Proteomics

Annual Review of Genomics and Human Genetics

Volumn 5, Issue , 2004, Pages 267-293

  De Hoog, Carmen L ^a   Mann, Matthias ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

Functional genomics; Mass spectrometry; Organellar proteomics; Protein arrays; Protein protein interactions; Systems biology

Indexed keywords

BIOINFORMATICS; CELL ORGANELLE; GENE SEQUENCE; GENETIC TRANSCRIPTION; GENOMICS; MASS SPECTROMETRY; METABOLITE; METABOLOMICS; MOLECULAR BIOLOGY; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN MICROARRAY; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEOMICS; REVIEW; RNA TRANSLATION; TECHNOLOGY;

GENOMICS; MASS SPECTROMETRY; PROTEIN BINDING; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOMICS;

EID: 5444223979     PISSN: 15278204     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.genom.4.070802.110305     Document Type: Review

References (123)

1. Abola E, Kuhn P, Earnest T, Stevens RC. 2000. Automation of X-ray crystallography. Nat. Struct. Biol. 7(Suppl.):973-77
2. Adam GC, Sorensen EJ, Cravatt BF. 2002. Chemical strategies for functional proteomics. Mol. Cell. Proteomics 1:781-90
3. Adkins JN, Varnum SM, Auberry KJ, Moore RJ, Angell NH, et al. 2002. Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol. Cell. Proteomics 1:947-55
4. Aebersold R, Mann M. 2003. Mass spectrometry-based proteomics. Nature 422:198-207
5. Aebersold R, Watts JD. 2002. The need for national centers for proteomics. Nat. Biotechnol. 20:651
6. Agaton C, Galli J, Hoiden Guthenberg I, Janzon L, Hansson M, et al. 2003. Affinity proteomics for systematic protein profiling of chromosome 21 gene products in human tissues. Mol. Cell. Proteomics 2:405-14
7. Andersen JS, Wilkinson CJ, Mayor T, Mortensen P, Nigg EA, Mann M. 2003. Proteomic characterization of the human centrosome by protein correlation profiling. Nature 426:570-74
8. Anderson DC, Li W, Payan DG, Noble WS. 2003. A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores. J. Proteome Res. 2:137-46
9. Anderson NL, Anderson NG. 2002. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics 1:845-67
10. Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW. 2001. BIND - The Biomolecular Interaction Network Database. Nucl. Acids Res. 29:242-45
11. Bader GD, Heilbut A, Andrews B, Tyers M, Hughes T, Boone C. 2003. Functional genomics and proteomics: charting a multidimensional map of the yeast cell. Trends Cell Biol. 13:344-56
12. Bader JS, Chaudhuri A, Rothberg JM, Chant J. 2004. Gaining confidence in high-throughput protein interaction networks. Nat. Biotechnol. 22:78-85
13. Bailey SN, Wu RZ, Sabatini DM. 2002. Applications of transfected cell microarrays in high-throughput drug discovery. Drug Discov. Today 7:S113-18
14. Baldwin MA. 2004. Protein identification by mass spectrometry: issues to be considered. Mol. Cell. Proteomics 3:1-9
15. Blagoev B, Kratchmarova I, Ong SE, Nielsen M, Foster LJ, Mann M. 2003. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat. Biotechnol. 21:315-18
16. Braun P, LaBaer J. 2003. High throughput protein production for functional proteomics. Trends Biotechnol. 21:383-88
17. Brunet S, Thibault P, Gagnon E, Kearney P, Bergeron JJ, Desjardins M. 2003. Organelle proteomics: looking at less to see more. Trends Cell Biol. 13:629-38
18. Coates PJ, Hall PA. 2003. The yeast two-hybrid system for identifying protein-protein interactions. J. Pathol. 199:4-7
19. Dahlberg AE. 2001. Ribosome structure. The ribosome in action. Science 292:868-69
20. Elia AE, Cantley LC, Yaffe MB. 2003. Proteomic screen finds pSer/pThr-binding domain localizing Plk1 to mitotic substrates. Science 299:1228-31
