Mass spectrometry-based functional proteomics: From molecular machines to protein networks

Nature Methods

Volumn 4, Issue 10, 2007, Pages 807-815

  Köcher, Thomas ^a   Superti Furga, Giulio ^a  

^a ERICH SCHMID INSTITUTE OF MATERIALS SCIENCE   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN; PROTEIN; PROTEOME;

ANALYTIC METHOD; BIOINFORMATICS; FUNCTIONAL PROTEOMICS; GENOMICS; HUMAN; MASS SPECTROMETRY; MOLECULE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; REVIEW;

COMPUTERS, MOLECULAR; MASS SPECTROMETRY; PROTEIN INTERACTION MAPPING; PROTEINS; PROTEOMICS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; VALIDATION STUDIES AS TOPIC;

EID: 35848955168     PISSN: 15487091     EISSN: 15491676     Source Type: Journal    
DOI: 10.1038/nmeth1093     Document Type: Review

References (100)

1. Steen, H. & Mann, M. The ABCs (and XYZ's) of peptide sequencing. Nat. Rev. Mol. Cell Biol. 5, 699-711 (2004).
2. Ferguson, P.L. & Smith, R.D. Proteome analysis by mass spectrometry. Annu. Rev. Biophys. Biomol. Struct. 32, 399-424 (2003).
3. Bouwmeester, T. et al. A physical and functional map of the human TNF-alpha NF-kappa B signal transduction pathway. Nat. Cell Bio. 6, 97-105 (2004).
4. Blagoev, B. et al. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat. Biotechnol. 21, 315-318 (2003).
5. Major, M.B. et al. Wilms tumor suppressor WTX negatively regulates WNT/betacatenin signaling. Science 316, 1043-1046 (2007).
6. Weston, A.D. & Hood, L Systems biology, proteomics, and the future of health care: Toward predictive, preventative, and personalized medicine. J. Proteome Res. 3, 179-196 (2004).
7. Anderson, N.L. & Anderson, N.G. The human plasma proteome - history, character, and diagnostic prospects. Mol. Cell. Proteomics 1 845-867 (2002).
8. Gavin, A.C. et al. Functional organization of the yeast prateome by systematic analysis of protein complexes. Nature 415: 141-147 (2002).
9. Ho, Y. et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415 180-183 (2002).
10. Riedel, C.G. et al. Protein phosphatase 2A protects centromeric sister chromatid cohesion during meiosis I. Nature 441, 53-61 (2006).
11. Vanacova, S. et al. A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol. 3, 986-997 (2005).
12. Bertwistle, D., Sugimoto, M. & Sherr, C.J. Physical and functional interactions of the Arf tumor suppressor protein with nucleophasmin/B23. Mol. Cell. Biol. 24, 985-996 (2004).
13. Lorentzen, E. et al. The archaeal exosome core is a hexameric ring structure with three catalytic subunits. Nat. Struct. Mol. Biol. 12, 575-581 (2005).
14. Hao, B., Oehlmann, S., Sowa, M.E., Harper, J.W. & Pavletich, N.P. Structure of a Fbw7-Skp1-cyclin E complex: Multisite-phosphorylated substrate recognition by SCF ubiquitinjigases. Mol, Cell 26, 131-143 (2007).
15. Nickell, S., Kofler, C., Lets, A.P. & Baumeister, W. A visual approach to proteomics. Not. Rev. Mol. Cell Biol. 7, 229-230 (2006).
16. Groll, M., Bochtler, M., Brandstetter, H., Clausen, T. & Huber, R. Molecular machines for protein degradation. ChemBioChem 6, 222-256 (2005).
17. Gorg, A., Weiss, W. & Dunn, M.J. Current two-dimensional electrophoresis technology for proteomics. Proteomics 4, 3665-3685 (2004).
18. Wulfkuhle, J.D. et al. Proteomics of human breast ductal carcinoma in-situ. Cancer. Res. 62, 6740-6749 (2002).
19. Le Naour, F. et al. Profiling changes in gene expression during differentiation and maturation of monocyte-derived dendritic cells using both oligonucleotide microarrays and proteomics. J. Biol. Chem. 276, 17920-17931 (2001).
20. Ong, S.E. & Mann, M. Mass spectrometry-baied proteomics turns quantitative. Nat. Chem. Biol. 1, 252-262 (2005).
