 1997.
77. Mørtz, E.S.T., Haebel, S., Julkunen, I., Roepstorff, P. Mass spectrometric characterization of glycosylated interferon-gamma variants separated by gel electrophoresis. Electrophoresis 17:925-931, 1996.
78. Mørtz, E.S.T., Julkunen, I., Roepstorff, P. Does matrix-assisted laser desorption/ionization mass spectrometry allow analysis of carbohydrate heterogeneity in glycoproteins? A study of natural human interferon-gamma. J. Mass Spectrom. 31:1109-1118, 1996.
79. Kuster, B., Wheeler, S.F., Hunter, A.P., Dwek, R.A., Harvey, D.J. Sequencing of N-linked oligosaccharides directly from protein gels: In-gel deglycosylation followed by MALDI mass spectrometry and normal phase HPLC. Anal. Biochem. 250:82-101, 1997.
80. Carr, S.A., Huddleston, M.J., Bean, M.F. Selective identification and differentiation of N- and O-linked oligosaccharides in glycoproteins by liquid chromatography-mass spectrometry. Protein Sci. 2:183-196, 1993.