Proteomics of extremophiles

Environmental Microbiology

Volumn 13, Issue 8, 2011, Pages 1934-1955

  Burg, Dominic ^a   Ng, Charmaine ^b   Ting, Lily ^c   Cavicchioli, Ricardo ^b  

^a Department of Microbiology and Infectious Diseases   (Australia)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ARCHAEON; BACTERIUM; GENE EXPRESSION PROFILING; MASS SPECTROMETRY; METABOLISM; PROTEIN DATABASE; PROTEOMICS; SEQUENCE ANALYSIS; SHORT SURVEY; STAINING;

ARCHAEA; BACTERIA; DATABASES, PROTEIN; GENE EXPRESSION PROFILING; MASS SPECTROMETRY; PROTEINS; PROTEOMICS; SEQUENCE ANALYSIS, PROTEIN; STAINING AND LABELING;

EID: 80051926124     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2011.02484.x     Document Type: Short Survey

References (265)

1. Aebersold, R., and Goodlett, D.R. (2001) Mass spectrometry in proteomics. Chem Rev 101: 269-296.
2. Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422: 198-207.
3. America, A., Cordewener, J., van Geffen, M., Lommen, A., Vissers, J., Bino, R., and Hall, R. (2006) Alignment and statistical difference analysis of complex peptide data sets generated by multidimensional LC-MS. Proteomics 6: 641-653.
4. 14N quantitation with LC-ESI-MS using an LTQ-FT mass spectrometer. J Proteome Res 5: 2039-2045.
5. 2 and spectral counting. Anal Bioanal Chem 398: 391-404.
6. Antranikian, G. (2008) Thermoacidophiles and their protein adaptation to low pH and high temperature. In Protein Adaptation in Extremophiles. Siddiqui, K.S., and Thomas, T. (eds). New York: Nova biomedical books, pp. 143-146.
7. Atwater, J., Wisdom, R., and Verma, I. (1990) Regulated mRNA stability. Annu Rev Genet 24: 519-541.
8. Bachmair, A., Finley, D., and Varshavsky, A. (1986) In vivo half-life of a protein is a function of its amino-terminal residue. Science 234: 179-186.
9. Baliga, N.S., Pan, M., Goo, Y.A., Yi, E.C., Goodlett, D.R., Dimitrov, K., etal. (2002) Coordinate regulation of energy transduction modules in Halobacterium sp. Analyzed by a global systems approach. Proc Natl Acad Sci USA 99: 14913-14918.
10. Banfield, J.F., VerBerkmoes, N.C., Hettich, R.L., and Thelen, M.P. (2005) Proteogenomic approaches for the molecular characterization of natural microbial communities. OMICS 4: 301-333.
11. Bantscheff, M., Schirle, M., Sweetman, G., Rick, J., and Kuster, B. (2007) Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem 389: 1017-1031.
12. Barry, R.C., Young, M.J., Stedman, K.M., and Dratz, E.A. (2006) Proteomic mapping of the hyperthermophilic and acidophilic archaeon Solfolobus solfataricus p2. Electrophoresis 27: 2970-2983.
13. Bastida, F., Moreno, J.L., Nicolas, C., Hernandez, T., and Garcia, C. (2009) Soil metaproteomics: a review of an emerging environmental science. Significance, methodology and perspectives. Eur J Soil Sci 60: 845-859.
14. Belle, A., Tanay, A., Bitincka, L., Shamir, R., and O'Shea, E.K. (2006) Quantification of protein half-lives in the budding yeast proteome. Proc Natl Acad Sci USA 103: 13004-13009.
15. Benndorf, D., Balcke, G.U., Harms, H., and Bergen, M.V. (2007) Functional metaproteome analysis of protein extracts from contaminated soil and groundwater. ISME J 1: 224-234.
16. Biemann, K. (1986) Mass spectrometry methods for protein sequencing. Anal Chem 58: 1288A-1300A.
17. Biron, D.G., Brun, C., Lefevre, T., Lebarbenchon, C., Loxdale, H.D., Chevenet, F., etal. (2006) The pitfalls of proteomics experiments without the correct use of bioinformatics tools. Proteomics 6: 5577-5596.
18. Bisle, B., Schmidt, A., Scheibe, B., Klein, C., Tebbe, A., Kellermann, J., etal. (2006) Quantitative profiling of the membrane proteome in a halophilic archaeon. Mol Cell Proteomics 5: 1543-1558.
19. Blackler, A.R., Speers, A.E., Ladinsky, M.S., and Wu, C.C. (2008) A shotgun proteomic method for the identification of membrane-embedded proteins and peptides. J Proteome Res 7: 3028-3034.
20. Blondeau, F., Ritter, B., Allaire, P., Wasiak, S., Girard, M., Hussain, N., etal. (2004) Tandem MS analysis of brain clathrin-coated vesicles reveals their critical involvement in synaptic vesicle recycling. Proc Natl Acad Sci USA 101: 3833-3838.
21. Blonder, J., Goshe, M.B., Moore, R.J., Pasa-Tolic, L., Masselon, C.D., Lipton, M.S., and Smith, R.D. (2002) Enrichment of integral membrane proteins for proteomic analysis using liquid chromatography-tandem mass spectrometry. J Proteome Res 1: 351-360.
22. Blonder, J., Conrads, T.P., Yu, L.R., Terunuma, A., Janini, G.M., Issaq, H.J., etal. (2004a) A detergent- and cyanogen bromide-free method for integral membrane proteomics: application to halobacterium purple membranes and the human epidermal membrane proteome. Proteomics 4: 31-45.
23. Blonder, J., Goshe, M.B., Xiao, W., Camp, D.G., 2nd, Wingerd, M., Davis, R.W., and Smith, R.D. (2004b) Global analysis of the membrane subproteome of Pseudomonas aeruginosa using liquid chromatography-tandem mass spectrometry. J Proteome Res 3: 434-444.
24. Blonder, J., Terunuma, A., Conrads, T.P., Chan, K.C., Yee, C., Lucas, D.A., etal. (2004c) A proteomic characterization of the plasma membrane of human epidermis by high-throughput mass spectrometry. J Invest Dermatol 123: 691-699.
25. Blumer-Schuette, S.E., Kataeva, I., Westpheling, J., Adams, M.W., and Kelly, R.M. (2008) Extremely thermophilic microorganisms for biomass conversion: status and prospects. Curr Opin Biotechnol 19: 210-217.
26. Boguski, M.S., and McIntosh, M.W. (2003) Biomedical informatics for proteomics. Nature 422: 233-237.
27. Bondarenko, P., Chelius, D., and Shaler, T. (2002) Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal Chem 74: 4741-4749.
28. Bouyssie, D., de Peredo, G., Mouton, E., Albigot, R., Roussel, L., Ortega, N., etal. (2007) Mascot file parsing and quantification (MFPaQ), a new software to parse, validate, and quantify proteomic data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomic study of membrane proteins from primary human endothelial cells. Mol Cell Proteomics 9: 1621-1637.
29. Brun, V., Masselon, C., Garin, J., and Dupuis, A. (2009) Isotope dilution strategies for absolute quantitative proteomics. J Proteomics 72: 740-749.