21. Zhang, H., Yan, W. & Aebersold, R. Chemical probes and tandem mass spectrometry: A strategy for the quantitative analysis of proteomes and subproteomes. Curr. Opin. Chem. Biol. 8, 66-75 (2004).
22. Jensen, O.N. Modification-specific proteomics: Characterization of posttranslational modifications by mass spectrometry. Curr. Opin. Chem. Biol. 8, 33-41 (2004).
23. Mann, M. & Jensen, O.N. Proteomic analysis of post-translational modificatiohs. Nat. Biotechnol. 21, 255-261 (2003).
24. Gygi, S.P., Rochon, Y., Franza, B.R. & Aebersold, R. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19, 1720-1730 (1999).
25. Ghaemmaghami, S. et al. Global analysis-of protein expression in yeast. Nature 425, 737-741 (2003).
26. Alberts, B. The cell as a collection of protein machines: Preparing the next generation of molecular biologists. Cell 92, 291-294 (1998).
27. Terpe, K. Overview of tag protein fusions: From molecular and biochémical fundamentals to commercial systems. Appl. Microbiol. Biotechnol. 60, 523-533 (2003).
28. Bauch, A. & Superti-Furga, G. Charting protein complexes, signaling pathways, and networks in the immune system. Immunol. Rev. 210 187-207 (2006).
29. Zhu, H. & Snyder, M. Protein chip technology. Curr. Opin. Chem. Biol. 7, 55-63 (2003).
30. Chien, C.T., Bartel, P.L., Sternglanz, R. & Fields, S. The 2-hybrid system - a method to identify and clone genes for proteins that interact with a protein of interest. Proc. Natl. Acad. Sci. USA 88, 9578-9582 (1991).
31. Giepmans, B.N.G., Adams, S.R., Ellisman, M.H. & Tsien, R.Y. The fluorescent toolbox for assessing protein location and function. Science 312, 217-224 (2006).
32. Barrios-Rodiles, M. et al. High-throughput mapping of a dynamic signaling network in mammalian cells. Science 307, 1621-1625 (2005).
33. Aloy, P. & Russell, R.B. Structural systems biology: Modelling protein interactions. Nat. Rev. Mol. Cell Biol. 7, 188-197 (2006).
34. Marcotte, E.M. et al. Detecting protein function and protein-protein interactions from genome sequences. Science 285 751-753 (1999).
35. Tornow, S. & Mewes, H.W. Functional modules by relating protein interaction networks and gene expression. Nucleic Acids Res. 31 6283-6289 (2003).
36. Sharan, R. & Ideker, T. Modeling cellular machinery through biological network comparison. Nat. Biotechnol. 24, 427-433 (2006).
37. Ranish, J.A. et al. The study of macromolecular complexes by quantitative proteomics. Nat. Genet. 33, 349-355 (2003).
38. Mann, M. Functional and quantitative proteomics using SILAC. Nat Rev. Mol. Cell Biol. 7, 952-958 (2006).
39. Hochleitner, E.O. et al. Protein stoichiometry of a multiprotein complex, the human spliceosomal U1 small nuclear ribonucleoprotein - absolute quantification using isotope-coded tags and mass spectrometry. J. Biol. Chem. 280, 2536-2542 (2005).
40. Fields, S. & Song, O.K. A novel genetic system to detect protein-protein interactions. Nature 340, 245-246 (1989).
41. Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198-207 (2003).
42. Fishman, M.C. & Porter, J.A. Pharmaceuticals - a new grammar for drug discovery. Nature 437, 491-493 (2005).
43. Rodi, D.J. & Makowski, L. Phage-display technology - finding a needle in a vast molecular haystack. Curr. Opin. Biotechnol. 10, 87-93 (1999).
44. Cahill, D.J. Protein and antibody arrays and their medical applications. J. Immunol. Methods 250, 81-91 (2001).
45. Zhu, H. et al. Global analysis of protein activities using proteome chips. Science 293, 2101-2105 (2001).
46. Paweletz, C.P. et al. Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene 20, 1981-1989 (2001).
47. Huang, R.P., Huang, R.C., Fan, Y. & Lin, Y. Simultaneous detection of multiple cytokines from conditioned media and patient's sera by an antibody-based protein array system. Anal. Biochem. 294, 55-62 (2001).
