Proteomics

Methods in Enzymology

Volumn 402, Issue , 2005, Pages 245-289

  Stults, John T ^b   Arnott, David ^a  

^a GENENTECH INC   (United States)

^b Predicant Biosciences   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; DRUG DEVELOPMENT; DRUG EFFICACY; DRUG TARGETING; DRUG TOXICITY; GEL ELECTROPHORESIS; GENOMICS; HEART MUSCLE CELL; HEART VENTRICLE HYPERTROPHY; HUMAN; HUMAN GENOME; MOLECULAR WEIGHT; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ISOLATION; PROTEIN MICROARRAY; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEOMICS; REVIEW; STRUCTURAL PROTEOMICS;

ANIMALS; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; HUMANS; PROTEINS; PROTEOMICS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 30144439996     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(05)02008-2     Document Type: Review

References (182)

1. Aebersold R., and Goodlett D.R. Mass spectrometry in proteomics Chem. Rev. 101 2001 269 295
2. Aebersold R., and Mann M. Mass spectrometry-based proteomics Nature 422 2003 198 207
3. Aicher L., Wahl D., Arce A., Grenet O., and Steiner S. New insights into cyclosporine A nephrotoxicity by proteome analysis Electrophoresis 19 1998 1998 2003
4. Alaiya A.A., Franzen B., Auer G., and Linder S. Cancer proteomics: From identification of novel markers to creation of artificial learning models for tumor classification Electrophoresis 21 2000 1210 1217
5. Andersen J.S., Lam Y.W., Leung A.K., Ong S.E., Lyon C.E., Lamond A.I., and Mann M. Nucleolar proteome dynamics Nature 433 2005 77 83
6. Andersen J.S., Lyon C.E., Fox A.H., Leung A.K., Lam Y.W., Steen H., Mann M., and Lamond A.I. Directed proteomic analysis of the human nucleolus Curr. Biol. 12 2002 1 11
7. Anderson L., and Seilhamer J. A comparison of selected mRNA and protein abundances in human liver Electrophoresis 18 1997 533 537
8. Anderson N.G., and Anderson N.L. The human protein index Clin. Chem. 28 1982 739 748
9. Anderson N.G., Matheson A., and Anderson N.L. Back to the future: The human protein index (HPI) and the agenda for post-proteomic biology Proteomics 1 2001 3 12
10. Anderson N.L., Esquer-Blasco R., Richardson F., Foxworthy P., and Eacho P. The effects of peroxisome proliferators on protein abundances in mouse liver Toxicol. Appl. Pharmacol. 137 1996 75 89
11. Anderson N.L., Matheson A.D., and Steiner S. Proteomics: Applications in basic and applied biology Curr. Opin. Biotechnol. 11 2000 408 412
12. Anderson N.L., Taylor J., Hofmann J.P., Esquer-Blasco R., Swift S., and Anderson N.G. Simultaneous measurement of hundreds of liver proteins: Application in assessment of liver function Toxicol. Pathol. 24 1996 72 76
13. Annan R.S., Huddleston M.J., Verma R., Deshaies R.J., and Carr S.A. A multidimensional electrospray MS-based approach to phosphopeptide mapping Anal. Chem. 73 2001 393 404
14. Arnott D., Henzel W., and Stults J.T. Rapid identification of comigrating gel-isolated proteins by ion trap-spectrometry Electrophoresis 19 1998 968 980
15. Arnott D., Kishiyama A., Luis E.A., Ludlum S.G., Marsters J.C. Jr., and Stults J.T. Selective detection of membrane proteins without antibodies: A mass spectrometric version of the Western blot Mol. Cell Proteom. 1 2002 148 156
16. Arnott D., O'Connell K., King K., and Stults J.T. An integrated approach to proteome analysis: Identification of proteins associated with cardiac hypertrophy Anal. Biochem. 258 1998 1 18
17. Ballif B.A., Villen J., Beausoleil S.A., Schwartz D., and Gygi S.P. Phosphoproteomic analysis of the developing mouse brain Mol. Cell Proteom. 3 2004 1093 1101
18. Banks R.E., Dunn M.J., Forbes M.A., Stanley A., Pappin D., Naven T., Gough M., Harnden P., and Selby P.J. The potential use of laser capture microdissection to selectively obtain distinct populations of cells for proteomic analysis - preliminary findings Electrophoresis 20 1999 689 700
19. Beausoleil S.A., Jedrychowski M., Schwartz D., Elias J.E., Villen J., Li J., Cohn M.A., Cantley L.C., and Gygi S.P. Large-scale characterization of HeLa cell nuclear phosphoproteins Proc. Natl. Acad. Sci. USA 101 2004 12130 12135
20. Bell A.W., Ward M.A., Blackstock W.P., Freeman H.N., Choudhary J.S., Lewis A.P., Chotai D., Fazel A., Gushue J.N., Paiement J., Palcy S., Chevet E., Lafreniere-Roula M., Solari R., Thomas D.Y., Rowley A., and Bergeron J.J. Proteomics characterization of abundant Golgi membrane proteins J. Biol. Chem. 276 2001 5152 5165
21. Bell A.W., Ward M.A., Blackstock W.P., Freeman H.N.M., Choudhary J.S., Lewis A.P., Chotai D., Fazel A., Gushue J.N., Paiement J., Palcy S., Chevet E., Lafreniere-Roula M., Solari R., Thomas D.Y., Rowley A., and Bergeron J.J.M. Proteomics characterization of abundant Golgi membrane proteins J. Biol. Chem. 276 2001 5152 5165