21. Ficarro SB, McCleland ML, Stukenberg PT, Burke DJ, Ross MM, et al. 2002. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 20:301-5
22. Fields S, Song O. 1989. A novel genetic system to detect protein-protein interactions. Nature 340:245-46
23. Florens L, Washburn MP, Raine JD, Anthony RM, Grainger M, et al. 2002. A proteomic view of the Plasmodium falciparum life cycle. Nature 419:520-26
24. Forler D, Kocher T, Rode M, Gentzel M, Izaurralde E, Wilm M. 2003. An efficient protein complex purification method for functional proteomics in higher eukaryotes. Nat. Biotechnol. 21:89-92
25. Foster LJ, de Hoog CL, Mann M. 2003. Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors. Proc. Natl. Acad. Sci. USA 100:5813-18
26. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW. 2002. Evolutionary rate in the protein interaction network. Science 296:750-52
27. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141-47
28. Gevaert K, Goethals M, Martens L, Van Damme J, Staes A, et al. 2003. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat. Biotechnol. 21:566-69
29. Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, et al. 2003. Global analysis of protein expression in yeast. Nature 425:737-41
30. Gibbs RA, Belmont JW, Hardenbol P, Willis TD, Yu F, et al. 2003. The International HapMap Project. Nature 426:789-96
31. Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, et al. 2003. A protein interaction map of Drosophila melanogaster. Science 302:1727-36
32. Glokler J, Angenendt P. 2003. Protein and antibody microarray technology. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 797:229-40
33. Godl K, Wissing J, Kurtenbach A, Habenberger P, Blencke S, et al. 2003. An efficient proteomics method to identify the cellular targets of protein kinase inhibitors. Proc. Natl. Acad. Sci. USA 100:15434-39
34. Goshe MB, Conrads TP, Panisko EA, Angell NH, Veenstra TD, Smith RD. 2001. dePhosphoprotein isotope-coded affinity tag approach for isolating and quantitating phosphopeptides in proteome-wide analyses. Anal. Chem. 73:2578-86
35. Graves PR, Haystead TA. 2002. Molecular biologist's guide to proteomics. Microbiol. Mol. Biol. Rev. 66:39-63
36. Grønborg M, Kristiansen TZ, Stensballe A, Andersen JS, Ohara O, et al. 2002. A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein, Frigg, as a protein kinase A substrate. Mol. Cell. Proteomics 1:517-27
37. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. 1999. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17:994-99
38. Hansen KC, Schmitt-Ulms G, Chalkley RJ, Hirsch J, Baldwin MA, Burlingame AL. 2003. Mass spectrometric analysis of protein mixtures at low levels using cleavable 13C-isotope-coded affinity tag and multidimensional chromatography. Mol. Cell. Proteomics 2:299-314
39. Hazbun TR, Malmstrom L, Anderson S, Graczyk BJ, Fox B, et al. 2003. Assigning function to yeast proteins by integration of technologies. Mol. Cell 12:1353-65
40. Hegde PS, White IR, Debouck C. 2003. Interplay of transcriptomics and proteomics. Curr. Opin. Biotechnol. 14:647-51
41. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, et al. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180-83
42. Horning S, Malek R, Wieghaus A, Senko MW, Syka JEP. 2003. A hybrid two-dimensional quadrupole ion trap/fourier transform ion cyclotron mass spectrometer: accurate mass and high resolution at a chromatography timescale. Presented at Am. Soc. Mass Spectrom. Conf. Mass Spectrom. Allied Top., 51st, Montreal, Canada
43. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, et al. 2003. Global analysis of protein localization in budding yeast. Nature 425:686-91
44. Huynen MA, Snel B, von Mering C, Bork P. 2003. Function prediction and protein networks. Curr. Opin. Cell Biol. 15:191-98
45. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98:4569-74
46. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, et al. 2003. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302:449-53
47. Jeong H, Mason SP, Barabasi AL, Oltvai ZN. 2001. Lethality and centrality in protein networks. Nature 411:41-42
48. Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, et al. 2004. EnsMart: a generic system for fast and flexible access to biological data. Genome. Res. 14:160-69
49. Keller A, Nesvizhskii AI, Kolker E, Aebersold R. 2002. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74:5383-92
50. Knight ZA, Schilling B, Row RH, Kenski DM, Gibson BW, Shokat KM. 2003. Phosphospecific proteolysis for mapping sites of protein phosphorylation. Nat. Biotechnol. 21:1047-54
51. Kononen J, Bubendorf L, Kallioniemi A, Barlund M, Schraml P, et al. 1998. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat. Med. 4:844-47
52. Krijgsveld J, Ketting RF, Mahmoudi T, Johansen J, Artal-Sanz M, et al. 2003. Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat. Biotechnol. 21:927-31
53. Kumar A, Agarwal S, Heyman JA, Matson S, Heidtman M, et al. 2002. Subcellular localization of the yeast proteome. Genes Dev. 16:707-19
54. Kuruvilla FG, Shamji AF, Sternson SM, Hergenrother PJ, Schreiber SL. 2002. Dissecting glucose signalling with diversity-oriented synthesis and small-molecule microarrays. Nature 416:653-57
55. Kuster B, Mortensen P, Andersen JS, Mann M. 2001. Mass spectrometry allows direct identification of proteins in large genomes. Proteomics 1:641-50
56. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921
57. Lasonder E, Ishihama Y, Andersen JS, Vermunt AM, Pain A, et al. 2002. Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature 419:537-42
58. Li J, Steen H, Gygi SP. 2003. Protein profiling with cleavable isotope-coded affinity tag (cICAT) reagents: the yeast salinity stress response. Mol. Cell. Proteomics 2:1198-204
59. Li S, Armstrong CM, Bertin N, Ge H, Milstein S, et al. 2004. A map of the interactome network of the Metazoan C. elegans. Science 303(5657):540-43
60. Lill J. 2003. Proteomic tools for quantitation by mass spectrometry. Mass Spectrom. Rev. 22:182-94
61. Lueking A, Possling A, Huber O, Beveridge A, Horn M, et al. 2003. A nonredundant human protein chip for antibody screening and serum profiling. Mol. Cell. Proteomics 2:1342-49
62. Lundgren DH, Eng J, Wright ME, Han DK. 2003. PROTEOME-3D: an interactive bioinformatics tool for large-scale data exploration and knowledge discovery. Mol. Cell. Proteomics 2:1164-76
63. MacCoss MJ, McDonald WH, Saraf A, Sadygov R, Clark JM, et al. 2002. Shotgun identification of protein modifications from protein complexes and lens tissue. Proc. Natl. Acad. Sci. USA 99:7900-5
64. Mann M, Jensen ON. 2003. Proteomic analysis of post-translational modifications. Nat. Biotechnol. 21:255-61
65. Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D. 1999. Detecting protein function and protein-protein interactions from genome sequences. Science 285:751-53
66. Marshall AG, Hendrickson CL, Jackson GS. 1998. Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom. Rev. 17:1-35
67. Medalia O, Weber I, Frangakis AS, Nicastro D, Gerisch G, Baumeister W. 2002. Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography. Science 298:1209-13
68. Michaud GA, Salcius M, Zhou F, Bangham R, Bonin J, et al. 2003. Analyzing antibody specificity with whole proteome microarrays. Nat. Biotechnol. 21:1509-12
69. Mootha VK, Bunkenborg J, Olsen JV, Hjerrild M, Wisniewski JR, et al. 2003. Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell 115:629-40
70. Mootha VK, Lepage P, Miller K, Bunkenborg J, Reich M, et al. 2003. Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics. Proc. Natl. Acad. Sci. USA 100:605-10
