Mass spectrometric identification of proteins in complex post-genomic projects: Soluble proteins of the metabolically versatile, denitrifying 'Aromatoleum' sp. strain EbN1

Journal of Molecular Microbiology and Biotechnology

Volumn 11, Issue 1-2, 2006, Pages 53-81

  Hufnagel, Peter ^a   Rabus, Ralf ^b,c  

^a BRUKER DALTONIK GMBH   (Germany)

^b MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^c UNIVERSITY OF OLDENBURG   (Germany)

Author keywords

2D DIGE; Anaerobic degradation; Aromatic compounds; Bioinformatics; High throughput; Ion trap; LC ESI; MALDI TOF; Mass spectrometry; MS MS; Protein identification; Proteomics; Quantitative proteomics; Robotics; Two dimensional gel electrophoresis

Indexed keywords

ALGORITHM; AROMATOLEUM; ARTICLE; AUTOMATION; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM; BIOINFORMATICS; CALIBRATION; DENITRIFICATION; GENOME ANALYSIS; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PROTEIN ANALYSIS; PROTEOMICS; REPRODUCIBILITY; TANDEM MASS SPECTROMETRY; TWO DIMENSIONAL GEL ELECTROPHORESIS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BETAPROTEOBACTERIA; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; MOLECULAR SEQUENCE DATA; PROTEOME; PROTEOMICS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

BACTERIA (MICROORGANISMS);

EID: 33745742167     PISSN: 14641801     EISSN: None     Source Type: Journal    
DOI: 10.1159/000092819     Document Type: Article

References (201)

1. Aivaliotis M, Corvey C, Tsirogianni I, Karas M, Tsiotis G (2004) Membrane proteome analysis of the green-sulfur bacterium Chlorobium tepidum. Electrophoresis 25:3468-3474.
2. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (1992) Current Protocols in Molecular Biology. John Wiley & Sons, New York.
3. Babnigg G, Giometti CS (2004) GELBANK: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes. Nucleic Acids Res 32:D582-D585.
4. Backert S, Kwok T, Schmid M, Selbach M, Moese S, Peek Jr RM, König W, Meyer TF, Jungblut PR (2005) Subproteomes of soluble and structure-bound Helicobacter pylori proteins analyzed by two-dimensional gel electrophoresis and mass spectrometry. Proteomics 5:1331-1345.
5. Bafna V, Edwards N (2001) SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database. Bioinformatics 17:S13-S21.
6. Bernardini G, Renzone G, Comanducci M, Mini R, Arena S, D'Ambrosio C, Bambini S, Trabalzini L, Grandi G, Martelli P, Achtman M, Scaloni A, Ratti G, Santucci A (2004) Proteome analysis of Neisseria meningitidis serogroup A. Proteomics 4:2893-2926.
7. Biemann K, Scoble HA (1987) Characterization by tandem mass spectrometry of structural modifications in proteins. Science 237:992-998.
8. Bier ME, Schwartz JC (1997) Electrospray-ionization quadrupole ion-trap mass spectrometry; in Cole RB (ed): Electrospray Ionization Mass Spectrometry. John Wiley & Sons Inc., New York, pp 235-288.
9. Bjellqvist B, Ek K, Righetti PG, Gianazza E, Görg A, Westermeier R, Postel W (1982) Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications. J Biochem Biophys Methods 6:317-339.
10. Blattner FR, Plunkett 3rd G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rhode CK, Mayhew GF, Gregor J, Wayne Davis N, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453-1462.
11. Bogdanov B, Smith RD (2005) Proteomics by FTI-CR mass spectrometry: top down and bottom up. Mass Spectrom Rev 24:168-200.
12. Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248-254.
13. Brown PO, Botstein D (1999) Exploring the new world of the genome with DNA microarrays. Nat Gen 21:33-37.
14. Carr S, Aebersold R, Baldwin M, Burlingame A, Clauser K, Nesvizshkii A (2004) The need for guidelines in publication of peptide and protein identification data. Mol Cell Proteomics 3.6:531-533.