22. Berndt P., Hobohm U., and Langen H. Reliable automatic protein identification from matrix-assisted laser desorption/ionization mass spectrometric peptide fingerprints Electrophoresis 20 1999 3521 3526
23. Bini L., Magi B., Marzocchi B., Arcuri F., Tripodi S., Cintorino M., Sanchez J.C., Frutiger S., Hughes G., Pallini V., Hochstrasser D.F., and Tosi P. Protein expression profiles in human breast ductal carcinoma and histologically normal tissue Electrophoresis 18 1997 2832 2841
24. Blackstock W., and Weir M. Proteomics: Quantitative and physical mapping of cellular proteins TibTech 17 1999 121 127
25. Blagoev B., Ong S.E., Kratchmarova I., and Mann M. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics Nat. Biotechnol. 22 2004 1139 1145
26. Brunet S., Thibault P., Gagnon E., Kearney P., Bergeron J.J., and Desjardins M. Organelle proteomics: Looking at less to see more Trends Cell Biol. 13 2003 629 638
27. Cao P., and Stults J.T. Phosphopeptide analysis by on-line immobilized metal-ion affinity chromatography-capillary electrophoresis-electrospray ionization mass spectrometry J. Chromatogr. 853 1999 225 235
28. Cash P., Argo E., Ford L., Lawrie L., and McKenzie H. A proteomic analysis of erythromycin resistance in Streptococcus pneumoniae Electrophoresis 20 1999 2259 2268
29. Celis J.E., Celis P., Ostergaard M., Basse B., Lauridsen J.B., Ratz G., Rasmussen H.H., Orntoft T.F., Hein B., Wolf H., and Celis A. Proteomics and immunohistochemistry define some of the steps involved in the squamous differentiation of the bladder transitional epithelium: A novel strategy for identifying metaplastic lesions Cancer Res. 59 1999 3003 3009
30. Celis J.E., Kruhoffer M., Gromova I., Frederiksen C., Ostergaard M., Thykjaer T., Gromov P., Yu J., Palsdottir H., Magnusson N., and Orntoft T.F. Gene expression profiling: Monitoring transcription and translation products using DNA microarrays and proteomics FEBS Lett. 480 2000 2 16
31. Celis J.E., Ostergaard M., Rasmussen H.H., Gromov P., Gromova I., Varmark H., Palsdottir H., Magnusson N., Andersen I., Basse B., Lauridsen J.B., Ratz G., Wolf H., Orntoft T.F., Celis P., and Celis A. A comprehensive protein resource for the study of bladder cancer Electrophoresis 20 1999 300 309 http://biobase.dk/cgi-bin/celis
32. Chaurand P., Schwartz S.A., and Caprioli R.M. Assessing protein patterns in disease using imaging mass spectrometry J. Proteom. Res. 3 2004 245 252
33. Chevalier S., Macdonald N., Tonge R., Rayner S., Rowlinson R., Shaw J., Young J., Davison M., and Roberts R.A. Proteomic analysis of differential protein expression in primary hepatocytes induced by EGF, tumour necrosis factor alpha or the peroxisome proliferator nafenopin Eur. J. Biochem. 267 2000 4624 4634
34. Chien C.T., Bartel P.L., Sternglanz R., and Fields S. The two-hybrid system: A method to identify and clone genes for proteins that interact with a protein of interest Proc. Natl. Acad. Sci. USA 88 1991 9578 9582
35. Clauser K.R., Baker P., and 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 1999 2871 2882
36. Corthals G.L., Wasinger V.C., Hochstrasser D.F., and Sanchez J.C. The dynamic range of protein expression: A challenge for proteomic research Electrophoresis 21 2000 1104 1115
37. Courchesne P., Luethy R., and Patterson S. Comparison of in-gel and on-membrane digestion methods at low to sub-pmol level for subsequent peptide and fragment-ion mass analysis using matrix-assisted laser-desorption/ionization mass spectrometry Electrophoresis 18 1997 369 381
38. Creasy D.M., and Cottrell J.S. Error tolerant searching of uninterpreted tandem mass spectrometry data Proteomics 2 2002 1426 1434
39. Cutler P., Bell D.J., Birrell H.C., Connelly J.C., Connor S.C., Holmes E., Mitchell B.C., Monte S.Y., Neville B.A., Pickford R., Polley S., Schneider K., and Skehel J.M. An integrated proteomic approach to studying glomerular nephrotoxicity Electrophoresis 20 1999 3647 3658
40. Dancik V., Addona T.A., Clauser K.R., Vath J.E., and Pevzner P.A. De novo peptide sequencing via tandem mass spectrometry J. Comput. Biol. 6 1999 327 342
41. Davis M., and Lee T. Variable flow liquid chromatography-tandem mass spectrometry and the comprehensive analysis of complex protein digest mixtures J. Am. Soc. Mass Spectrom. 8 1997 1059 1069
42. Davis M.T., Spahr C.S., McGinley M.D., Robinson J.H., Bures E.J., Beierle J., Mort J., Yu W., Luethy R., and Patterson S.D. Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry, II. Limitations of complex mixture analyses Proteomics 1 2001 108 117
43. de Wildt R.M., Mundy C.R., Gorick B.D., and Tomlinson I.M. Antibody arrays for high-throughput screening of antibody-antigen interactions Nat. Biotechnol. 18 2000 989 994