48. Zhu, H. et al. Analysis of yeast protein kinases using protein chips. Nat. Genet. 26, 283-289 (2000).
49. Hamelinck, D. et al. Optimized normalization for antibody microarrays and application to serum-protein profiling. Mol. Cell. Proteomics 4, 773-784 (2005).
50. Davies, H., Lomas, L. & Austen, B. Profiling of amyloid beta peptide variants using SELDI ProteinChip (R) arrays. Biotechniques 27 1258-1261 (1999).
51. Hua, S., To, W.Y., Nguyen, T.T., Wong, M.L. & Wang, C.C. Purification and characterization of proteasomes from Trypanosoma brucei. Mol. Biochem. Parasitol. 78, 33-46 (1996).
52. Huang, L. et al. Functional assignment of the 20S proteasome from Trypanosoma brucei using mass spectrometry and new bioinformatics approaches. J. Biol. Chem. 276, 28327-28339 (2001).
53. Harlow, E. & Lane, D. Antibodies: A Laboratory Manual (Cold Spring Harbor Laboratory Press, Cold Springs Harbor, New York, 1998).
54. Uhlen, M. & Ponten, F. Antibody-based proteomics for human tissue profiling. Mol. Cell. Proteomics 4, 384-393 (2005).
55. Nord, K. et al. Binding proteins selected from combinatorial libraries of an alpha-helical bacterial receptor domain. Nat. Biotechnol. 15, 772-777 (1997).
56. Hermann, T. & Patel, D.J. Biochemistry - Adaptive recognition by nucleic acid aptamers. Science 287, 820-825 (2000).
57. Waugh, D.S. Making the most of affinity tags. Trends Biotechnol. 23, 316-320 (2005).
58. de Boer, E. et al. Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice. Proc. Natl. Acad. Sci. USA 100, 7480-7485 (2003).
59. Neubauer, G. et al. Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry. Proc. Natl. Acad. Sci. USA 94, 385-390 (1997).
60. Puig, O. et al. The tandem affinity purification (TAP) method: A general procedure of protein complex purification. Methods 24 218-229 (2001).
61. Rigaut, G. et al. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17, 1030-1032 (1999).
62. Burckstummer, T. et al. An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells. Nat. Methods 3, 1013-1019 (2006).
63. Forler, D. et al. An efficient protein complex purification method for functional proteomics in higher eukaryotes. Nat. Biotechnol. 21, 89-92 (2003).
64. Drakas, R., Prisco, M. & Baserga, R. A modified tandem affinity purification tag technique for the purification of protein complexes in mammalian cells. Proteomics 5, 132-137 (2005).
65. Knuesel, M. et al. Identification of novel protein-protein interactions using a versatile mammalian tandem affinity purification expression system. Mol. Cell. Proteomics 2, 1225-1233 (2003).
66. Westermarck, J. et al. The DEXD/H-box RNA helicase RHII/Gu is a co-factor for c-Jun-activated transcription. EMBO J. 21, 451-460 (2002).
67. Gavin, A.C. & Superti-Furga, G. Protein complexes and proteome organization from yeast to man. Curr. Opin. Chem. Biol. 7, 21-27 (2003).
68. Benesch, J.L.P., Aquilina, J.A., Ruotolo, B.T., Sobott, F. & Robinson, C.V. Tandem mass spectrometry reveals the quaternary organization of macromolecular assemblies. Chem. Biol. 13, 597-605 (2006).
69. Kelleher, N.L. et al. Top down versus bottom up protein characterization by tandem high-resolution mass spectrometry. J. Am. Chem. Soc. 121, 806-812 (1999).
70. Benjamin, D.R., Robinson, C.V., Hendrick, J.P., Hartl, F.U. & Dobson, C.M. Mass spectrometry of ribosomes and ribosomal subunits. Proc. Natl. Acad. Sci. USA 95, 7391-7395 (1998).
71. Sharon, M., Taverner, T., Ambroggio, X.I., Deshaies, R.J. & Robinson, C.V. Structural organization of the 19S proteasome lid: Insights from MS of intact complexes. PLoS Biol. 4, 1314-1323 (2006).