15. Carrillo CD, Taboada E, Nash JHE, Lanthier P, Kelly J, Lau PC, Verhulp R, Mykytczuk O, Sy J, Findlay WA, Amoako K, Gomis S, Willson P, Austin JW, Potter A, Babiuk L, Allan B, Szymanski CM (2004) Genome-wide expression analyses of Campylobacter jejuni NCTC11168 reveals coordinate regulation of motility and virulence by flhA. J Biol Chem 279:20327-20338.
16. Celestino PBS, de Carvalho LR, de Freitas LM, Dorella FA, Martins NF, Pacheco LGC, Miyoshi A, Azevedo V (2004) Update of microbial genome programs for bacteria and archaea. Gen Mol Res 3:421-431.
17. Chamrad DC, Körting G, Gobom J, Thiele H, Klose J, Meyer HE, Blüggel M (2003) Interpretation of mass spectrometry data for high-throughput proteomics. Anal Bioanal Chem 376:1014-1022.
18. Chamrad DC, Körting G, Stühler K, Meyer HE, Klose J, Blüggel M (2004) Evaluation of algorithms for protein identification from sequence databases using mass spectrometry data. Proteomics 4:619-628.
19. Chao C-C, Chelius D, Zhang T, Daggle L, Ching W-M (2004) Proteome analysis of Madrid E strain of Rickettsia prowazekii. Proteomics 4:1280-1292.
20. Chernushevich IV, Loboda AV, Thomson BA (2001) An introduction to quadrupole-time-of-flight mass spectrometry. J Mass Spectrom 36:849-865.
21. Clauser KR, Baker P, Burlingame AL (1999) Role of accurate mass measurement (±10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal Chem 71:2871-2882.
22. Coelho A, de Oliveira Santos E, da Hora Faria ML, de Carvalho DP, Soares MR, von Kruger WMA, Bisch PM (2004) A proteome reference map for Vibrio cholerae El Tor. Proteomics 4:1491-1504.
23. Colinge J, Chiappe D, Lagache S, Moniatte M, Bougueleret L (2005) Differential proteomics via probabilistic peptide identification scores. Anal Chem 77:596-606.
24. Conway T, Schoolnik GK (2003) Microarray expression profiling: capturing a genome-wide portrait of the transcriptome. Mol Microbiol 47:879-889.
25. Cordwell SJ, Nouwens AS, Verrills NM, Basseal DJ, Walsh BJ (2000) Subproteomics based upon protein cellular location and relative solubilities in conjunction with composite two-dimensional electrophoresis. Electrophoresis 21:1094-1103.
26. Cordwell SJ, Nouwens AS, Verrills NM, McPherson JC, Hains PG, Van Dyk DD, Walsh BJ (1999) The microbial proteome database - an automated laboratory catalogue for monitoring protein expression in bacteria. Electrophoresis 20:3580-3588.
27. Cramer R, Gobom J, Nordhoff E (2005) High-throughput proteomics using matrix-assisted laser desorption/ionization mass spectrometry. Expert Rev Proteomics 2:407-420.
28. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27:4636-4641.
29. Djordjevic MA (2004) Sinorhizobium meliloti metabolism in the root nodule: a proteomic perspective. Proteomics 4:1859-1872.
30. Doherty NS, Littman BH, Reilly K, Swindell AC, Buss JM, Anderson NL (1998) Analysis of changes in acute-phase plasma proteins in an acute inflammatory response and in rheumatoid arthritis using two-dimensional gel electrophoresis. Electrophoresis 19:355-363.
31. Drews O, Görg A (2005) DynaProt 2D: an advanced proteomic database for dynamic online access to proteomes and two-dimensional electrophoresis gels. Nucleic Acids Res 33:D583-D587.
32. Drews O, Reil G, Parlar H, Görg A (2004) Setting up standards and a reference map for the alkaline proteome of the Gram-positive bacterium Lactococcus lactis. Proteomics 4:1293-1304.
33. Dworzanski JP, Snyder AP (2005) Classification and identification of bacteria using mass-spectrometry-based proteomics. Expert Rev Proteomics 2:863-878.
34. Elias DA, Monroe ME, Marshall MJ, Romine MF, Belieav AS, Fredrickson JK, Anderson GA, Smith RD, Lipton MS (2005) Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS-based proteomics. Proteomics 5:3120-3130.
35. Encarnación S, Guzmán Y, Dunn MF, Hernández M, del Carmen Vargas M, Mora J (2003) Proteome analysis of aerobic and fermentative metabolism of Rhizobium etli CE3. Proteomics 3:1077-1085.