30. Budde, I., Steil, L., Scharf, C., Volker, U., and Bremer, E. (2006) Adaptation of Bacillus subtilis to growth at low temperature: a combined transcriptomic and proteomic appraisal. Microbiology 152: 831-853.
31. Burg, D.W., Lauro, F.M., Williams, T.J., Raftery, M.J., Guilhaus, M., and Cavicchioli, R. (2010) Analyzing the hydrophobic proteome of the Antarctic archaeon Methanococcoides burtonii using differential solubility fractionation. J Proteome Res 9: 664-676.
32. Campanaro, S., Williams, T.J., Burg, D.W., De Francisci, D., Treu, L., Lauro, F.M., and Cavicchioli, R. (2010) Temperature-dependent global gene expression in the Antarctic archaeon Methanococcoides burtonii. Environ Microbiol (in press): doi:10.1111/j.1462-2920.2010.02367.x.
33. Cannataro, M. (2008) Computational proteomics: management and analysis of proteomics data. Brief Bioinform 9: 97-101.
34. Carr, S., Aebersold, R., Baldwin, M., Burlingame, A., Clauser, K., and Nesvizhskii, A. (2004) The need for guidelines in publication of peptide and protein identification data: working group on publication guidelines for peptide and identification data. Mol Cell Proteomics 3: 531-533.
35. Cavicchioli, R. (2002) Extremophiles and the search for extra-terrestrial life. Astrobiology 2: 281-292.
36. Cavicchioli, R., and Thomas, T. (2004) Extremophiles. In The Desk Encyclopedia of Microbiology. Schaechter, M. (ed.). London: Elsevier, pp. 434-451.
37. Cavicchioli, R., Goodchild, A., and Raftery, M. (2006) Proteomics of archaea. In Microbial Proteomics - Functional Biology of Whole Organisms. Humphery-Smith, I., and Hecker, M. (eds). New York: Wiley, pp. 57-72.
38. Celis, J.E. (2004) Gel-based proteomics: what does MCP expect? Mol Cell Proteomics 3: 949.
39. Chelius, D., and Bondarenko, P.V. (2002) Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J Proteome Res 1: 317-323.
40. Chen, G., Gharib, T.G., Huang, C.C., Taylor, J.M.G., Misek, D.E., Kardia, S.L.R., etal. (2002) Discordant protein and mRNA expression in lung adenocarcinomas. Mol Cell Proteomics 1: 304-313.
41. Chen, X., Sun, L., Yu, Y., Xue, Y., and Yang, P. (2007) Amino acid-coded tagging approaches in quantitative proteomics. Expert Rev Proteomics 4: 25-37.
42. Chiappetta, G., Ndiaye, S., Igbaria, A., Kumar, C., Vinh, J., and Toledano, M.B. (2010) Proteome screens for cys residues oxidation: the redoxome. Methods Enzymol 473: 199-216.
43. Chich, J.-F., David, O., Villers, F., Schaeffer, B., Lutomski, D., and Huet, S. (2007) Statistics for proteomics: experimental design and 2-DE differential analysis. J Chromatogr B 849: 261-272.
44. Choe, L., D'Ascenzo, M., Relkin, N., Pappin, D., Ross, P., Williamson, B., etal. (2007) 8-plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for alzheimer's disease. Proteomics 7: 3651-3660.
45. Chong, P.K., Wright, P.C., Gan, C.S., and Pham, T.K. (2005) Identification and characterization of the Sulfolobus solfataricus p2 proteome. J Proteome Res 4: 1789-1798.
46. Chong, P.K., Burja, A.M., Radianingtyas, H., Fazeli, A., and Wright, P.C. (2007) Proteome analysis of Sulfolobus solfataricus p2 propanol metabolism. J Proteome Res 6: 1430-1439.
47. 15N-metabolic labeling. Anal Chem 73: 2132-2139.
48. Corthals, G.L., Wasinger, V.C., Hochstrasser, D.F., and Sanchez, J.C. (2000) The dynamic range of protein expression: a challenge for proteomic research. Electrophoresis 21: 1104-1115.
49. Cox, J., and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26: 1367-1372.
50. Craig, R., and Beavis, R.C. (2004) TANDEM: matching proteins with mass spectra. Bioinformatics 20: 1466-1467.
51. Craig, R., Cortens, J., and Beavis, R. (2005) The use of proteotypic peptide libraries for protein identification. Rapid Commun Mass Spectrom 19: 1844-1850.
52. Dayon, L., Hainard, A., Licker, V., Turck, N., Kuhn, K., Hochstrasser, D.F., etal. (2008) Relative quantification of proteins in human cerebrospinal fluids by ms/ms using 6-plex isobaric tags. Anal Chem 80: 2921-2931.
53. Ehler, M.M., and Cloete, T.E. (1999) Comparing protein profiles of 21 different activated sludge systems after SDS-PAGE. Water Res 33: 1181-1186.
54. Eithier, M., Hou, W.M., Duewel, H.S., and Figeys, D. (2006) The proteomic reactor: a microfluidic device for processing minute amounts of protein prior to mass spectrometry analysis. J Proteome Res 5: 2754-2759.
55. Ellen, A.F., Albers, S.V., and Driessen, A.J. (2009) Comparative study of the extracellular proteome of sulfolobus species reveals limited secretion. Extremophiles 14: 87-98.
56. Eng, J.K., McCormack, A.L., and Yates, J.R., III (1994) 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.
57. Engen, J.R., Bradbury, E.M., and Chen, X. (2002) Using stable-isotope-labeled proteins for hydrogen exchange studies in complex mixtures. Anal Chem 74: 1680-1686.
58. Everberg, H., Gustavsson, N., and Tjerneld, F. (2008) Enrichment of Membrane Proteins by Partitioning in Detergent/Polymer Aqueous Two-Phase Systems. Methods in Molecular Biology. A. Posch. Totowa, NJ: Humana press.
59. Everley, P.A., Krijgsveld, J., Zetter, B.R., and Gygi, S.P. (2004) Quantitative cancer proteomics: stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research. Mol Cell Proteomics 3: 729-735.
60. Fenselau, C. (2007) A review of quantitative methods for proteomic studies. J Chromatogr B 855: 14-20.
61. Fey, S.J., Larsen, P.M., Görg, A., München, F., Weihenstephan, G., and Odense, D. (2000) Towards higher resolution: two-dimensional electrophoresis of Saccharomyces cerevisiae proteins using overlapping narrow immobilized pH gradients. Electrophoresis 21: 2610-2616.
62. Gan, C.S., Chong, P.K., Pham, T.K., and Wright, P.C. (2007) Technical, experimental, and biological variations in isobaric tags for relative and absolute quantitation (iTRAQ). J Proteome Res 6: 821-827.
63. Gerber, S., Rush, J., Stemman, O., Kirschner, M., and Gygi, S. (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci USA 100: 6940-6945.
64. Gibson, F., Anderson, L., Babnigg, G., Baker, M., Berth, M., Binz, P.A., etal. (2008) Guidelines for reporting the use of gel electrophoresis in proteomics. Nat Biotechnol 26: 863.