72. Hernandez, H., Dziembowski, A., Taverner, T., Seraphin, B. Robinson, C.V. Subunit architecture of multimeric complexes isolated directly from cells. EMBO Rep. 7, 605-610 (2006).
73. Rappsilber, J., Siniossoglou, S., Hurt, E.C. & Mann, M. A generic strategy to analyze the spatial organization of multi-protein complexes by cross-linking and mass spectrometry. Anal. Chem. 72, 267-275 (2000).
74. Vasilescu, J., Guo, X.C. & Kast, J. Identification of protein-protein interactions using in vivo cross-linking and mass spectrometry. Proteomics 4, 3845-3854 (2004).
75. Shevchenko, A., Tomas, H., Havlis, J., Olsen, J. V. & Mann, M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protoc. 1, 2856-2860 (2006).
76. Havlis, J. & Shevchenko, A. Absolute quantification of proteins in solutions and in polyacrylamide gels by mass spectrometry. Anal. Chem. 76, 3029-3036 (2004).
77. Link, A.J. et al. Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17, 676-682 (1999).
78. Washburn, M.P., Wolters, D. & Yates, J.R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247 (2001).
79. Wilm, M. et al. Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 379, 466-469 (1996).
80. Wilm, M. & Mann, M. Analytical properties of the nanoelectrospray ion source. Anal. Chem. 68, 1-8 (1996).
81. Fenn, J.B., Mann, M., Meng, C.K., Wong, S.F. & Whitehouse, C.M. Electrospray ionization for mass-spectrometry of large biomolecules. Science 246, 64-71 (1989).
82. Karas, M., Bachmann, D., Bahr, U. & Hillenkamp, F. Matrix-assisted ultraviolet-laser desorption of nonvolatile compounds. Int. J. Mass Spectrom. Ion Process. 78, 53-68 (1987).
83. Clauser, K.R., Baker, P. & Burlingame, A.L. Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem. 71, 2871-2882 (1999).
84. Perkins, D.N., Pappin, D.J.C., Creasy, D.M. & Cottrell, J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567 (1999).
85. Eng, J.K., McCormack, A.L. & Yates, J.R. An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976-989 (1994).
86. Elias, J.E. & Gygi, S.P. Target-decoy search strategy for increased-confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207-214 (2007).
87. Olson, J.V. & Mann, M. Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc. Natl. Acad. Sci. USA 101, 13417-13422 (2004).
88. Nesvizhskii, A.I. & Aebersold, R. Interpretation of shotgun proteomic data - the protein inference problem. Mol. Cell. Proteomics 4 1419-1440 (2005).
89. Brazma, A., Krestyaninova, M. & Sarkans, U. Standards for systems biology. Nat. Rev. Genet. 7, 593-605 (2006).
90. Taylor, C. F. et al. The minimum information about a proteomics experiment (MIAPE). Nat. Biotechnol. 25, 837-893 (2007).
91. Orchard, S. et al. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat. Biotechnol. 25 894-898 (2007).
92. Gerber, S.A., Rush, J., Stemman, O., Kirschner, M.W. & Gygi, S.P. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. USA 100, 6940-6945 (2003).
93. Aloy, P. et al. Structure-based assembly of protein complexes in yeast. Science 303, 2026-2029 (2004).
94. Schirle, M. Heurtier, M.A. & Kuster, B. Profiling core proteomes of human cell lines by one-dimensional PAGE and liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteomics 2, 1297-1305 (2003).
95. Krogan, N.J. et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643 (2006).
96. Gavin, A.C. et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636 (2006).
97. Uetz, P. et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627 (2000).
98. Ito, T. et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98, 4569-4574 (2001).
99. Andersen, J.S. & Mann, M. Organellar proteomics: Turning inventories into insights. EMBO Rep. 7, 874-879 (2006).
100. Goh, K.I. et al. The human disease network. Proc. Natl. Acad. Sci. USA 104, 8685-8690 (2007).