36. Encheva V, Wait R, Gharbia SE, Begum S, Shah HN (2005) Proteome analysis of serovars Typhimurium and Pullorum of Salmonella enterica subspecies I. BMC Microbiol 5:42.
37. Eng JK, McCormack AL, Yates 3rd JR (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.
38. Eymann C, Dreisbach A, Albrecht D, Bernhardt J, Becher D, Gentner S, Tam LT, Büttner K, Buurman G, Scharf C, Venz S, Völker U, Hecker M (2004) A comprehensive proteome map of growing Bacillus subtilis cells. Proteomics 4:2849-2876.
39. Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246:64-71.
40. Fenyö D (2000) Identifying the proteome: software tools. Curr Opin Biotechnol 11:391-395.
41. Fenyö D, Qin J, Chait BT (1998) Protein identification using mass spectrometric information. Electrophoresis 19:998-1005.
42. Field HI, Fenyö D, Beavis RC (2002) RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimizes protein identification, and archives data in a relational database. Proteomics 2:36-47.
43. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb J-F, Dougherty BA, Merrick JM, McKenney K, Sutton G, FitzHugh W, Fields C, Gocyne JD, Scott J, Shirley R, Liu L-I, Glodek A, Kelley JM, Weidman JF, Phillips CA, Spriggs T, Hedblom E, Cotton MD, Utterback TR, Hanna MC, Nguyen DT, Saudek DM, Brandon RC, Fine LD, Fritchman JL, Fuhrmann JL, Geoghagen NSM, Gnehm CL, McDonald LA, Small KV, Fraser CM, Smith HO, Venter JG (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512.
44. Fodor IK, Nelson DO, Alegria-Hartman M, Robbins K, Langlois RG, Turteltaub KW, Corzett TH, McCutchen-Maloney SL (2005) Statistical challenges in the analysis of two-dimensional difference gel electrophoresis experiments using DeCyder™. Bioinformatics 21:3733-3740.
45. Folio P, Chavant P, Chafsey I, Belkorchia A, Chambon C, Hébraud M (2004) Two-dimensional electrophoresis database of Listeria monocytogenes EGDe proteome and proteomic analysis of mid-log and stationary growth phase cells. Proteomics 4:3187-3201.
46. Fournier M, Aubert C, Dermoun Z, Durand M-C, Moinier D, Dolla A (2005) Response of the anaerobe Desulfovibrio vulgaris Hildenborough to oxidative conditions: proteome and transcript analysis. Biochemie 88:85-94.
47. Franzen J, Gabling R-H, Schubert M, Wang Y (1995) Nonlinear ion traps in practical aspects of ion trap mass spectrometry; in March RE, Todd JFJ (eds): Fundamentals of Ion Trap Mass Spectrometry, Volume I. CRC Press, Boca Raton, pp. 49-167.
48. Frishman D, Mironov A, Mewes H-W, Gelfand M (1998) Combining diverse evidence for gene recognition in completely sequenced bacterial genomes. Nucleic Acids Res 26:2941-2947.
49. Gade D, Gobom J, Rabus R (2005a) Proteomic analysis of carbohydrate catabolism and regulation in the marine bacterium Rhodopirellula baltica. Proteomics 5:3672-3683.
50. Gade D, Stührmann T, Reinhardt R, Rabus R (2005b) Growth phase dependent regulation of protein composition in Rhodopirellula baltica. Environ Microbiol 7:1074-1084.
51. Gade D, Theiss D, Lange D, Mirgorodskaya E, Lombardot T, Glöckner FO, Kube M, Reinhardt R, Amann R, Lehrach H, Rabus R, Gobom J (2005c) Towards the proteome of the marine bacterium Rhodopirellula baltica: mapping the soluble proteins. Proteomics 5:3654-3671.
52. Gade D, Thiermann J, Markowsky D, Rabus R (2003) Evaluation of two-dimensional difference gel electrophoresis for protein profiling. Soluble proteins of the marine bacterium Pirellula sp. strain 1. J Mol Microbiol Biotechnol 5:240-251.