65. Goo, Y.A., Yi, E.C., Baliga, N.S., Tao, W.A., Pan, M., Aebersold, R., etal. (2003) Proteomic analysis of an extreme halophilic archaeon, Halobacterium sp. NRC-1. Mol Cell Proteomics 2: 506-524.
66. Goodchild, A., Raftery, M., Saunders, N.F., Guilhaus, M., and Cavicchioli, R. (2004a) Biology of the cold adapted archaeon, Methanococcoides burtonii determined by proteomics using liquid chromatography-tandem mass spectrometry. J Proteome Res 3: 1164-1176.
67. Goodchild, A., Saunders, N.F.W., Ertan, H., Raftery, M., Guilhaus, M., Curmi, P.M.G., and Cavicchioli, R. (2004b) A proteomic determination of cold adaptation in the Antarctic archaeon, Methanococcoides burtonii. Mol Microbiol 53: 309-321.
68. Goodchild, A., Raftery, M., Saunders, N.F., Guilhaus, M., and Cavicchioli, R. (2005) Cold adaptation of the Antarctic archaeon, Methanococcoides burtonii assessed by proteomics using ICAT. J Proteome Res 4: 473-480.
69. Goodlett, D.R., and Yi, E.C. (2002) Proteomics without polyacrylamide: qualitative and quantitative uses of tandem mass spectrometry in proteome analysis. Funct Integr Genomics 2: 138-153.
70. Gorg, A., Obermaier, C., Boguth, G., Harder, A., Scheibe, B., Wildgruber, R., and Weiss, W. (2000) The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 21: 1037-1053.
71. Graham, R.L., O'Loughlin, S.N., Pollock, C.E., Ternan, N.G., Weatherly, D.B., Jackson, P.J., etal. (2006a) A combined shotgun and multidimensional proteomic analysis of the insoluble subproteome of the obligate thermophile, Geobacillus thermoleovorans t80. J Proteome Res 5: 2465-2473.
72. Graham, R.L.J., Pollock, C.E., Ternan, N.G., and McMullan, G. (2006b) Top-down proteomic analysis of the soluble sub-proteome of the obligate thermophile, Geobacillus thermoleovorans t80: insights into its cellular processes. J Prot Res 5: 822-828.
73. Graham, R.L., Pollock, C.E., O'Loughlin, S.N., Ternan, N.G., Weatherly, D.B., Tarleton, R.L., and McMullan, G. (2007) Multidimensional analysis of the insoluble sub-proteome of Oceanobacillus iheyensis hte831, an alkaliphilic and halotolerant deep-sea bacterium isolated from the Iheya Ridge. Proteomics 7: 82-91.
74. Graumann, J., Hubner, N.C., Kim, J.B., Ko, K., Moser, M., Kumar, C., etal. (2008) Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5, 111 proteins. Mol Cell Proteomics 7: 672-683.
75. Griffin, T.J., Han, D.K., Gygi, S.P., Rist, B., Lee, H., Aebersold, R., and Parker, K.C. (2001) Toward a high-throughput approach to quantitative proteomic analysis: expression-dependent protein identification by mass spectrometry. J Am Soc Mass Spectrom 12: 1238-1246.
76. Gygi, S.P., Rochon, Y., Franza, B.R., and Aebersold, R. (1999a) Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19: 1720-1730.
77. Gygi, S.P., Rist, B., Gerber, S.A., Turecek, F., Gelb, M.H., and Aebersold, R. (1999b) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17: 994-999.
78. Gygi, S.P., Corthals, G.L., Zhang, Y., Rochon, Y., and Aebersold, R. (2000) Evaluation of two-dimensional gel electrophoresis based proteome analysis technology. Proc Natl Acad Sci USA 97: 9390-9305.
79. Gygi, S.P., Rist, B., Griffin, T.J., Eng, J.K., and Aebersold, R. (2002) Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinty tags. J Proteome Res 1: 47-54.
80. Halligan, B.D., Slyper, R.Y., Twigger, S.N., Hicks, W., Olivier, M., and Greene, A.S. (2005) ZoomQuant: an application for the quantitation of stable isotope labeled peptides. J Am Soc Mass Spectrom 16: 302-306.
81. Han, X., Aslanian, A., and Yates, J.R., III (2008) Mass spectrometry for proteomics. Curr Opin Chem Biol 12: 483-490.
82. Heck, A.J.R. (2008) Native mass spectrometry: a bridge between interactomics and structural biology. Nat Methods 5: 927-933.
83. Hendrickson, E., Xia, Q., Wang, T., Leigh, J., and Hackett, M. (2006) Comparison of spectral counting and metabolic stable isotope labeling for use with quantitative microbial proteomics. Analyst 131: 1335-1341.
84. Hengst, L., and Reed, S.I. (1996) Translational control of p27KIP1 accumulation during the cell cycle. Science 271: 1861-1864.
85. Hillenkamp, F., and Peter-Katalinic, J. (2007) A Practical Guide to MALDI-MS. Instrumentation, Methods and Applications. New York: Wiley.
86. Horvatovich, P., Govorukhina, N., Reijmers, T.H., van der Zee, G.J., Suits, F., and Bischoff, R. (2007) Chip-LC-MS for label-free profiling of human serum. Electrophoresis 28: 4493-4505.
87. Hu, J., Coombes, K.R., Morris, J.S., and Baggerly, K.A. (2005a) The importance of experimental design in proteomic mass spectrometry experiments: some cautionary tales. Brief Funct Genomic Proteomic 3: 322-331.
88. Hu, Q., Noll, R.J., Li, H., Makarov, A.A., Hardman, M., and Cooks, R.G. (2005b) The orbitrap: a new mass spectrometer. J Mass Spectrom 40: 430-443.
89. Hunt, D.F., and Yates, J.R., III (1986) Protein sequencing by tandem mass spectrometry. Proc Acad Sci USA 83: 6233-6237.
90. Hunt, S.M.N., Thomas, M.R., Sebastian, L.T., Pedersen, S.K., Harcourt, R.L., Sloane, A.J., and Wilkins, M.R. (2005) Optimal replication and the importance of experimental design for gel-based quantitative proteomics. J Proteome Res 4: 809-819.
91. Ishihama, Y., Oda, Y., Tabata, T., Sato, T., Nagasu, T., Rappsilber, J., and Mann, M. (2005) Exponentially modified protein abundance index (EMPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics 4: 1265-1272.
92. Issaq, H.J., Chan, K.C., Janini, G.M., Conrads, T.P., and Veenstra, T.D. (2005) Multidimensional separation of peptides for effective proteomic analysis. J Chromatogr B 817: 35-47.
93. Jaffe, J.D., Mani, D.R., Leptos, K.C., Church, G.M., Gillette, M.A., and Carr, S.A. (2006) PEPPeR, a platform for experimental proteomic pattern recognition. Mol Cell Proteomics 5: 1927-1941.
94. Jemlich, N., Schmidt, F., Harwich, M., von Bergen, M., Richnow, H.-H., and Vogt, C. (2008) Incorporation of carbon and nitrogen atoms into proteins measured by protein-based stable isotope probing (Protein-SIP). Rapid Commun Mass Spectrom 22: 2889-2897.