44. Dunn M.J. Studying heart disease using the proteomic approach Drug Discov. Today 5 2000 76 84
45. Eckerskorn C., Strupat K., Schleuder D., Hochstrasser D., Sanchez J.C., Lottspeich F., and Hillenkamp F. Analysis of proteins by direct scanning infrared-MALDI mass spectrometry after PD PAGE separation and electroblotting Anal. Chem. 69 1997 2888 2892
46. Ekstrom S., Onnerfjord P., Nilsson J., Bengtsson M., Laurell T., and Marko-Varga G. Integrated microanalytical technology enabling rapid and automated protein identification Anal. Chem. 72 2000 286 293
47. Eng J.K., McCormack A.L., and 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 1994 976 989
48. Engen J.R., and Smith D.L. Investigating protein structure and dynamics by hydrogen exchange MS Anal. Chem. 73 2001 256A 265A
49. Epstein L., Smith D., Matsui N., Tran H., Sullican C., Raineri I., Burlingame A., Clauser K., Hall S., and Andrews L. Identification of cytokine-regulated proteins in normal and malignant cells by the combination of two-dimensional polyacrylamide gel electrophoresis, mass spectrometry, Edman degradation and immunoblotting and approaches to the analysis of their functional roles Electrophoresis 17 1996 1655 1670
50. Erdjument-Bromage H., Lui M., Lacomis L., Grewal A., Annan R., McNulty D., Carr S., and Tempst P. Examination of micro-tip reversed-phase liquid chromatographic extraction of peptide pools for mass spectrometry analysis J. Chromatogr. A 826 1998 167 181
51. Eriksson J., Chait B.T., and Fenyo D. A statistical basis for testing the significance of mass spectrometric protein identification results Anal. Chem. 72 2000 999 1005
52. Fenn J.B., Mann M., Meng C.K., Wong S.F., and Whitehouse C.M. Electrospray ionization for mass spectrometry of large biomolecules Science 246 1989 64 67
53. Fenyo D., Qin J., and Chait B.T. Protein identification using mass spectrometric information Electrophoresis 19 1998 998 1005
54. Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F., and White F.M. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae Nat. Biotechnol. 20 2002 301 305
55. Fields S. Proteomics. Proteomics in genomeland Science 291 2001 1221 1224
56. Figeys D., Gygi S., McKinnon G., and Aebersold R. An integrated microfluidics-Tandem mass spectrometry system automated protein analysis Anal. Chem. 70 1998 3728 3734
57. Florens L., Washburn M.P., Raine J.D., Anthony R.M., Grainger M., Haynes J.D., Moch J.K., Muster N., Sacci J.B., Tabb D.L., Witney A.A., Wolters D., Wu Y., Gardner M.J., Holder A.A., SInden R.E., Yates J.R., and Carucci D.J. A proteomic view of the Plasmodium falciparum life cycle Nature 419 2002 520 526
58. Fox A.H., Lam Y.W., Leung A.K., Lyon C.E., Andersen J., Mann M., and Lamond A.I. Paraspeckles: A novel nuclear domain Curr. Biol. 12 2002 13 25
59. Garin J., Diez R., Kieffer S., Dermine J.F., Duclos S., Gagnon E., Sadoul R., Rondeau C., and Desjardins M. The phagosome proteome: Insight into phagosome functions J. Cell Biol. 152 2001 165 180
60. Gatlin C., Kleemann G., Hays L., Link A., and Yates J. Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography-microspray and nanospray mass spectrometry Anal. Biochem. 263 1998 93 101
61. Geng M.H., Ji J.Y., and Regnier F.E. Signature-peptide approach to detecting proteins in complex mixtures J. Chromatogr. 870 2000 295 313
62. Gerhold D., Rushmore T., and Caskey C.T. DNA chips: Promising toys have become powerful tools Trends Biochem. Sci. 24 1999 168 173
63. Gevaert K., and Vandekerckhove J. Protein identification methods in proteomics Electrophoresis 21 2000 1145 1154
64. Gharahdaghi F., Weinberg C., Meagher D., Imai B., and Mische S. Mass spectrometry identification of proteins from silver-stained polyacrylamide gel: A method for the removal of silver ions to enhance sensitivity Electrophoresis 20 1999 601 605
65. Gobom J., Nordhoff E., Mirgorodskaya E., Ekman R., and Roepstorff P. Sample purification and preparation technique based on nano-scale reversed-phase columns for the sensitive analysis of complex peptide mixtures by matrix-assisted laser desorption/ionization mass spectrometry J. Mass Spectrom. 34 1999 105 116
66. Godovac-Zimmermann J., and Brown L.R. Perspectives for mass spectrometry and functional proteomics Mass Spectrom. Rev. 20 2001 1
67. Goodlett D.R., Bruce J.E., Anderson G.A., Rist B., Pasa-Tolic L., Fiehn O., Smith R.D., and Aebersold R. Protein identification with a single accurate mass of a cysteine-containing peptide and constrained database searching Anal. Chem. 72 2000 1112 1118
68. Griffin T.J., Gygi S.P., Rist B., Aebersold R., Loboda A., Jilkine A., Ens W., and Standing K.G. Quantitative proteomic analysis using a MALDI quadrupole time-of-flight mass spectrometer Anal. Chem. 73 2001 978 986
69. Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.F., Mann M., and Jensen O.N. Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway Mol. Cell Proteom. 4 2005 310 327
70. Gygi S.P., Corthals G.L., Zhang Y., Rochon Y., and Aebersold R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology Proc. Natl. Acad. Sci. USA 97 2000 9390 9395
71. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., and Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags Nat. Biotechnol. 17 1999 994 999
72. Gygi S.P., Rochon Y., Franza B.R., and Aebersold R. Correlation between protein and mRNA abundance in yeast Mol. Cell Biol. 19 1999 1720 1730
73. Haab B.B., and Zhou H. Multiplexed protein analysis using spotted antibody microarrays Methods Mol. Biol. 264 2004 33 45
74. Han D.K., Eng J., Zhou H.L., and Aebersold R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry Nat. Biotechnol. 19 2001 946 951
75. Hanisch F.G., Jovanovic M., and Peter-Katalinic J. Glycoprotein identification and localization of O-glycosylation sites by mass spectrometric analysis of deglycosylated/alkylaminylated peptide fragments Anal. Biochem. 290 2001 47 59
76. Harry J.L., Wilkins M.R., Herbert B.R., Packer N.H., Gooley A.A., and Williams K.L. Proteomics: Capacity versus utility Electrophoresis 21 2000 1071 1081
77. Heid C.A., Stevens J., Livak K.J., and Williams P.M. Real time quantitative PCR Genome Resl. 6 1996 986 994
78. Henzel W.J., Aswad D.W., and Stults J.T. Structural Analysis of Protein Carboxyl Methyltransferase Utilizing Tandem Mass Spectrometry T.E. Hugli "Techniques in Protein Chemistry" 1989 Academic Press San Diego 127 134
79. Holt L.J., Bussow K., Walter G., and Tomlinson I.M. By-passing selection: Direct screening for antibody-antigen interactions using protein arrays Nucl. Acids Res. 28 2000 E72
80. Hunter T. Signaling - 2000 and beyond Cell 100 2000 113 127
81. Husi H., Ward M.A., Choudhary J.S., Blackstock W.P., and Grant S.G. Proteomic analysis of NMDA receptor-adhesion protein signaling complexes Nat. Neurosci. 3 2000 661 669
82. James P., Quadroni M., Carafoli E., and Gonnet G. Protein identification by mass profile fingerprinting Biochem. Biophys. Res. Commun. 195 1993 58 64
83. James P. Mass spectrometry and the proteome. Quo Vadis P. James "Proteome Research: Mass Spectrometry" 2001 Springer-Verlag Berlin 259 270
84. James P. "Proteome Research: Mass Spectrometry." 2001 Springer-Verlag Berlin
85. Jenkins R.E., and Pennington S.R. Arrays for protein expression profiling: Towards a viable alternative to two-dimensional gel electrophoresis? Proteomics 1 2001 13 29
86. Ji J.Y., Chakraborty A., Geng M., Zhang X., Amini A., Bina M., and Regnier F. Strategy for qualitative and quantitative analysis in proteomics based on signature peptides J. Chromatogr. B 745 2000 197 210
87. Jung E., Heller M., Sanchez J.C., and Hochstrasser D.F. Proteomics meets cell biology: The establishment of subcellular proteomes Electrophoresis 21 2000 3369 3377
88. Jungblut P.R., Zimny-Arndt U., Zeindl-Eberhart E., Stulik J., Koupilova K., Pleissner K.P., Otto A., Muller E.C., Sokolowska-Kohler W., Grabher G., and Stoffler G. Proteomics in human disease: Cancer, heart and infectious diseases Electrophoresis 20 1999 2100 2110
89. Karas M., and Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons Anal. Chem. 60 1988 2299 2301
90. Keough T., Lacey M.P., Fieno A.M., Grant R.A., Sun Y.P., Bauer M.D., and Begley K.B. Tandem mass spectrometry methods for definitive protein identification in proteomics research Electrophoresis 21 2000 2252 2265
91. 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 1975 231 243
92. Kononen J., Bubendorf L., Kallioniemi A., Barlund M., Schraml P., Leighton S., Torhorst J., Mihatsch M.J., Sauter G., and Kallioniemi O.P. Tissue microarrays for high-throughput molecular profiling of tumor specimens Nat. Med. 4 1998 844 847
93. Krone J.R., Nelson R.W., Dogruel D., Williams P., and Granzow R. BIA/MS: Interfacing biomolecular interaction analysis with mass spectrometry Anal. Biochem. 244 1997 124 132
94. Lahm H.W., and Langen H. Mass spectrometry: A tool for the identification of proteins separated by gels Electrophoresis 21 2000 2105 2114
95. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., Fitz Hugh W., Funke R., Gage D., Harris K., Heaford A., Howland J., Kann L., Lehoczky J., Le Vine R., McEwan P., McKernan K., Meldrim J., Mesirov J.P., Miranda C., Morris W., Naylor J., Raymond C., Rosetti M., Santos R., Sheridan A., Sougnez C., Stange-Thomann N., Stojanovic N., Subramanian A., Wyman D., Rogers J., Sulston J., Ainscough R., Beck S., Bentley D., Burton J., Clee C., Carter N., Coulson A., Deadman R., Deloukas P., Dunham A., Dunham I., Durbin R., French L., Grafham D., Gregory S., Hubbard T., Humphray S., Hunt A., Jones M., Lloyd C., McMurray A., Matthews L., Mercer S., Milne S., Mullikin J.C., Mungall A., Plumb R., Ross M., Shownkeen R., Sims S., Waterston R.H., Wilson R.K., Hillier L.W., McPherson J.D., Marra M.A., Mardis E.R., Fulton L.A., Chinwalla A.T., Pepin K.H., Gish W.R., Chissoe S.L., Wendl M.C., Delehaunty K.D., Miner T.L., Delehaunty A., Kramer J.B., Cook L.L., Fulton R.S., Johnson D.L., Minx P.J., Clifton S.W., Hawkins T., Branscomb E., Predki P., Richardson P., Wenning S., Slezak T., Doggett N., Cheng J.F., Olsen A., Lucas S., Elkin C., Uberbacher E., and Frazier M. Initial sequencing and analysis of the human genome Nature 409 2001 860 921
96. Langen H., Takacs B., Evers S., Berndt P., Lahm H.W., Wipf B., Gray C., and Fountoulakis M. Two-dimensional map of the proteome of Haemophilus influenzae Electrophoresis 21 2000 411 429
97. Larsen M.R., Sorensen G.L., Fey S.J., Larsen P.M., and Roepstorff P. Phospho-proteomics: Evaluation of the use of enzymatic de-phosphorylation and differential mass spectrometric peptide mass mapping for site specific phosphorylation assignment in proteins separated by gel electrophoresis Proteomics 1 2001 223 238
98. Li J., Wang C., Kelly J.F., Harrison D.J., and Thibault P. Rapid and sensitive separation of trace level protein digests using microfabricated devices coupled to a quadrupole-time-of-flight mass spectrometer Electrophoresis 21 2000 198 210
99. Link A.J. "2-D Proteome Analysis Protocols." 1999 Humana Press Totowa, NJ
100. Link A.J., Eng J., Schieltz D.M., Carmack E., Mize G.J., Morris D.R., Garvik B.M., and Yates J.R. Direct analysis of protein complexes using mass spectrometry Nat. Biotechnol. 17 1999 676 682
101. Loo J., Brown J., Critchley G., Mitchell C., Andrews P., and Ogorzalek Loo R. High sensitivity mass spectrometry methods for obtaining intact molecular weights from gel-separated proteins Electrophoresis 20 1999 743 748
102. Lopez M.F., Berggren K., Chernokalskaya E., Lazarev A., Robinson M., and Patton W.F. A comparison of silver stain and SYPRO Ruby Protein Gel Stain with respect to protein detection in two-dimensional gels and identification by peptide mass profiling Electrophoresis 21 2000 3673 3683
103. Mac Beath G., and Schreiber S.L. Printing proteins as microarrays for high-throughput function determination Science 289 2000 1760 1763
104. Mahajan N.P., Linder K., Berry G., Gordon G.W., Heim R., and Herman B. Bcl-2 and Bax interactions in mitochondria probed with green fluorescent protein and fluorescence resonance energy transfer Nat. Biotechnol. 16 1998 547 552
105. Mann M., Hojrup P., and Roepstorff P. Use of mass spectrometric molecular weight information to identify proteins in sequence databases Biol. Mass Spectrom. 22 1993 338 345
106. Mann M., and Wilm M. Error-tolerant identification of peptides in sequence databases by peptide sequence tags Anal. Chem. 66 1994 4390 4399
107. Marcotte E.M., Pellegrini M., Ng H.L., Rice D.W., Yeates T.O., and Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences Science 285 1999 751 753
108. Martin S.E., Shabanowitz J., Hunt D.F., and Marto J.A. Subfemtomole MS and MS/MS peptide sequence analysis using nano-HPLC micro-ESI Fourier transform ion cyclotron resonance mass Anal. Chem. 72 2000 4266 4274
109. Medzihradszky K.F., Campbell J.M., Baldwin M.A., Falick A.M., Juhasz P., Vestal M.L., and Burlingame A.L. The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF Tandem mass spectrometer Anal. Chem. 72 2000 552 558
110. Miranker A., Robinson C.V., Radford S.E., and Dobson C.M. Investigation of protein folding by mass spectrometry FASEB J. 10 1996 93 101
111. Mirgorodskaya E., Hassan H., Clausen H., and Roepstorff P. Mass spectrometric determination of O-glycosylation sites using beta-elimination and partial acid hydrolysis Anal. Chem. 73 2001 1263 1269
112. Molloy M.P., Herbert B.R., Slade M.B., Rabilloud T., Nouwens A.S., Williams K.L., and Gooley A.A. Proteomic analysis of the Escherichia coli outer membrane Eur. J. Biochem. 267 2000 2871 2881
113. Muzio M., Chinnaiyan A.M., Kischkel F.C., O'Rourke K., Shevchenko A.J.N., Scaffidi C., Bretz J.D., Zhang M., Gentz R., Mann M., Krammer P.H., Peter M.E., and Dixit V.M. FLICE, a novel FADD-homologous ICE/CED-3-like protease, is recruited to the CD95 (Fas/APO-1) death-inducing signaling complex Cell 85 1996 817 827
114. Nelson P.S., Han D., Rochon Y., Corthals G.L., Lin B., Monson A., Nguyen V., Franza B.R., Plymate S.R., Aebersold R., and Hood L. Comprehensive analyses of prostate gene expression: Convergence of expressed sequence tag databases, transcript profiling and proteomics Electrophoresis 21 2000 1823 1831