53. Galperin MY (2005) The molecular biology database collection: 2005 update. Nucleic Acids Res 33:D5-D24.
54. Garwood K, McLaughlin T, Garwood C, Joens S, Morrison N, Taylor CF, Carroll K, Evans C, Whetton AD, Hart S, Stead D, Yin Z, Brown AJP, Hesketh A, Chater K, Hansson L, Mewissen M, Ghazal P, Howard J, Lilley KS, Gaskell SJ, Brass A, Hubbard SJ, Oliver SG, Paton NW (2004) PEDRo: A database for storing, searching and disseminating experimental proteomics data. BMC Genomics 5:68.
55. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server; in Walker JM (ed): The Proteomics Protocols Handbook. Humana Press, Totowa/NJ, pp. 571-607.
56. Geer LY, Markey SR, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH (2004) Open mass spectrometry search algorithm. J Proteome Res 3:958-964.
57. Giard J-C, Laplace J-M, Rincé A, Pichereau V, Benachour A, Leboeuf C, Flahaut S, Auffray Y, Hartke A (2001) The stress proteome of Enterococcus faecalis. Electrophoresis 22:2947-2954.
58. Giometti CS, Reich C, Tollaksen S, Babnigg G, Lim H, Zhu W, Yates 3rd JR, Olsen G (2002) Global analysis of a 'simple' proteome: Methanococcus jannaschii. J Chromatogr B 782:227-243.
59. Gobom J, Schürenberg M, Müller M, Theiss D, Lehrach H, Nordhoff E (2001) α-Cyano-4-hydroxycinnamic acid affinity sample preparation. A protocol for MALDI-MS peptide analysis in proteomics. Anal Chem 73:434-438.
60. Goesmann A, Linke B, Bartels B, Dondrup M, Krause L, Neuweger H, Oehm S, Paczian T, Wilke A, Meyer F (2005) BRIGEP - the BRIDGE-based genome-transcriptome-proteome browser. Nucleic Acids Res 33:W710-W716.
61. Goodchild A, Raftery M, Saunders NFW, Guilhaus M, Cavicchioli R (2004) Biology of the cold adapted archaeon, Methanococcoides burtonii determined by proteomics using liquid chromatography-tandem mass spectrometry. J Proteome Res 3:1164-1176.
62. Görg A, Boguth G, Köpf A, Reil G, Parlar H, Weiss W (2002) Sample prefractionation with Sephadex isoelectric focusing prior to narrow pH range two-dimensional gels. Proteomics 2:1652-1657.
63. Görg A, Obermaier C, Boguth G, Harder A, Scheibe B, Wildgruber R, Weiss W (2000) The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 21:1037-1053.
64. Görg A, Weiss W, Dunn MJ (2004) Current two-dimensional electrophoresis technology for proteomics. Proteomics 4:3665-3685.
65. Graham DRM, Elliott ST, Van Eyk JE (2005) Broad-based proteomic strategies: a practical guide to proteomics and functional screening. J Physiol 563:1-9.
66. Gras R, Müller M, Gasteiger E, Gay S, Binz P-A, Bienvenut W, Hoogland C, Sanchez J-C, Bairoch A, Hochstrasser DF, Appel RD (1999) Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection. Electrophoresis 20:3535-3550.
67. Grünenfelder B, Rummel G, Vohradsky J, Röder D, Langen H, Jenal U (2001) Proteomic analysis of the bacterial cell cycle. Proc Natl Acad Sci USA 98:4681-4686.
68. Gygj SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17:994-999.
69. Hardman M, Makarov AA (2003) Interfacing the Orbitrap mass analyzer to an electrospray ion source. Anal Chem 75:1699-1705.
70. Haveman SA, Brunelle V, Voordouw JK, Voordouw G, Heidelberg JF, Rabus R (2003) Gene expression analysis of energy metabolism mutants of Desulfovibrio vulgaris Hildenborough indicates an important role of alcohol dehydrogenase. J Bacteriol 185:4345-4353.
71. Hecker M, Engelmann S, Cordwell SJ (2003) Proteomics of Staphylococcus aureus - current state and future challenges. J Chromatogr B 787:179-195.
72. Hecker M, Völker U (2004) Towards a comprehensive understanding of Bacillus subtilis cell physiology by physiological proteomics. Proteomics 4:3727-3750.