95. Jemlich, N., Schmidt, F., Taubert, M., Seifert, J., von Bergen, M., Richnow, H.-H., and Vogt, C. (2009) Comparison of methods for simultaneous identificatiopn of bacterial species and determination of metabolic activity by protein based stable isotope probing (Protein-SIP) experiments. Rapid Commun Mass Spectrom 23: 1871-1878.
96. Jemlich, N., Schmidt, F., Taubert, M., Seifert, J., Bastida, F., von Bergen, M., etal. (2010) Protein based stable isotope probing. Nat Protoc 5: 1957-1966.
97. 18O peptide ion ratios for the relative quantification of proteomes. J Am Soc Mass Spectrom 15: 437-445.
98. Julka, S., and Regnier, F. (2004) Quantification in proteomics through stable isotope coding: a review. J Proteome Res 3: 350-363.
99. Kaiser, J. (2002) Public-private group maps out initiatives. Science 296: 827.
100. Kan, J., Hanson, T.E., Ginter, J.M., Wang, K., and Chen, F. (2005) Metaproteomic analysis of Chesapeake Bay microbial communities. Saline Systems 1: 1-7.
101. Karp, N.A., Spencer, M., Lindsay, H., O'Dell, K., and Lilley, K.S. (2005) Impact of replicate types on proteomic expression analysis. J Proteome Res 4: 1867-1871.
102. Karp, N.A., McCormick, P.S., Russell, M.R., and Lilley, K.S. (2007) Experimental and statistical considerations to avoid false conclusions in proteomic studies using differential in-gel electrophoresis. Mol Cell Proteomics 6: 1354-1364.
103. Karp, N.A., Huber, W., Sadowski, P.G., Charles, P.D., Hester, S.V., and Lilley, K.S. (2010) Addressing accuracy and precision issues in iTRAQ quantitation. Mol Cell Proteomics 9: 1885-1897.
104. Kawamoto, J., Kurihara, T., Kitagawa, M., Kato, I., and Esaki, N. (2007) Proteomic studies of an antarctic cold-adapted bacterium, Shewanella livingstonensis ac10, for global identification of cold-inducible proteins. Extremophiles 11: 819-826.
105. Keller, A., and Shteynberg, D. (2011) Software pipeline and data analysis for ms/ms proteomics: the trans-proteomic pipeline. Methods Mol Biol 694: 169-189.
106. Keller, A., Eng, J., Zhang, N., Li, X., and Aebersold, R. (2005) A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol 2: 1-8.
107. Keller, M., and Hettich, R. (2009) Environmental proteomics: a paradigm shift in characterizing microbial activities at the molecular level. Microbiol Mol Biol Rev 73: 62-70.
108. Kiley, P.J., and Storz, G. (2004) Exploiting thiol modifications. PLoS Biol 2: e400.
109. Kirkland, P.A., Humbard, M.A., Daniels, C.J., and Maupin-Furlow, J.A. (2008) Shotgun proteomics of the haloarchaeon Haloferax volcanii. J Proteome Res 7: 5033-5039.
110. Kirkpatrick, D., Gerber, S., and Gygi, S. (2005) The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods 35: 265-273.
111. Klaassens, E.S., de Vos, W.M., and Vaughan, E.E. (2007) Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestional tract. Appl Environ Microbiol 73: 1388-1392.
112. Klein, C., Garcia-Rizo, C., Bisle, B., Scheffer, B., Zischka, H., Pfeiffer, F., etal. (2005) The membrane proteome of Halobacterium salinarum. Proteomics 5: 180-197.
113. Klein, C., Aivaliotis, M., Olsen, J.V., Falb, M., Besir, H., Scheffer, B., etal. (2007) The low molecular weight proteome of Halobacterium salinarum. J Proteome Res 6: 1510-1518.
114. Konstantinidis, K., Tebbe, A., Klein, C., Scheffer, B., Aivaliotis, M., Bisle, B., etal. (2007) Genome-wide proteomics of Natronomonas pharaonis. J Proteome Res 6: 185-193.
115. Krijgsveld, J., and Heck, A.J.R. (2004) Quantitative proteomics by metabolic labeling with stable isotopes. Drug Discov Today: Targets 3: S11-S15.
116. Krijgsveld, J., Ketting, R.F., Mahmoudi, T., Johansen, J., Artal-Sanz, M., Verrijzer, C.P., etal. (2003) Metabolic labeling of C.elegans and D.melanogaster for quantitative proteomics. Nat Biotechnol 21: 927-931.
117. Kumsta, C., Thamsen, M., and Jakob, U. (2010) Effects of oxidative stress on behavior, physiology, and the redox thiol proteome of Caenorhabditis elegans. Antioxid Redox Signal 14: 1023-1037.
118. Kwon, S.O., Kang, S.G., Park, S.H., Kim, Y.H., Choi, J.S., Lee, J., and Kim, S.I. (2009) Proteomic characterization of the sulfur-reducing hyperthermophilic archaeon Thermococcus onnurineus na1 by 2-DE/MS-MS. Extremophiles 13: 379-387.
119. Lacerda, C.M.R., and Reardon, K.F. (2009) Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology. Brief Funct Genomic Proteomic 8: 75-87.
120. Lacerda, C.M.R., Choe, L.H., and Reardon, K.F. (2007) Metaproteomic analysis of bacterial community response to cadmium exposure. J Proteome Res 6: 1145-1152.
121. Lange, R., and Hengge-Aronis, R. (1994) The cellular concentration of the sigma s subunit of RNA polymerase in Escherichia coli is controlled at the levels of transcription, translation, and protein stability. Gene Dev 8: 1600-1612.
122. Lasonder, E., Ishihama, Y., Andersen, J.S., Vermunt, A.M.W., Pain, A., Sauerwein, R.W., etal. (2002) Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature 419: 537-542.
123. Lauro, F.M., DeMaere, M.Z., Yau, S., Brown, M., Ng, C., Wilkins, D., etal. (2010) An integrative study of a meromictic lake ecosystem in Antarctica. ISME J (in press) doi:10.1038/ismej.2010.185.
124. Lee, A.M., Sevinsky, J.R., Bundy, J.L., Grunden, A.M., and Stephenson, J.L., Jr (2009) Proteomics of Pyrococcus furiosus, a hyperthermophilic archaeon refractory to traditional methods. J Proteome Res 8: 3844-3851.
125. Lefevre, F., Jarrin, C., Ginolhac, A., Auriol, D., and Nalin, R. (2007) Environmental metagenomics: an innovative resource for industrial biocatalysis. Biocatal Biotransform 25: 242-250.
126. Leichert, L.I., Gehrke, F., Gudiseva, H.V., Blackwell, T., Ilbert, M., Walker, A.K., etal. (2008) Quantifying changes in the thiol redox proteome upon oxidative stress in vivo. Proc Natl Acad Sci USA 105: 8197-8202.
127. Leptos, K.C., Sarracino, D.A., Jaffe, J.D., Krastins, B., and Church, G.M. (2006) MapQuant: open-source software for large-scale protein quantification. Proteomics 6: 1770-1782.