71. Nesvizhskii AI, Keller A, Kolker E, Aebersold R. 2003. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75:4646-58
72. Neubauer G, King A, Rappsilber J, Calvio C, Watson M, et al. 1998. Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex. Nat. Genet. 20:46-50
73. Nielsen UB, Cardone MH, Sinskey AJ, MacBeath G, Sorger PK. 2003. Profiling receptor tyrosine kinase activation by using Ab microarrays. Proc. Natl. Acad. Sci. USA 100:9330-35
74. Nishizuka S, Charboneau L, Young L, Major S, Reinhold WC, et al. 2003. Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc. Natl. Acad. Sci. USA 100:14229-34
75. Oda Y, Nagasu T, Chait BT. 2001. Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat. Biotechnol. 19:379-82
76. Oda Y, Owa T, Sato T, Boucher B, Daniels S, et al. 2003. Quantitative chemical proteomics for identifying candidate drug targets. Anal. Chem. 75:2159-65
77. Olsen JV, Ong SE, Mann M. 2004. Trypsin cleaves exclusively C-terminal to Arginine and lysine residues. Mol. Cell. Proteomics http://www.ncbi.nlm.nih. gov:80/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt= Abstract&list_uids=15034119
78. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, et al. 2002. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1:376-86
79. Ong SE, Kratchmarova I, Mann M. 2003. Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J. Proteome Res. 2:173-81
80. Orchard S, Hermjakob H, Apweiler R. 2003. The proteomics standards initiative. Proteomics 3:1374-76
81. Paigen K, Eppig JT. 2000. A mouse phenome project. Mamm. Genome 11:715-17
82. Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP. 2003. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J. Proteome Res. 2:43-50
83. Peng J, Schwartz D, Elias JE, Thoreen CC, Cheng D, et al. 2003. A proteomics approach to understanding protein ubiquitination. Nat. Biotechnol. 21:921-26
84. Petricoin EF, Ardekani AM, Hitt BA, Levine PJ, Fusaro VA, et al. 2002. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359:572-77
85. Phizicky E, Bastiaens PI, Zhu H, Snyder M, Fields S. 2003. Protein analysis on a proteomic scale. Nature 422:208-15
86. Pieper R, Gatlin CL, Makusky AJ, Russo PS, Schatz CR, et al. 2003. The human serum proteome: display of nearly 3700 chromatographically separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins. Proteomics 3:1345-64
87. Ranish JA, Yi EC, Leslie DM, Purvine SO, Goodlett DR, et al. 2003. The study of macromolecular complexes by quantitative proteomics. Nat. Genet. 33:349-55
88. Rappsilber J, Ryder U, Lamond AI, Mann M. 2002. Large-scale proteomic analysis of the human spliceosome. Genome Res. 12:1231-45
89. Reboul J, Vaglio P, Rual JF, Lamesch P, Martinez M, et al. 2003. C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat. Genet. 34:35-41
90. Sali A, Glaeser R, Earnest T, Baumeister W. 2003. From words to literature in structural proteomics. Nature 422:216-25
91. Salwinski L, Eisenberg D. 2003. Computational methods of analysis of protein-protein interactions. Curr. Opin. Struct. Biol. 13:377-82
92. Schirle M, Heurtier MA, Kuster B. 2003. Profiling core proteomes of human cell lines by one-dimensional PAGE and liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteomics 2:1297-305
93. Schulze WX, Mann M. 2004. A novel proteomic screen for peptide-protein interactions. J. Biol. Chem. 279:10756-64
94. Schweitzer B, Kingsmore SF. 2002. Measuring proteins on microarrays. Curr. Opin. Biotechnol. 13:14-19
95. Schweitzer B, Predki P, Snyder M. 2003. Microarrays to characterize protein interactions on a whole-proteome scale. Proteomics 3:2190-99
96. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13:2498-504