73. Heider J, Fuchs G (1997) Anaerobic metabolism of aromatic compounds. Eur J Biochem 243:577-596.
74. Heim S, Ferrer M, Heuer H, Regenhardt D, Nimtz M, Timmis KN (2003) Proteome reference map of Pseudomonas putida strain KT2440 for genome expression profiling: distinct responses of KT2440 and Pseudomonas aeruginosa strain PAO1 to iron deprivation and a new form of superoxide dismutase. Environ Microbiol 5:1257-1269.
75. Hesketh AR, Chandra G, Shaw AD, Rowland JJ, Kell DB, Bibb MJ, Chater KF (2002) Primary and secondary metabolism, and post-translational protein modifications, as portrayed by proteomic analysis of Streptomyces coelicolor. Mol Microbiol 46:917-932.
76. Heukeshoven J, Dernick R (1988) Improved silver staining procedure for fast staining in Phast-System Development Unit. I. Staining of sodium dodecyl sulfate gels. Electrophoresis 9:28-32.
77. Holmes K, Mulholland F, Pearson BM, Pin C, McNicholl-Kennedy J, Ketley JM, Wells JM (2005) Campylobacter jejuni gene expression in response to iron limitation and the role of Fur. Microbiology 151:243-257.
78. Hoogland C, Mostaguir K, Sanchez J-C, Hochstrasser DF, Appel RD (2004) SWISS-2DPAGE, ten years later. Proteomics 4:2352-2356.
79. Houthaeve T, Gausepohl H, Mann M, Ashman K (1995) Automation of micro-preparation and enzymatic cleavage of gel electrophoretically separated proteins. FEBS Lett 376:91-94.
80. Hu Q, Noll RJ, Hongyan L, Makarov A, Hardman M, Cooks RG (2005) The Orbitrap: a new mass spectrometer. J Mass Spectrom 40:430-443.
81. Hubálek M, Hernychová L, Havlasová J, Kasalová I, Neubauerová V, Stulík J, Macela A, Lundqvist M, Larsson P (2003) Towards proteome database of Francisella tularensis. J Chromatogr B 787:149-177.
82. Hunsucker SW, Klage K, Slaughter SM, Potts M, Helm RF (2004) A preliminary investigation of the Nostoc punctiforme proteome. Biochem Biophys Res Commun 317:1121-1127.
83. Hunt DF, Shabanowitz J, Yates 3rd JR, Zhu N-Z, Russell DH, Castro ME (1987) Tandem quadrupole Fourier-transform mass spectrometry of oligopeptides and small proteins. Proc Natl Acad Sci USA 84:620-623.
84. Jacobs JM, Yang X, Luft BJ, Dunn JJ, Camp II DG, Smith RD (2005) Proteomic analysis of Lyme disease: global protein comparison of three strains of Borrelia burgdorferi. Proteomics 5:1446-1453.
85. Jaffe JD, Stange-Thomann N, Smith C, DeCaprio D, Fisher S, Butler J, Calvo S, Elkins T, FitzGerald MG, Hafez N, Kodira CD, Major J, Wang S, Wilkinson J, Nicol R, Nusbaum C, Birren B, Berg HC, Church GM (2004) The complete genome and proteome of Mycoplasma mobile. Genome Res 14:1447-1461.
86. Johnson RS, Martin SA, Biemann K, Stults JT, Watson JT (1987) Novel fragmentation process of peptides by collision-induced decomposition in a tandem mass spectrometer: differentiation of leucine and isoleucine. Anal Chem 59:2621-2625.
87. Jungblut PR, Bumann D, Haas G, Zimny-Arndt U, Holland P, Lamer S, Siejak F, Aebischer A, Meyer TF (2000) Comparative proteome analysis of Helicobacter pylori. Mol Microbiol 36:710-725.
88. Kajiwara H, Kaneko T, Ishizaka M, Tajima S, Kouchi H (2003) Protein profile of symbiotic bacteria Mesorhizobium loti MAFF303099 in mid-growth phase. Biosci Biotechnol Biochem 67:2668-2673.
89. Kao W-C, Chen Y-R, Yi EC, Lee H, Tian Q, Wu K-M, Tsai S-F, Yu SS-F, Chen Y-J, Aebersold R, Chan SI (2004) Quantitative proteomic analysis of metabolic regulation by copper ions in Methylococcus capsulatus (Bath). J Biol Chem 279:51554-51560.