128. Leroy, B., Rosier, C., Erculisse, V., Leys, N., Mergeay, M., and Wattiez, R. (2010) Differential proteomic analysis using isotope-coded protein-labeling strategies: comparison, improvements and application to simulated microgravity effect on Cupriavidus metallidurans ch34. Proteomics 10: 2281-2291.
129. Leuko, S., Raftery, M.J., Burns, B.P., Walter, M.R., and Neilan, B.A. (2009) Global protein level responses of Halobacterium salinarum NRC-1 to prolonged changes in external sodium chloride concentrations. J Proteome Res 8: 2218-2225.
130. Li, X.J., Zhang, H., Ranish, J.A., and Aebersold, R. (2003) Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal Chem 75: 6648-6657.
131. Lim, H., Eng, J., Yates, J.R., III, Tollaksen, S., Giometti, C., Holden, J., etal. (2003) Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to μLC-ESI tandem mass spectrometry. J Am Soc Mass Spectrom 14: 957.
132. Lin, W.T., Hung, W.N., Yian, Y.H., Wu, K.P., Han, C.L., Chen, Y.R., etal. (2006) Multi-Q: a fully automated tool for multiplexed protein quantitation. J Proteome Res 5: 2328-2338.
133. Link, A.J., Eng, J.K., Schieltz, D.M., Carmack, E., Mize, G.J., Morris, D.R., etal. (1999) Direct analysis of protein complexes using mass spectrometry detection. Nat Biotechnol 17: 676-682.
134. Lopez, M.F., Berggren, K., Chernokalskaya, E., Lazarev, A., Robinson, M., and Patton, W.F. (2000) 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: 3673-3683.
135. Lu, P., Vogel, C., Wang, R., Yao, X., and Marcotte, E.M. (2006) Absolute protein expressionprofiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol 25: 117-124.
136. Lu, X., and Zhu, H. (2005) Tube-gel digestion: a novel proteomic approach for high throughput analysis of membrane proteins. Mol Cell Proteomics 4: 1948-1958.
137. Ma, B., Zhang, K., Hendrie, C., Liang, C., Li, M., Doherty-Kirby, A., and Lajoie, G. (2003) PEAKS: powerful softwate for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom 17: 2337-2342.
138. MacCoss, M.J., and Matthews, D.E. (2005) Quantitative MS for proteomics: teaching a new dog old tricks. Anal Chem 77: 294A-302A.
139. MacCoss, M.J., Wu, C.C., Liu, H., Sadygov, R., and Yates, J.R., III (2003) A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal Chem 75: 6912-6921.
140. MacCoss, M.J., Wu, C.C., Matthews, D.E., and Yates, J.R., III (2005) Measurement of the isotope enrichment of stable isotope-labeled proteins using high-resolution mass spectra of peptides. Anal Chem 77: 7646-7653.
141. Mann, M., and Jensen, O. (2003) Proteomic analysis of post-translational modifications. Nat Biotechnol 21: 255-261.
142. Maron, P.A., Coeur, C., Pink, C., Clays-Josserand, A., Lensi, R., Richaume, A., and Poetier, P. (2003) Use of polyclonal antibodies to detect and quantify the NOR protein of nitriteoxidizers in complex environments. J Microbiol Methods 53: 87-95.
143. Maron, P.A., Richaume, A., Poetier, P., Lata, J.C., and Lensi, R. (2004) Immunological method for direct assessment of the functionality of a denitrifying strain of Pseudomonas fluorescens in soil. J Microbiol Methods 53: 13-21.
144. Maron, P.A., Christophe, M., Severine, S., Houria, A., Philippe, L., and Lionel, R. (2006) Protein extraction and fingerprinting optimization of bacterial communities in natural Environment. Microb Ecol 53: 426-434.
145. Maron, P.A., Ranjard, L., Mougel, C., and Lemanceau, P. (2007) Metaproteomics: a new approach for studying functional microbial ecology. Microb Ecol 53: 486-493.
146. Marouga, R., David, S., and Hawkins, E. (2005) The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal Bioanal Chem 382: 669-678.
147. Mary, I., Oliver, A., Skipp, P., Holland, R., Topping, J., Tarran, G., etal. (2010) Metaproteomic and metagenomic analyses of defined oceanic microbial populations using microwave cell fixation and flow cytometric sorting. FEMS Microbiol Ecol 74: 10-18.
148. May, D., Fitzgibbon, M., Liu, Y., Holzman, T., Eng, J., Kemp, C.J., etal. (2007) A platform for accurate mass and time analyses of mass spectrometry data. J Proteome Res 6: 2685-2694.
149. Mesbah, N.M., Cook, G.M., and Wiegel, J. (2009) The halophilic alkalithermophile Natranaerobius thermophilus adapts to multiple environmental extremes using a large repertoire of Na(K)/H antiporters. Mol Microbiol 74: 270-281.
150. Mitra, S.K., Gantt, J.A., Ruby, J.F., Clouse, S.D., and Goshe, M.B. (2007) Membrane proteomic analysis of Arabidopsis thalania using alternative solubilisation techniques. J Proteome Res 6: 1933-1950.
151. 18O-labeling strategies for quantitative proteomics. Mass Spectrom Rev 26: 121-136.
152. Miyazaki, K. (2005) A hyperthermophilic laccase from Thermus thermophilus hb27. Extremophiles 9: 415-425.
153. Molloy, M.P., Herbert, B.R., Slade, M.B., Rabilloud, T., Nouwens, A.S., Williams, K.L., and Gooley, A.A. (2000) Proteomic analysis of the Escherichia coli outer membrane. Eur J Biochem 267: 2871-2881.
154. Molloy, M.P., Brzezinsk, E.E., Hang, J., McDowell, M.T., and VanBogelen, R.A. (2003) Overcoming technical variation and biological variation in quantitative proteomics. Proteomics 3: 1912-1919.
155. Monroe, M.E., Shaw, J.L., Daly, D.S., Adkins, J.N., and Smith, R.D. (2008) Masic: a software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features. Comput Biol Chem 32: 215-217.
156. Morris, R.M., Nunn, B.L., Frazar, C., Goodlett, D.R., Ting, Y.S., and Rocap, G. (2010) Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction. ISME J 4: 673-685.
157. 2. Anal Bioanal Chem 398: 377-389.
158. Nesvizhskii, A.I., Vitek, O., and Aebersold, R. (2007) Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods 4: 787-797.
159. Ng, C., DeMaere, M.Z., Williams, T.J., Lauro, F.M., Raftery, M., Gibson, J., etal. (2010) Metaproteogenomic analysis of a dominant green sulfur bacterium of Ace Lake, Antarctica. ISME J 4: 1002-1019.
160. Oda, Y., Huang, K., Cross, F.R., Cowburn, D., and Chait, B.T. (1999) Accurate quantitation of protein expression and site-specific phosphorylation. Proc Natl Acad Sci U S A 96: 6591-6596.
161. Ogunseitan, O.A. (1993) Direct extraction of proteins from environmental samples. J Microbiol Methods 17: 273-281.
162. Old, W.M., Meyer-Arendt, K., Aveline-Wolf, L., Pierce, K.G., Mendoza, A., Sevinsky, J.R., etal. (2005) Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics 4: 1487-1502.