115. Nelson R.W., Nedelkov D., and Tubbs K.A. Biomolecular interaction analysis mass spectrometry. BIA/MS can detect and characterize protiens in complex biological fluids at the low- to subfemtomole level Anal. Chem. 72 2000 404A 411A
116. Neubauer G., King A., Rappsilber J., Calvio C., Watson M., Ajuh P., Sleeman J., Lamond A., and Mann M. Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex Nat. Genet. 20 1998 46 50
117. Neugebauer J., Moseley M.A., Vissers J.P.C., and Moyer M. Comparison of nanospray and fully automated nanoscale capillary LC/MS/MS for protein identification "ASMS Conference on Mass Spectrometry and Allied Topics." 1999 Dallas TX
118. Nielsen U.B., and Geierstanger B.H. Multiplexed sandwich assays in microarray format J. Immunol. Methods 290 2004 107 120
119. Nordhoff E., Krogsdam A.M., Jorgensen H.F., Kallipolitis B.H., Clark B.F., Roepstorff P., and Kristiansen K. Rapid identification of DNA-binding proteins by mass spectrometry Nat. Biotechnol. 17 1999 884 888
120. Nuwaysir L.M., and Stults J.T. Electrospray ionization mass spectrometry of phosphopeptides isolated by on-line immobilized metal-ion affinity chromatography J. Am. Soc. Mass Spectrom. 4 1993 662 669
121. Oda Y., Huang K., Cross F.R., Cowburn D., and Chait B.T. Accurate quantitation of protein expression and site-specific phosphorylation Proc. Natl. Acad. Sci. USA 96 1999 6591 6596
122. Oda Y., Nagasu T., and Chait B.T. Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome Nat. Biotechnol. 19 2001 379 382
123. O'Farrell P.H. High resolution two-dimensional electrophoresis of proteins J. Biol. Chem. 250 1975 4007 4021
124. Ong S.E., Blagoev B., Kratchmarova I., Kristensen D.B., Steen H., Pandey A., and Mann M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics Mol. Cell Proteom. 1 2002 376 386
125. Orchard S., Hermjakob H., and Apweiler R. The proteomics standards initiative Proteomics 3 2003 1374 1376
126. Ornstein D.K., Gillespie J.W., Paweletz C.P., Duray P.H., Herring J., Vocke C.D., Topalian S.L., Bostwick D.G., Linehan W.M., Petricoin E.F. 3rd, and Emmert-Buck M.R. Proteomic analysis of laser capture microdissected human prostate cancer and in vitro prostate cell lines Electrophoresis 21 2000 2235 2242
127. Ostergaard M., Rasmussen H.H., Nielsen H.V., Vorum H., Orntoft T.F., Wolf H., and Celis J.E. Proteome profiling of bladder squamous cell carcinomas: Identification of markers that define their degree of differentiation Cancer Res. 57 1997 4111 4117
128. Ostergaard M., Wolf H., Orntoft T.F., and Celis J.E. Psoriasin (S100A7): A putative urinary marker for the follow-up of patients with bladder squamous cell carcinomas Electrophoresis 20 1999 349 354
129. Page M.J., Amess B., Rohlff C., Stubberfield C., and Parekh R. Proteomics: A major new technology for the drug discovery process Drug Discov. Today 4 1999 55 62
130. Page M.J., Amess B., Townsend R.R., Parekh R., Herath A., Brusten L., Zvelebil M.J., Stein R.C., Waterfield M.D., Davies S.C., and O'Hare M.J. Proteomic definition of normal human luminal and myoepithelial breast cells purified from reduction mammoplasties Proc. Natl. Acad. Sci. USA 96 1999 12589 12594
131. Pan S., Zhang H., Rush J., Eng J., Zhang N., Patterson D., Comb M.J., and Aebersold R. High throughput proteome screening for biomarker detection Mol. Cell Proteom. 4 2005 182 190
132. Pandey A., Fernandez M.M., Steen H., Blagoev B., Nielsen M.M., Roche S., Mann M., and Lodish H.F. Identification of a novel immunoreceptor tyrosine-based activation motif-containing molecule, STAM2, by mass spectrometry and its involvement in growth factor and cytokine receptor signaling pathways J. Biol. Chem. 275 2000 38633 38639
133. Pandey A., and Mann M. Proteomics to study genes and genomes Nature 405 2000 837 846
134. Pandey A., Podtelejnikov A.V., Blagoev B., Bustelo X.R., Mann M., and Lodish H.F. Analysis of receptor signaling pathways by mass spectrometry: Identification of vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors Proc. Natl. Acad. Sci. USA 97 2000 179 184
135. Pappin D.J.C., Hojrup P., and Bleasby A.J. Rapid identification of proteins by peptide-mass fingerprinting Curr. Biol. 3 1993 327 332
136. Pawson T., and Nash P. Protein-protein interactions define specificity in signal transduction Genes Dev. 14 2000 1027 1047
137. Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G., Roelofs J., Finley D., and Gygi S.P. A proteomics approach to understanding protein ubiquitination Nat. Biotechnol. 21 2003 921 926
138. Perkins D.N., Pappin D.J.C., Creasy D.M., and Cottrell S. Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 20 1999 3551 3567