90. Kapp EA, Schütz F, Connolly LM, Chakel JA, Meza JE, Miller CA, Fenyo D, Eng JK, Adkins JN, Omenn GS, Simpson RJ (2005) An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis. Proteomics 5:3475-3490.
91. Karas M, Hillenkamp F (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem 60:2299-2301.
92. Kazemi-Pour N, Condemine G, Hugouvieux-Cotte-Pattat N (2004) The secretome of the plant pathogenic bacterium Erwinia chrysanthemi. Proteomics 4:3177-3186.
93. Kim E-A, Kim JY, Kim S-J, Park KR, Chung H-J, Leem S-H, Kim SI (2004) Proteomic analysis of Acinetobacter lwoffii K24 by 2-D gel electrophoresis and electrospray ionization quadrupole-time of flight mass spectrometry. J Microbiol Methods 57:337-349.
94. Klein C, Garcia-Rizo C, Bisle B, Scheffer B, Zischka H, Pfeiffer F, Siedler F, Oesterhelt D (2005) The membrane proteome of Halobacterium salinarum. Proteomics 5:180-197.
95. Klose J (1975) Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 26:231-243.
96. Kolker E, Purvine S, Galperin MY, Stolyar S, Goodlett DR, Nesvizhskii AI, Keller A, Xie T, Eng JK, Yi E, Hood L, Picone AF, Cherny T, Tjaden BC, Siegel AF, Reilly TJ, Markarova KS, Palsson BO, Smith AL (2003) Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. J Bacteriol 185:4593-4602.
97. Kramer R, Cohen D (2004) Functional genomics to new drug targets. Nat Rev Drug Discov 3:965-972.
98. Kube M, Heider J, Amann J, Hufnagel P, Kühner S, Beck A, Reinhardt R, Rabus R (2004) Genes involved in the anaerobic degradation of toluene in a denitrifying bacterium, strain EbN1. Arch Microbiol 181:182-194.
99. Kühner S, Wöhlbrandt L, Fritz I, Wruck W, Hultschig C, Hufnagel P, Kube M, Reinhardt R, Rabus R (2005) Substrate-dependent regulation of anaerobic degradation pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1. J Bacteriol 187:1493-1503.
100. Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessières P, Bolotin A, Borchert S, Borriss R, Boursier L, Brans A, Braun M, Brignell SC, Bron S, Brouillet S, Bruschi CV, Caldwell B, Capuano V, Carter NM, Choi S-K, Codani J-J, Connerton IF, Cummings NJ, Daniel RA, Denizot F, Devine KM, Düsterhöft A, Ehrlich SD, Emmerson PT, Entian KD, Errington J, Fabret C, Ferrari E, Foulger D, Fritz C, Fujita M, Fujita Y, Fuma S, Galizzi A, Galleron N, Ghim S-Y, Glaser P, Goffeau A, Golightly EJ, Grandi G, Guiseppi G, Guy BJ, Haga K, Haiech J, Harwood CR, Hénaut A, Hilbert H, Holsappel S, Hosono S, Hullo M-F, Itaya M, Jones L, Joris B, Karamata D, Kasahara Y, Klaerr-Blanchard M, Klein C, Kobayashi Y, Koetter P, Koningstein G, Krogh S, Kumano M, Kurita K, Lapidus A, Lardinois S, Lauber J, Lazarevic V, Lee S-M, Levine A, Liu H, Masuda S, Mauël C, Médigue C, Medina N, Mellado RP, Mizuno M, Moestl D, Nakai S, Noback M, Noone M, O'Reilly M, Ogawa K, Ogiwara A, Oudega B, Park S-H, Parro V, Pohl TM, Portetelle D, Porwollik S, Prescott AM, Presecan E, Pujic P, Purnelle B, Rapoport G, Rey M, Reynolds S, Rieger M, Rivolta C, Rocha E, Roche B, Rose M, Sadaie Y, Sato T, Scanlan E, Schleich S, Schroeter R, Scoffone F, Sekiguchi J, Sekowska A, Seror SJ, Serror P, Shin B-S, Soldo B, Sorokin A, Tacconi E, Takagi T, Takahashi H, Takemaru K, Takeuchi M, Tamakoshi A, Tanaka T, Terpstra P, Tognoni A, Tosato V, Uchiyama S, Vandenbol M, Vannier F, Vassarotti A, Viari A, Wambutt R, Wedler E, Wedler H, Weitzenegger T, Winters P, Wipat A, Yamamoto H, Yamane K, Yasumoto K, Yata K, Yoshida K, Yoshikawa H-F, Zumstein E, Yoshikawa H, Danchin A (1997) The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390:249-256.