163. Ong, S.E., Blagoev, B., Kratchmarova, I., Kristensen, D.B., Steen, H., Pandey, A., and Mann, M. (2002) Stable isotope labeling by amino acids in cell culture, silac, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1: 376-386.
164. Ong, S.E., Foster, L.J., and Mann, M. (2003a) Mass spectrometric-based approaches in quantitative proteomics. Methods 29: 124-130.
165. 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J Proteome Res 2: 173-181.
166. Onsongo, G., Stone, M.D., Van Riper, S.K., Chilton, J., Wu, B., Higgins, L., etal. (2010) LTQ-iQuant: a freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments. Proteomics 10: 3533-3538.
167. Ostrowski, M., Fegatella, F., Wasinger, V., Corthals, G., Guilhaus, M., and Cavicchioli, R. (2004) Cross species identification of proteins from proteome profiles of the marine oligotrophic ultramicrobacterium, Sphingopyxis alaskensis. Proteomics 4: 1779-1788.
168. Ow, S.Y., Salim, M., Noirel, J., Evans, C., Rehman, I., and Wright, P.C. (2009) Itraq underestimation in simple and complex mixtures: 'The good, the bad and the ugly'. J Proteome Res 8: 5347-5355.
169. Palagi, P.M., Walther, D., Quadroni, M., Catherinet, S., Burgess, J., Zimmermann-Ivol, C., etal. (2005) MSight: an image analysis software for liquid chromatography-mass spectrometry. Proteomics 5: 2381-2384.
170. Pandey, A., and Mann, M. (2000) Proteomics to study genes and genomes. Nature 405: 837-846.
171. Paoletti, A.C., Parmely, T.J., Tomomori-Sato, C., Sato, S., Zhu, D., Conaway, R.C., etal. (2006) Quantitative proteomic analysis of distinct mammalian mediator complexes using normalized spectral abundance factors. Proc Natl Acad Sci USA 103: 18928-18933.
172. Paradela, A., Marcilla, M., Navajas, R., Ferreira, L., Ramos-Fernandez, A., Fernandez, M., etal. (2010) Evaluation of isotope-coded protein labeling (ICPL) in the quantitative analysis of complex proteomes. Talanta 80: 1496-1502.
173. Park, S.K., Venable, J.D., Xu, T., and Yates, J.R., III (2008) Aquantitative analysis software tool for mass spectrometry-based proteomics. Nat Methods 5: 319-322.
174. Pasa-Tolic, L., Jensen, P.K., Anderson, G.A., Lipton, M.S., Peden, K.K., Martinovic, S., etal. (1999) High throughput proteome-wide precision measurements of protein expression using mass spectrometry. J Am Chem Soc 121: 7949-7950.
175. Patterson, S.D. (1994) From electrophoretically separated protein to identification: strategies for sequence and mass analysis. Anal Biochem 221: 1-15.
176. Patton, W.F. (2000) A thousand points of light: the application of fluorescence detection technologies to two-dimensional gel electrophoresis and proteomics. Electrophoresis 21: 1123-1144.
177. Patton, W.F., Schulenberg, B., and Steinberg, T.H. (2002) Two-dimensional gel electrophoresis; better than a poke in the ICAT? Curr Opin Biotechnol 13: 321-328.
178. Pavelka, N., Fournier, M.L., Swanson, S.K., Pelizzola, M., Ricciardi-Castagnoli, P., Florens, L., and Washburn, M.P. (2008) Statistical similarities between transcriptomics and quantitative shotgun proteomics data. Mol Cell Proteomics 7: 631-644.
179. Peng, J., and Gygi, S.P. (2001) Proteomics: the move to mixtures. J Mass Spectrom 36: 1083-1091.
180. Perkins, D.N., Pappin, D.J., Creasy, D.M., and Cottrell, J.S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20: 3551-3567.
181. Pichler, P., Kocher, T., Holzmann, J., Mazanek, M., Taus, T., Ammerer, G., and Mechtler, K. (2010) Peptide labeling with isobaric tags yields higher identification rates using iTRAQ 4-plex compared to TMT 6-plex and iTRAQ 8-plex on LTQ orbitrap. Anal Chem 82: 6549-6558.
182. Pohlschroder, M., Gimenez, M.I., and Jarrell, K.F. (2005) Protein transport in archaea: sec and twin arginine translocation pathways. Curr Opin Microbiol 8: 713-719.
183. Prosinecki, V., Botelho, H.M., Francese, S., Mastrobuoni, G., Moneti, G., Urich, T., etal. (2006) A proteomic approach toward the selection of proteins with enhanced intrinsic conformational stability. J Proteome Res 5: 2720-2726.
184. Pulido, M.A., Koga, Y., Takano, K., and Kanaya, S. (2007) Directed evolution of tk-subtilisin from a hyperthermophilic archaeon: identification of a single amino acid substitution responsible for low-temperature adaptation. Protein Eng Des Sel 20: 143-153.
185. Rabilloud, T. (2002) Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs up the mountains. Proteomics 2: 3-10.
186. Ram, R.J., VerBerkmoes, N.C., Thelen, M.P., Tyson, G.W., Baker, B.J., Blake, R.C., II, etal. (2005) Community proteomics of a natural microbial biofilm. Science 308: 1915-1920.
187. Ramos, Y., Garcia, Y., Llopiz, A., and Castellanos-Serra, L. (2008) Selectivity of bacterial proteome fractionation based on differential solubility: a mass spectrometry evaluation. Anal Biochem 377: 134-140.
188. 18O labeling with a correction for labeling efficiency. Mol Cell Proteomics 6: 1274-1286.
189. Rappsilber, J., Ryder, U., Lamond, A., and Mann, M. (2002) Large-scale proteomic analysis of the human spliceosome. Genome Res 12: 1231-1245.
190. Righetti, P.G., Castagna, A., Antonioli, P., and Boschetti, E. (2005) Prefractionation techniques in proteome analysis: the mining tools of the third millennium. Electrophoresis 26: 297-319.
191. Rocke, D.M. (2004) Design and analysis of experiments with high throughput biological assay data. Semin Cell Dev Biol 15: 703-713.
192. Ross, P.L., Huang, Y.N., Marchese, J.N., Williamson, B., Parker, K., Hattan, S., etal. (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3: 1154-1169.
193. Saunders, N.F., Ng, C., Raftery, M., Guilhaus, M., Goodchild, A., and Cavicchioli, R. (2006) Proteomic and computational analysis of secreted proteins with type 1 signal peptides from the Antarctic archaeon Methanococcoides burtonii. J Proteome Res 5: 2457-2464.
194. Savitski, M.M., Nielsen, M.L., Kjeldsen, F., and Zubarev, R.A. (2005) Proteomics-grade de novo sequencing approach. J Proteome Res 4: 2348-2354.
195. Schloss, P.D., and Handelsman, J. (2003) Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14: 303-310.
196. Schmeisser, C., Steele, H., and Streit, W.R. (2007) Metagenomics, biotechnology with non-culturable microbes. Appl Microbiol Biotechnol 75: 955-962.
197. Schmidt, A., Kellermann, J., and Lottspeich, F. (2005) A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5: 4-15.