139. Petricoin E.F., Ardekani A.M., Hitt B.A., Levine P.J., Fusaro V.A., Steinberg S.M., Mills G.B., Simone C., Fishman D.A., Kohn E.C., and Liotta L.A. Use of proteomic patterns in serum to identify ovarian cancer Lancet 359 2002 572 577
140. Pieper R., Su Q., Gatlin C.L., Huang S.T., Anderson N.L., and Steiner S. Multi-component immunoaffinity subtraction chromatography: An innovative step towards a comprehensive survey of the human plasma proteome Proteomics 3 2003 422 432
141. Posewitz M.C., and Tempst P. Immobilized gallium(III) affinity chromatography of phosphopeptides Anal. Chem. 71 1999 2883 2892
142. Ransohoff D.F. Lessons from controversy: Ovarian cancer screening and serum proteomics J. Natl. Cancer. Inst. 97 2005 315 319
143. Rappsilber J., Siniossoglou S., Hurt E.C., and Mann M. A generic strategy to analyze the spatial organization of multi-protein complexes by cross-linking and mass spectrometry Anal. Chem. 72 2000 267 275
144. Reymond M.A., Sanchez J.C., Hughes G.J., Gunther K., Riese J., Tortola S., Peinado M.A., Kirchner T., Hohenberger W., Hochstrasser D.F., and Kockerling F. Standardized characterization of gene expression in human colorectal epithelium by two-dimensional electrophoresis Electrophoresis 18 1997 2842 2848
145. Rigaut G., Shevchenko A., Rutz B., Wilm M., Mann M., and Seraphin B. A generic protein purification method for protein complex characterization and proteome exploration Nat. Biotechnol. 17 1999 1030 1032
146. Rout M.P., Aitchison J.D., Suprapto A., Hjertaas K., Zhao Y., and Chait B.T. The yeast nuclear pore complex: Composition, architecture, and transport mechanism J. Cell Biol. 148 2000 635 652
147. Rudd P.M., Colominas C., Royle l., Murphy N., Hart E., Merry A., Heberstreit H., and Dwek R.A. Glycoproteomics; High-Throughput Sequencing of Oligosaccharide Modifications to Proteins P. James "Proteome Research: Mass Spectrometry" 2001 Springer-Verlag Berlin 207 228
148. Santoni V., Molloy M., and Rabilloud T. Membrane proteins and proteomics: Un amour impossible? Electrophoresis 21 2000 1054 1070
149. Scheele G.A. Two-dimensional gel analysis of soluble proteins. Characterization of guinea pig exocrine pancreatic proteins J. Biol. Chem. 250 1975 5375 5385
150. Schleuder D., Hillenkamp F., and Strupat K. IR-MALDI-mass analysis of electroblotted proteins directly from the membrane: Comparison of different membranes, application to on-membrane digestion, and protein identification by database searching Anal. Chem. 71 1999 3238 3247
151. Shalon D., Smith S.J., and Brown P.O. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization Genome Res. 6 1996 639 645
152. Shevchenko A., Loboda A., Ens W., and Standing K.G. MALDI quadrupole time-of-flight mass spectrometry: A powerful tool for proteomic research Anal. Chem. 72 2000 2132 2141
153. Shevchenko A., Wilm M., Vorm O., and Mann M. Mass spectrometric sequencing of proteins from silver stained polyacrylamide gels Anal. Chem. 68 1996 850 858
154. Simone N.L., Bonner R.F., Gillespie J.W., Emmert-Buck M.R., and Liotta L.A. Laser-capture microdissection: Opening the microscopic frontier to molecular analysis Trends Genet. 14 1998 272 276
155. Simpson R.J., Connolly L.M., Eddes J.S., Pereira J.J., Moritz R.L., and Reid G.E. Proteomic analysis of the human colon carcinoma cell line (LIM 1215): Development of a membrane protein database Electrophoresis 21 2000 1707 1732
156. Sobott F., and Robinson C.V. Protein complexes gain momentum Curr. Opin. Struct. Biol. 12 2002 729 734
157. Spahr C.S., Davis M.T., McGinley M.D., Robinson J.H., Bures E.J., Beierle J., Mort J., Courchesne P.L., Chen K., Wahl R.C., Yu W., Luethy R., and Patterson S.D. Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry I. Profiling an unfractionated tryptic digest Proteomics 1 2001 93 107
158. Srinivas P.R., Srivastava S., Hanash S., and Wright G.L. Jr. Proteomics in early detection of cancer Clin. Chem. 47 2001 1901 1911
159. Steiner S., Aicher L., Raymackers J., Meheus L., Esquer-Blasco R., Anderson N.L., and Cordier A. Cyclosporine A decreases the protein level of the calcium-binding protein calbindin-D 28 kDa in rat kidney Biochem. Pharmacol. 51 1996 253 258
160. Steiner S., Wahl D., Varela M.D.C., Aicher L., and Prieto P. Protein variability in male and female Wistar rat liver proteins Electrophoresis 16 1995 1969 1976
161. Steiner S., and Witzmann F.A. Proteomics: Applications and opportunities in preclinical drug development Electrophoresis 21 2000 2099 2104
162. Stulik J., Koupilova K., Osterreicher J., Knizek J., Macela A., Bures J., Jandik P., Langr F., Dedic K., and Jungblut P.R. Protein abundance alterations in matched sets of macroscopically normal colon mucosa and colorectal carcinoma Electrophoresis 20 1999 3638 3646