101. Lamonica JM, Wagner MA, Eschenbrenner M, Williams LE, Miller TL, Patra G, DelVecchio VG (2005) Comparative secretome analyses of three Bacillus anthracis strains with variant plasmid contents. Infect Immun 73:3646-3658.
102. Langen H, Takács B, Evers S, Berndt P, Lahm H-W, Wipf B, Gray C, Fountoulakis M (2000) Two-dimensional map of the proteome of Haemophilus influenzae. Electrophoresis 21:411-429.
103. Laukel M, Rossignol M, Borderies G, Völker U, Vorholt JA (2004) Comparison of the proteome of Methylobacterium extorquens AM1 grown under methylotrophic and nonmethylotrophic conditions. Proteomics 4:1247-1264.
104. Lebeau I, Lammertyn E, De Buck E, Maes L, Geukens N, Van Mellaert L, Arckens L, Anné J, Clerens S (2005) First proteomic analysis of Legionella pneumophila based on its developing genome sequence. Res Microbiol 156:119-129.
105. Lee PS, Lee KH (2003) Escherichia coli - a model system that benefits from and contributes to the evolution of proteomics. Biotechnol Bioeng 84:801-814.
106. Len ACL, Cordwell SJ, Harty DWS, Jacques NA (2003) Cellular and extracellular proteome analysis of Streptococcus mutans grown in a chemostat. Proteomics 3:627-646.
107. Leverrier P, Vissers JPC, Rouault A, Boyaval P, Jan G (2004) Mass spectrometry proteomic analysis of stress adaptation reveals both common and distinct response pathways in Propionibacterium freudenreichii. Arch Microbiol 181:215-230.
108. Li Q, Li L, Rejtar T, Karger BL, Ferry JG (2005) Proteome of Methanosarcina acetivorans. Part I: An expanded view of the biology of the cell. J Proteome Res 4:112-128.
109. Liao X, Ying T, Wang H, Wang J, Shi Z, Feng E, Wei K, Wang Y, Zhang X, Huang L, Su G, Huang P (2003) A two-dimensional proteome map of Shigella flexneri. Electrophoresis 24:2864-2882.
110. Lipton MS, Paša-Tolić L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolić N, Udseth HR, Venkateswaran A, Wong K-K, Zhao R, Smith RD (2002) Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc Natl Acad Sci USA 99:11049-11054.
111. Mann M, Hendrickson RC, Pandey A (2001) Analysis of proteins and proteomes by mass spectrometry. Annu Rev Biochem 70:437-473.
112. Mann M, Wilm M (1994) Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal Chem 66:4390-4399.
113. Manso MA, Léonil J, Piot M, Gagnaire V (2005) Isolation and characterization of a Lactobacillus helveticus ITG LH1 peptidase-rich sub-proteome. Int J Food Microbiol 105:119-129.
114. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y-J, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim J-B, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380.
115. Marouga R, David S, Hawkins E (2005) The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal Bioanal Chem 382:669-678.
116. Marques MAM, Espinosa BJ, da Silveira EKX, Pessolani MCV, Chapeaurouge A, Perales J, Dobos KM, Belisle JT, Spencer JS, Brennan PJ (2004) Continued proteomic analysis of Mycobacterium leprae subcellular fractions. Proteomics 4:2942-2953.
117. Martens L, Hermjakob H, Jones P, Adamski M, Taylor C, States D, Gevaert K, Vandekerckhove J, Apweiler R (2005) PRIDE: The proteomics identifications database. Proteomics 5:3537-3545.
118. McLuckey SA, Van Berkel GJ, Goeringer DE, Glish GL (1994) Ion trap mass spectrometry. Using high-pressure ionization. Anal Chem 66:737A-743A.
119. Moritz B, Meyer HE (2003) Approaches for the quantification of protein concentration ratios. Proteomics 3:2208-2220.