198. Schneider, T., and Riedel, K. (2010) Environmental proteomics: analysis of structure and function of microbial communities. Proteomics 10: 785-798.
199. Schulze, W.X., and Mann, M. (2004) A novel proteomic screen for peptide-protein interactions. J Biol Chem 279: 10756-10764.
200. Sergeant, K., Beeumen, J.V., and Samyn, B. (2009) De novo sequence analysis of N-terminal sulfonated peptides after in-gel guanidination. Methods Mol Biol 519: 495-506.
201. Shadforth, I.P., Dunkley, T.P., Lilley, K.S., and Bessant, C. (2005) i-Tracker: for quantitative proteomics using iTRAQ. BMC Genomics 6: 145-151.
202. Shen, Y., Jacobs, J., Camp, D., 2nd, Fang, R., Moore, R., Smith, R., etal. (2004) Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome. Anal Chem 76: 1134-1144.
203. Shevchenko, A., Thomas, H., Havli, J., Olsen, J.V., and Mann, M. (2007) In-gel digestion for mass spectrometric characterisation of proteins and proteomes. Nat Protoc 1: 2856-2860.
204. Shirai, T., Kobayashi, T., Ito, S., and Horikoshi, K. (2008) Alkaline adaptation of proteins. In Protein Adaptation in Extremophiles. Siddiqui, K.S., and Thomas, T. (eds). New York: Nova biomedical books, pp. 105-141.
205. Siddiqui, K.S., and Thomas, T. (eds) (2008) Protein Adaptation in Extremophiles. Molecular anatomy and physiologyof proteins Uversky, V.N (series ed.) New York: Nova Biomedical Books.
206. Singleton, I., Merringto, G., Colvan, S., and Delahunty, J.S. (2003) The potential of soilprotein-based methods to indicate metal contamination. Appl Soil Ecol 654: 1-8.
207. Siuti, N., and Kelleher, N.L. (2007) Decoding protein modifications using top-down mass spectrometry. Nat Methods 4: 817-821.
208. Song, X., Bandow, J., Sherman, J., Baker, J.D., Brown, P.W., McDowell, M.T., and Molloy, M.P. (2008) iTRAQ experimental design for plasma biomarker discovery. J Proteome Res 7: 2952-2958.
209. Sowell, S.M., Wilhelm, L.J., Norbeck, A.D., Lipton, M.S., Nicora, C.D., Barofsky, D.F., etal. (2009) Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J 3: 93-105.
210. Srbek, J., Eickhoff, J., Effelsberg, U., Kraiczek, K., van de Goor, T., and Coufal, P. (2007) Chip-based nano-LC-MS/MS identification of proteins in complex biological samples using a novel polymer microfluidic device. J Sep Sci 30: 2046-2052.
211. Stasyk, T., and Huber, L.A. (2004) Zooming in: fractionation strategies in proteomics. Proteomics 4: 3704-3716.
212. Stead, D., Paton, N.W., Missier, P., Embury, S.M., Hedeler, C., Jin, B., etal. (2008) Information quality in proteomics. Brief Bioinform 9: 174-188.
213. Sun, N., Pan, C., Nickell, S., Mann, M., Baumeister, W., and Nagy, I. (2010) Quantitative proteome and transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions. J Proteome Res 9: 4839-4850.
214. Syka, J.E., Marto, J.A., Bai, D.L., Horning, S., Senko, M.W., Schwartz, J.C., etal. (2004) Novel linear quadrupole ion trap/FT mass spectrometer: performance characterization and use in the comparative analysis of histone H3 post-translational modification. J Proteome Res 3: 621-626.
215. Tang, H., Arnold, R., Alves, P., Xun, Z., Clemmer, D., Novotny, M., etal. (2006) A computational approach toward label-free protein quantification using predicted peptide detectability. Bioinformatics 22: e481-e488.
216. Tang, X., Yi, W., Munske, G.R., Adhikari, D.P., Zakharova, N.L., and Bruce, J.E. (2007) Profiling the membrane proteome of Shewanella oneidensis mr-1 with new affinity labeling probes. J Proteome Res 6: 724-734.
217. Taylor, C.F., Hermjakob, H., Julian, R.K., Jr, Garavelli, J.S., Aebersold, R., and Apweiler, R. (2006) The work of the human proteome organisation's proteomics standards initiative (HUPO PSI). OMICS 10: 145-151.
218. Taylor, C.F., Paton, N.W., Lilley, K.S., Binz, P.A., Julian, R.K., Jones, A.R., etal. (2007) The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol 25: 887.
219. Taylor, C.F., Binz, P.A., Aebersold, R., Affolter, M., Barkovich, R., Deutsch, E.W., etal. (2008) Guidelines for reporting the use of mass spectrometry in proteomics. Nat Biotechnol 26: 860.
220. Tebbe, A., Schmidt, A., Konstantinidis, K., Falb, M., Bisle, B., Klein, C., etal. (2009) Life-style changes of a halophilic archaeon analyzed by quantitative proteomics. Proteomics 9: 3843-3855.
221. Ting, L., Cowley, M.J., Hoon, S.L., Guilhaus, M., Raftery, M.J., and Cavicchioli, R. (2009) Normalization and statistical analysis of quantitative proteomics data generated by metabolic labeling. Mol Cell Proteomics 8: 2227-2242.
222. Ting, L., Williams, T.J., Cowley, M.J., Lauro, F.M., Guilhaus, M., Raftery, M.J., and Cavicchioli, R. (2010) Cold adaptation in the marine bacterium, Sphingopyxis alaskensis, assessed using quantitative proteomics. Environ Microbiol 12: 2658-2676.
223. Trauger, S.A., Kalisak, E., Kalisiak, J., Morita, H., Weinberg, M.V., Menon, A.L., etal. (2008) Correlating the transcriptome, proteome, and metabolome in the environmental adaptation of a hyperthermophile. J Proteome Res 7: 1027-1035.
224. Unlu, M., Morgan, M., and Minden, J. (1997) Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18: 2071-2077.
225. Usaite, R., Wohlschlegel, J., Venable, J.D., Park, S.K., Nielsen, J., Olsson, L., and Yates, J.R., III (2008) Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression Saccharomyces cerevisiae strains: the comparison of two quantitative methods. J Proteome Res 7: 266-275.
226. Vellaichamy, A., Tran, J.C., Catherman, A.D., Lee, J.E., Kellie, J.F., Sweet, S.M.M., etal. (2010) Size-sorting combined with improved nanocapillary liquid chromatography-mass spectrometry for identification of intact proteins up to 80kDa. Anal Chem 82: 1234-1244.
227. Venable, J.D., Dong, M.Q., Wohlschlegel, J., Dillin, A., and Yates, J.R., III (2004) Automated approach for quantitative analysis of complex mixtures from tandem mass spectra. Nat Methods 1: 1-7.
228. VerBerkmoes, N.C., Denef, V.J., Hettich, R.L., and Banfield, J.F. (2009) Functional analysis of natural microbial consortia using community proteomics. Nat Rev Microbiol 7: 196-205.
229. Wang, H., Clouthier, S.G., Galchev, V., Misek, D.E., Duffner, U., Min, C.-K., etal. (2005) Intact-protein-based high resolution three dimensional quantitative analysis system for proteome profiling of biological fluids. Mol Cell Prot 4: 618-625.