97. Sidhu SS, Bader GD, Boone C. 2003. Functional genomics of intracellular peptide recognition domains with combinatorial biology methods. Curr. Opin. Chem. Biol. 7:97-102
98. Specht KM, Shokat KM. 2002. The emerging power of chemical genetics. Curr. Opin. Cell Biol. 14:155-59
99. Speers AE, Cravatt BF. 2004. Chemical strategies for activity-based proteomics. Chembiochemistry 5:41-47
100. Stagljar I. 2003. Finding partners: emerging protein interaction technologies applied to signaling networks. 2003. Sci. STKE pe56
101. Steen H, Mann M. 2002. A new derivatization strategy for the analysis of phosphopeptides by precursor ion scanning in positive ion mode. J. Am. Soc. Mass. Spectrom 13:996-1003
102. Steen H, Mann M. 2004. The abc's (and xyz's) of peptide sequencing. Nat. Rev. Mol. Cell Biol. In press
103. Steen H, Pandey A, Andersen JS, Mann M. 2002. Analysis of tyrosine phosphorylation sites in signaling molecules by a phosphotyrosine-specific immonium ion scanning method. 2002. Sci. STKE PL16
104. Taylor CF, Paton NW, Garwood KL, Kirby PD, Stead DA, et al. 2003. A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat. Biotechnol. 21:247-54
105. Tirumalai RS, Chan KC, Prieto DA, Issaq HJ, Conrads TP, Veenstra TD. 2003. Characterization of the low molecular weight human serum proteome. Mol. Cell. Proteomics 2:1096-103
106. Tong AH, Drees B, Nardelli G, Bader GD, Brannetti B, et al. 2002. A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 295:321-24
107. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, et al. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623-27
108. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, et al. 2001. The sequence of the human genome. Science 291:1304-51
109. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, et al. 2002. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417:399-403
110. Wilkins MR, Pasquali C, Appel RD, Ou K, Golaz O, et al. 1996. From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology 14:61-65
111. Winssinger N, Ficarro S, Schultz PG, Harris JL. 2002. Profiling protein function with small molecule microarrays. Proc. Natl. Acad. Sci. USA 99:11139-44
112. Wouters FS, Verveer PJ, Bastiaens PI. 2001. Imaging biochemistry inside cells. Trends Cell Biol. 11:203-11
113. Wulfkuhle JD, Liotta LA, Petricoin EF. 2003. Proteomic applications for the early detection of cancer. Nat. Rev. Cancer 3:267-75
114. Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, Eisenberg D. 2002. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucl. Acids Res. 30:303-5
115. Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G. 2002. MINT: a Molecular INTeraction database. FEBS Lett. 513:135-40
116. Zhang H, Li XJ, Martin DB, Aebersold R. 2003. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat. Biotechnol. 21:660-66
117. Zhou H, Ranish JA, Watts JD, Aebersold R. 2002. Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nat. Biotechnol. 20:512-15
118. Zhou H, Watts JD, Aebersold R. 2001. A systematic approach to the analysis of protein phosphorylation. Nat. Biotechnol. 19:375-78
119. Zhou Z, Licklider LJ, Gygi SP, Reed R. 2002. Comprehensive proteomic analysis of the human spliceosome. Nature 419:182-85
120. Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, et al. 2001. Global analysis of protein activities using proteome chips. Science 293:2101-5
121. Zhu H, Klemic JF, Chang S, Bertone P, Casamayor A, et al. 2000. Analysis of yeast protein kinases using protein chips. Nat. Genet. 26:283-89
122. Zhu H, Snyder M. 2003. Protein chip technology. Curr. Opin. Chem. Biol. 7:55-63
123. Ziauddin J, Sabatini DM. 2001. Microarrays of cells expressing defined cDNAs. Nature 411:107-10