Going global: Protein expression profiling using shotgun mass spectrometry

Current Opinion in Molecular Therapeutics

Volumn 5, Issue 3, 2003, Pages 285-293

  Kislinger, Thomas ^a   Emili, Andrew ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

Bioinformatics; Expression profiling; Mass spectrometry; Peptide sequencing; Protein quantitation; Shotgun proteomics

Indexed keywords

PROTEIN;

BLOOD ANALYSIS; DATA ANALYSIS; GENE EXPRESSION PROFILING; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MEDICAL RESEARCH; MONITORING; NONHUMAN; PLASMODIUM FALCIPARUM; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN ANALYSIS; PROTEIN DETERMINATION; PROTEIN EXPRESSION; PROTEIN PROCESSING; PROTEOMICS; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW;

ANIMALS; BLOOD; CELL MEMBRANE; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; HUMANS; MASS SPECTROMETRY; ORYZA SATIVA; PLASMODIUM FALCIPARUM; PROTEIN ARRAY ANALYSIS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOMICS;

PLASMODIUM FALCIPARUM;

EID: 0141613681     PISSN: 14648431     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (64)

1. Wasinger VC, Cordwell SJ, Cerpa-Poljak A, Yan JX, Gooley AA, Wilkins MR, Duncan MW, Harris R, Williams KL, Humphery-Smith I: Progress with gone-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis (1995) 16(7):1090-1094.
2. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD et al: The sequence of the human genome. Science (2001) 291(5507):1304-1351.
3. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwall P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE et al. Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 420(6915):520-562.
4. Karas M, Hillenkamp F: Laser desorption ionization of proteins with molecular masses exceeding 10,000 Daltons. Anal Chem (1988) 60(20):2299-2301.
5. Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM: Electrospray ionization for mass spectrometry of large biomolecules. Science (1989) 246(4926):64-71.
6. Beavis RC, Chait BT: Matrix-assisted laser-desorption mass spectrometry using 365 nm radiation. Rapid Commun Mass Spectrom (1989) 3(12):436-439.
7. Cleveland DW, Fischer SG, Kirschner MW, Laemmli UK: Peptide mapping by limited proteolysis in sodium dodecyl sulfate and analysis by gel electrophoresis. J Biol Chem (1977) 252(3):1102-1106.
8. James P, Quadroni M, Carafoli E, Gonnet G: Protein identification by mass profile fingerprinting. Biochem Biophys Res Commun (1993) 195(1):58-64.
9. Whitehouse CM, Dreyer RN, Yamashita M, Fenn JB: Electrospray interface for liquid chromatographs and mass spectrometers. Anal Chem (1985) 57(3):675-679.
10. Eng JK, McCormack AL, Yates JR 3rd: An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom (1994) 5(11):976-989.
11. O'Farrell PH: High resolution two-dimensional electrophoresis of proteins. J Biol Chem (1975) 250(10):4007-4021.
12. Fountoulakis M, Juranville JF, Dierssen M, Lubec G: Proteomic analysis of the fetal brain. Proteomics (2002) 2(11):1547-1576.
13. Gygi SP, Corthals GL, Zhang Y, Rochon Y, Aebersold R: Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc Natl Acad Sci USA (2000) 97(17):9390-9395.
14. Neverova I, Van Eyk JE: Application of reversed phase high performance liquid chromatography for subproteomic analysis of cardiac muscle. Proteomics (2002) 2(1):22-31.
15. Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ, Morris DR, Garvik BM, Yates JR 3rd: Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol (1999) 17(7):676-682.
16. Wilm M, Mann M: Analytical properties of the nanoelectrospray ion source. Anal Chem (11996) 68(1):1-8.
17. Washburn MP, Wolters D, Yates JR 3rd: Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol (2001) 19(3):242-247.
18. Koller A, Washburn MP, Lange BM, Andon NL, Deciu C, Haynes PA, Hays L, Schieltz D, Ulaszek R, Wei J, Wolters D et al: From the cover: Proteomic survey of metabolic pathways in rice. Proc Natl Acad Sci USA (2002) 99(18):11969-11974.
19. Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 419(6906):498-511.
20. Lasonder E, Ishihama Y, Andersen JS, Vermunt AM, Pain A, Sauerwein RW, Eling WM, Hall N, Waters AP, Stunnenberg HG, Mann M: Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature (2002) 419(6906):537-542.