230. Wang, W., Zhou, H., Lin, H., Roy, S., Shaler, T., Hill, L., etal. (2003) Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal Chem 75: 4818-4826.
231. Wang, X., Li, X., and Li, Y. (2007) A modified coomassie brilliant blue staining method at nanogram sensitivity compatible with proteomic analysis. Biotechnol Lett 29: 1599-1603.
232. 15N-metabolic labeling/mass spectrometry for comparative proteomics and rapid identification of protein markers/targets. Rapid Commun Mass Spectrom 16: 1389-1397.
233. Washburn, M.P., and Yates, J.R. (2000) Analysis of the microbial proteome. Curr Opin Microbiol 3: 292-297.
234. Washburn, M.P., Wolters, D., and Yates, J.R., 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19: 242-247.
235. Washburn, M.P., Ulaszek, R., Deciu, C., Schieltz, D.M., and Yates, J.R., III (2002a) Analysis of quantitative proteomic data generated via multidimensional protein identification technology. Anal Chem 74: 1650-1657.
236. Washburn, M.P., Ulaszek, R., Deciu, C., Schieltz, D.M., and Yates, J.R., III (2002b) Analysis of quantitative proteomic data generated via multidimensional protein identification technology. Anal Chem 74: 1650-1657.
237. Wasinger, V.C., Cordwell, S.J., Cerpa-Poljak, A., Yan, J.X., Gooley, A.A., Wilkins, M.R., etal. (1995) Progress with gene-product mapping of the mollicutes: Mycoplasma genitalium. Electrophoresis 16: 1090-1094.
238. Whitehead, K., Kish, A., Pan, M., Kaur, A., Reiss, D.J., King, N., etal. (2006) An integrated systems approach for understanding cellular responses to gamma radiation. Mol Syst Biol 2: 47.
239. Wilkins, M.R., Pasquali, C., Appel, R.D., Ou, K., Golaz, O., Sanchez, J., etal. (1996) From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Bio/Technology 14: 61-65.
240. Wilkins, M.R., Appel, R.D., Van Eyk, J.E., Chung, M.C.M., Gorg, A., Hecker, M., etal. (2006) Guidelines for the next 10 years of proteomics. Proteomics 6: 4-8.
241. Williams, T.J., Burg, D.W., Ertan, H., Raftery, M.J., Poljak, A., Guilhaus, M., and Cavicchioli, R. (2010a) Global proteomic analysis of the insoluble, soluble, and supernatant fractions of the psychrophilic archaeon Methanococcoides burtonii. Part ii: the effect of different methylated growth substrates. J Proteome Res 9: 653-663.
242. Williams, T.J., Burg, D.W., Raftery, M.J., Poljak, A., Guilhaus, M., Pilak, O., and Cavicchioli, R. (2010b) Global proteomic analysis of the insoluble, soluble, and supernatant fractions of the psychrophilic archaeon Methanococcoides burtonii. Part i: the effect of growth temperature. J Proteome Res 9: 640-652.
243. Williamson, B.L., Purkayastha, S., Hunter, C.L., Nuwaysir, L., Hill, J., Easterwood, L., and Hill, J. (2011) Quantitative protein determination for CYP induction via LC-MS/MS. Proteomics 11: 33-41.
244. Wilm, M., Shevchenko, A., Houthaeve, T., Breit, S., Schweigerer, L., Fotsis, T., and Mann, M. (1996) Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 379: 466-469.
245. Wilmes, P., and Bond, P.L. (2004) The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environ Microbiol 6: 911-920.
246. Wilmes, P., and Bond, P.L. (2006) Metaprotemics: studying functional gene expression in microbial ecosystems. Trends Microbiol 14: 92-97.
247. Wittke, S., Kaiser, T., and Mischak, H. (2004) Differential polypeptide display: the search for the elusive target. J Chromatogr B 803: 17-26.
248. Wu, C.C., MacCoss, M.J., Howell, K.E., and Yates, J.R., 3rd (2003) A method for the comprehensive proteomic analysis of membrane proteins. Nat Biotechnol 21: 532-538.
249. Xia, Q., Hendrickson, E.L., Zhang, Y., Wang, T., Taub, F., Moore, B.C., etal. (2006) Quantitative proteomics of the archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR. Mol Cell Proteomics 5: 868-881.
250. Xia, Q., Wang, T., Park, Y., Lamont, R.J., and Hackett, M. (2007) Differential quantitative proteomics of Porphyromonas gingivalis by linear ion trap mass spectrometry: non-label methods comparison, q-values and lowess curve fitting. Int J Mass Spectrom 259: 105-116.
251. Yan, W., and Chen, S.S. (2005) Mass spectrometry-based quantitative proteomic profiling. Brief Funct Genomic Proteomic 4: 1-12.
252. 18O exchange of truncated peptide substrates. J Proteome Res 2: 147-152.
253. Yates, J.R., III (2004) Mass spectral analysis in proteomics. Annu Rev Bioph Biom 33: 297-316.
254. Yates, J.R., III, and Snyder, M. (2004) Proteomics and genomics. Curr Opin Chem Biol 8: 1-2.
255. Ye, M., Zou, H., Liu, Z., and Ni, J. (2000) Separation of peptides by strong cation-exchange capillary electrochromatography. J Chromatogr A 869: 385-394.
256. Zaparty, M., Esser, D., Gertig, S., Haferkamp, P., Kouril, T., Manica, A., etal. (2010) 'Hot standards' For the thermoacidophilic archaeon Sulfolobus solfataricus. Extremophiles 14: 119-142.
257. 18O labeling. J Proteome Res 9: 2160-2169.
258. Zhang, N., Chen, R., Young, N., Wishart, D., Winter, P., Weiner, J.H., and Li, L. (2007) Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for escherichia coli membrane proteome analysis by 2-D LC-MS/MS. Proteomics 7: 484-493.
259. Zheng, J., Wei, C., Leng, W., Dong, J., Li, R., Li, W., etal. (2007) Membrane subproteomic analysis of Mycobacterium bovis bacillus calmette-guerin. Proteomics 7: 3919-3931.
260. 15N-labeled and unlabeled peptides for efficient protein identification and de novo peptide sequencing. J Proteome Res 3: 1155-1163.
261. Zhu, W., Reich, C.I., Olsen, G.J., Giometti, C.S., and Yates, J.R., 3rd (2004) Shotgun proteomics of Methanococcus jannaschii and insights into methanogenesis. J Proteome Res 3: 538-548.
262. TM reagent technology for protein complex and profiling studies. J Exp Bot 57: 1501-1508.
263. Zivanovic, Y., Armengaud, J., Lagorce, A., Leplat, C., Guerin, P., etal. (2009) Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the archaea. Genome Biol 10: R70.
264. Zybailov, B., Coleman, M.K., Florens, L., and Washburn, M.P. (2005) Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal Chem 77: 6218-6224.
265. Zybailov, B., Mosley, A.L., Sardiu, M.E., Coleman, M.K., Florens, L., and Washburn, M.P. (2006) Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res 5: 2339-2347.