163. Taylor J., and Johnson R. Sequence database searches in de novo peptide sequencing by Tandem mass spectrometry Rapid Commun. Mass Spectrom. 11 1997 1067 1075
164. Ünlü M., Morgan M.E., and Minden J.S. Difference gel electrophoresis: A single gel method for detecting changes in protein extracts Electrophoresis 18 1997 2071 2077
165. VanBogelen R.A., Greis K.D., Blumenthal R.M., Tani T.H., and Matthews R.G. Mapping regulatory networks in microbial cells Trends Microbiol. 7 1999 320 328
166. Veenstra T.D., Conrads T.P., Hood B.L., Avellino A.M., Ellenbogen R.G., and Morrison R.S. Biomarkers: Mining the biofluid proteome Mol. Cell Proteom. 4 2005 409 418
167. Velculescu V.E., Vogelstein B., and Kinzler K.W. Analysing uncharted transcriptomes with SAGE Trends Genet. 16 2000 423 425
168. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans C.A., Holt R.A., Gocayne J.D., Amanatides P., Ballew R.M., Huson D.H., Wortman J.R., Zhang Q., Kodira C.D., Zheng X.H., Chen L., Skupski M., Subramanian G., Thomas P.D., Zhang J., Gabor Miklos G.L., Nelson C., Broder S., Clark A.G., Nadeau J., McKusick V.A., Zinder N., Levine A.J., Roberts R.J., Simon M., Slayman C., Hunkapiller M., Bolanos R., Delcher A., Dew I., Fasulo D., Flanigan M., Florea L., Halpern A., Hannenhalli S., Kravitz S., Levy S., Mobarry C., Reinert K., Remington K., Abu-Threideh J., Beasley E., Biddick K., Bonazzi V., Brandon R., Cargill M., Chandramouliswaran I., Charlab R., Chaturvedi K., Deng Z., Di Francesco V., Dunn P., Eilbeck K., Evangelista C., Gabrielian A.E., Gan W., Ge W., Gong F., Gu Z., Guan P., Heiman T.J., Higgins M.E., Ji R.R., Ke Z., Ketchum K.A., Lai Z., Lei Y., Li Z., Li J., Liang Y., Lin X., Lu F., Merkulov G.V., Milshina N., Moore H.M., Naik A.K., Narayan V.A., Neelam B., Nusskern D., Rusch D.B., Salzberg S., Shao W., Shue B., Sun J., Wang Z., Wang A., Wang X., Wang J., Wei M., Wides R., Xiao C., and Yan C. The sequence of the human genome Science 291 2001 1304 1351
169. Walter G., Bussow K., Cahill D., Lueking A., and Lehrach H. Protein arrays for gene expression and molecular interaction screening Curr. Opin. Microbiol. 3 2000 298 302
170. Washburn M.P., Wolters D., and Yates J.R. 3rd. Large-scale analysis of the yeast proteome by multidimensional protein identification technology Nat. Biotechnol. 19 2001 242 247
171. Wilkins M., Sanchez J., Gooley A., Appel R., Humphry-Smith I., Hochstrasser D., and Williams K. Progress with proteome projects: Why all proteins expressed by a genome should be identified and how to do it Biotechnol. Genet. Eng. Rev. 13 1995 19 50
172. Wilkins M.R., Williams R.D., Appel R.D., and Hochstrasser D.F. M.R. Wilkins K.L. Williams R.D. Appel D.F. Hochstrasser "Proteome Research: New Frontiers in Functional Genomics," 1997 Springer-Verlag Berlin 243
173. Wilm M., and Mann M. Analytical properties of the nanoelectrospray ion source Anal. Chem. 68 1996 1 8
174. Wilm M., Shevchenko A., Houthaeve T., Breit S., Schweigerer L., Fotsis T., and Mann M. Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry Nature 379 1996 466 469
175. Wolters D.A., Washburn M.P., and Yates J.R. 3rd. An automated multidimensional protein identification technology for shotgun proteomics Anal. Chem. 73 2001 5683 5690
176. Yates J.R. III, Speicher S., Griffin P.R., and Hunkapiller T. Peptide mass maps: A highly informative approach to protein identification Anal. Biochem. 214 1993 397 408
177. Young M.M., Tang N., Hempel J.C., Oshiro C.M., Taylor E.W., Kuntz I.D., Gibson B.W., and Dollinger G. High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry Proc. Natl. Acad. Sci. USA 97 2000 5802 5806
178. Zhang W.Z., and Chait B.T. Profound: An expert system for protein identification using mass spectrometric peptide mapping information Anal. Chem. 72 2000 2482 2489
179. Zhang X.L., Herring C.J., Romano P.R., Szczepanowska J., Brzeska H., Hinnebusch A.G., and Qin J. Identification of phosphorylation sites in proteins separated by polyacrylamide gel electrophoresis Anal. Chem. 70 1998 2050 2059
180. Zhang Z., Li W., Logan T.M., Li M., and Marshall A.G. Human recombinant [C22A] FK506-binding protein amide hydrogen exchange rates from mass spectrometry match and extend those from NMR Protein Sci. 6 1997 2203 2217
181. Zhou W., Merrick B.A., Khaledi M.G., and Tomer K.B. Detection and sequencing of phosphopeptides affinity bound to immobilized metal ion beads by matrix-assisted laser desorption/ionization mass spectrometry J. Am. Soc. Mass Spectrom. 11 2000 273 282
182. Zhu W., Reich C.I., Olsen G.J., Giometti C.S., and Yates J.R. 3rd. Shotgun proteomics of Methanococcus jannaschii and insights into methanogenesis J. Proteome Res. 3 2004 538 548