21. Florens L, Washburn MP, Raine JD, Anthony RM, Grainger M, Haynes JD, Moch JK, Muster N, Sacci JB, Tabb DL, Wittney AA et al: A proteomic view of the Plasmodium falciparum life cycle. Nature (2002) 419(6906):520-526.
22. Wolters DA, Washburn MP, Yates JR 3rd: An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem (2001) 73(23):5683-5690.
23. Kislinger T, Rahman K, Radulovic D, Cox B, Rossant J, Emili A: PRISM, a generic large-scale proteomic investigation strategy for mammals. Mol Cell Proteomics (2003) 2(2):96-106.
24. Gagnon E, Duclos S, Rondeau C, Chevet E, Cameron PH, Steele-Mortimer O, Paiement J, Bergeron JJ, Desjardins M: Endoplasmic reticulum-mediated phagocytosis is a mechanism of entry into macrophages. Cell (2002) 110(1):119-131.
25. Garin J, Diez R, Kieffer S, Dermine JF, Duclos S, Gagnon E, Sadoul R, Rondeau C, Desjardins M: The phagosome proteome: Insight into phagosome functions. J Cell Biol (2001) 152(1):165-180.
26. Andersen JS, Lyon CE, Fox AH, Leung AK, Lam YW, Steen H, Mann M, Lamond AI: Directed proteomic analysis of the human nucleolus. Cuff Biol (2002) 12(1):1-11.
27. Scherl A, Couté Y, Déon C, Callé A, Kindbeiter K, Sanchez JC, Greco A, Hochstrasser D, Diaz JJ: Functional proteomic analysis of human nucleolus. Mol Biol Cell (2002) 13(11):4100-4109.
28. Taylor SW, Fahy E, Zhang B, Glenn GM, Warnock DE, Wiley S, Murphy AN, Gaucher SP, Capaldi RA, Gibson BW, Ghosh SS: Characterization of the human heart mitochondrial proteome. Nat Biotechnol (2003) 21(3):281-286.
29. Journet A, Chapel A, Kieffer S, Roux F, Garin J: Proteomic analysis of human lysosomes: Application to monocytic and breast cancer cells. Proteomics (2002) 2(8):1026-1040.
30. Dreger M, Bengtsson L, Schöneberg T, Otto H, Hucho F: Nuclear envelope proteomics: Novel integral membrane proteins of the inner nuclear membrane. Proc Natl Acad Sci USA (2001) 98(21):11943-11948.
31. Ferro M, Salvi D, Riviere-Rolland H, Vermat T, Seigneurin-Berny D, Grunwald D, Garin J, Joyard J, Rolland N: Integral membrane proteins of the chloroplast envelope: Identification and subcellular localization of new transporters. Proc Natl Acad Sci USA (2002) 99(17):11487-11492.
32. Anderson NL, Anderson NG: The human plasma proteome: History, character, and diagnostic prospects. Mol Cell Proteomics (2002) 1(11):845-867.
33. Adkins A Varnum SM, Auberry KJ, Moore RJ, Angell NH, Smith RD, Springer DL, Pounds JG: Toward a human blood serum proteome: Analysis by multidimensional separation coupled with mass spectrometry. Mol Cell Proteomics (2002) 1(12):947-955.
34. Smith RD, Anderson GA, Lipton MS, Pasa-Tolic L, Shen Y, Conrads TP, Veenstra TD, Udseth HR: An accurate mass tag strategy for quantitative and high-throughput proteome measurements. Proteomics (2002) 2(5):513-523.
35. Lipton MS, Pasa-Tolic L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C et al: Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc Natl Acad Sci USA (2002) 99(17):11049-11054.
36. Goshe MB, Smith RD: Stable isotope-coded proteomic mass spectrometry. Curr Opin Biotechnol (2003) 14(1):101-109.
37. Tao WA, Aebersold R: Advances in quantitative proteomics via stable isotope tagging and mass spectrometry. Curr Opin Biotechnol (2003) 14(1):110-118.
38. 18O labeling: A tool for proteomics. Rapid Commun Mass Spectrom (2001) 15(24):2456-2465.
39. Gygi SP, Rist B, Griffin TJ, Eng J, Aebersold R: Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags. J Proteome Res (2002) 1(1):47-54.
40. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R: Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol (1999) 17(10):994-999.
41. Han DK, Eng J, Zhou H, Aebersold R: Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat Biotechnol (2001) 19(10):946-951.
42. Shiio Y, Donohoe S, Yi EC, Goodlett DR, Aebersold R, Eisenman RN: Quantitative proteomic analysis of Myc oncoprotein function. EMBO J (2002) 21(19):5088-5096.
43. Washburn MP, Ulaszek R, Deciu C, Schieltz DM, Yates JR 3rd: Analysis of quantitative proteomic date generated via multidimensional protein identification technology. Anal Chem (2002) 74(7):1650-1657.
44. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M: Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics (2002) 1(5):376-386.
45. Blagoev B, Kratchmarova I, Ong SE, Nielsen M, Foster LJ, Mann M: A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat Biotechnol (2003) 21(3):315-318.
46. Cagney G, Emili A: De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging. Nat Biotechnol (2002) 20(8):163-170.
47. Chelius D, Bondarenko PV: Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J Proteome Res (2002) 1(4):317-323.
48. Fenyo D, Beavis RC: A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal Chem (2003) 75(4):768-774.
49. Keller A, Nesvizhskii AI, Kolker E, Aebersold R: Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem (2002) 74(20):5383-5392.
50. MacCoss MJ, Wu CC, Yates JR 3rd: Probability-based validation of protein identifications using a modified SEQUEST algorithm. Anal Chem (2002) 74(21):5593-5599.
51. Miyagi M, Sakaguchi H, Darrow RM, Yan L, West KA, Aulak KS, Stuehr DJ, Hollyfield JG, Organisciak DY, Crabb JW: Evidence that light modulates protein nitration in rat retina. Mol Cell Proteomics (2002) 1(4):293-303.
52. Castegna A, Aksenov M, Aksenova M, Thongboonkerd V, Klein JB, Pierce WM, Booze R, Markesbery WR, Butterfield DA: Proteomic identification of oxidatively modified proteins in Alzheimers disease brain. Part I: Crestine kinase BB, glutamine synthase, and ubiquitin carboxy-terminal hydrolase L-1. Free Radic Biol Med (2002) 33(4):562-571.
53. Humeny A, Kislinger T, Becker CM, Pischetsrieder M: Qualitative determination of specific protein glycation products by matrix-assisted laser desorption/ionization mass spectrometry peptide mapping. J Agric Food Chem (2002) 50(7):2153-2160.
54. Kislinger T, Humeny A, Peich CC, Zhang X, Niwa T, Pischetsrieder M, Becker C-M: Relative quantification of N(E)-(carboxymethyl)lysine, imidazolone A, and the Amadori product in glycated lysozyme by MALDI-TOF mass spectrometry. J Agric Food Chem (2003) 51(1):51-57.
55. Hewitson KS, McNeill LA, Riordan MV, Tian YM, Bullock AN, Welford RW, Elkins JM, Oldham NJ, Bhattacharya S, Gleadle JM, Ratcliffe PJ et al: Hypoxia-inducible factor (HIF) asparagine hydroxylase is identical to factor inhibiting HIF (FIH) and is related to the cupin structural family. J Biol Chem (2002) 277(29):26351-26355.
56. Dell A, Morris HR: Glycoprotein structure determination by mass spectrometry. Science (2001) 291(5512):2351-2356.
57. Oda Y, Nagasu T, Chait BT: Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat Biotechnol (2001) 19(4):379-382.
58. Pandey A, Podtelejnikov AV, Blagoev B, Bustelo XR, Mann M, Lodish HF: 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 (2000) 97(1):179-184.
59. Ficarro SB, McCleland ML, Stukenberg PT, Burke DJ, Ross MM, Shabanowitz J, Hunt DF, White FM: Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces corovisiae. Nat Biotechnol (2002) 20(3):301-305.
60. Salomon AR, Ficarro SB, Brill LM, Brinker A, Phung QT, Ericson C, Sauer K, Brock A, Horn DM, Schultz PG, Peters EC et al. Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry. Proc Natl Acad Sci USA (2003) 100(2):443-448.
61. Ficarro S, Chertihin O, Westbrook VA, White F, Jayes F, Kalab P, Marto JA, Shabanowitz J, Herr JC, Hunt DF, Visconti PE: Phosphoproteome analysis of capacitated human sperm. Evidence of tyrosine phosphorylation of a kinase anchoring protein 3 and valosin containing protein/P97 during capacitation. J Biol Chem (2003) 278(13):11579-11589.
62. MacCoss W, McDonald WH, Saraf A, Sadygov R, Clark JM, Tasto JJ, Gould KL, Wolters D, Washburn M, Weiss A, Clark JI et al: Shotgun identification of protein modifications from protein complexes and lens tissue. Proc Natl Acad Sci USA (2002) 99(12):7900-7905.
63. Tabb DL, McDonald WH, Yates JR 3rd: DTASelect and Contrast: Tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res (2002) 1(1):21-26.
64. Ashbumer M, Ball CA, Blake A Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA et al: Germ ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 25(1):25-29.