120. Moslavac S, Bredemeier R, Mirus O, Granvogel B, Eichacker LA, Schleiff E (2005) Proteomic analysis of the outer membrane of Anabaena sp. strain PCC 7120. J Proteome Res 4:1330-1338.
121. Nijtmans LGJ, Henderson NS, Holt IJ (2002) Blue Native electrophoresis to study mitochondrial and other protein complexes. Methods 26:327-334.
122. Noël-Georis I, Vallaeys T, Chauvaux R, Monchy S, Falmagne P, Mergeay M, Wattiez R (2004) Global analysis of the Ralstonia metallidurans proteome: prelude for the large-scale study of heavy metal response. Proteomics 4:151-179.
123. Nordhoff E, Egelhofer V, Giavalisco P, Eickhoff H, Horn M, Przewieslik T, Theiss D, Schneider U, Lehrach H, Gobom J (2001) Large-gel two-dimensional electrophoresis-matrix assisted laser desorption/ionization-time of flight-mass spectrometry: an analytical challenge for studying complex protein mixtures. Electrophoresis 22:2844-2855.
124. Nouwens AS, Willcox MDP, Walsh BJ, Cordwell SJ (2002) Proteomic comparison of membrane and extracellular proteins from invasive (PAO1) and cytotoxic (6206) strains of Pseudomonas aeruginosa. Proteomics 2:1325-1346.
125. Oda Y, Huang K, Cross FR, Cowburn D, Chait BT (1999) Accurate quantitation of protein expression and site-specific phosphorylation. Proc Natl Acad Sci USA 96:6591-6596.
126. O'Farrell PH (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250:4007-4021.
127. Olsen JV, Ong S-E, Mann M (2004) Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol Cell Proteomics 3.6:608-614.
128. Ong S-E, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, 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 1.5:376-386.
129. Orchard S, Hermjakob H, Taylor CF, Potthast F, Jones P, Zhu W, Julian Jr RK, Apweiler R (2005) Second proteomics standards initiative spring workshop. Expert Rev Proteomics 2:287-289.
130. Ostrowski M, Fegatella F, Wasinger V, Guilhaus M, Corthals GL, Cavicchioli R (2004) Cross-species identification of proteins from proteome profiles of the marine oligotrophic ultra-microbacterium, Sphingopyxis alaskensis. Proteomics 4:1779-1788.
131. Ou K, Ong C, Kok SY, Rodrigues F, Sim SH, Wong D, Ooi CH, Ng KC, Jikuya H, Yau CC, Soon SY, Kesuma D, Lee AN, Tan P (2005) Integrative genomic, transcriptional, and proteomic diversity in natural isolates of the human pathogen Burkholderia pseudomallei. J Bacteriol 187:4276-4285.
132. Pappin DJ, Hojrup P, Bleasby AJ (1993) Rapid identification of proteins by peptide-mass fingerprinting. Curr Biol 3:327-332.
133. Park M-R, Lee E-G, Kim Y-H, Jung T-S, Shin Y-S, Shin G-W, Cha H-G, Kim G-S (2003) Reference map of soluble proteins from Salmonella enterica serovar enteritidis by two-dimensional electrophoresis. J Vet Sci 4:143-149.
134. Park SJ, Lee SY, Cho J, Kim TY, Lee JW, Park JH, Han M-J (2005) Global physiological understanding and metabolic engineering of microorganisms based on omics studies. Appl Microbiol Biotechnol (doi 10.1007/s00253-005-0081-z).
135. Patton WF, Lopez MF, Barry P, Skea WM (1992) A mechanically strong matrix for protein electrophoresis with enhanced silver staining properties. Biotechniques 12:580-585.
136. Pedersen S, Bloch PL, Reeh S, Neidhardt FC (1978) Patterns of protein synthesis in E. coli: a catalog of the amount of 140 individual proteins at different growth rates. Cell 14:179-190.
137. Pedrioli PGA, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian Jr RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R (2004) A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol 22:1459-1466.
138. Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP (2003) Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J Proteome Res 2:43-50.
139. Perkins DN, Pappin DJC, Creasy DM, Cottrell JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551-3567.
140. Petricoin EF, Zoon KC, Kohn EC, Barrett JC, Liotta LA (2002) Clinical proteomics: translating benchside promise into bedside reality. Nat Rev Drug Discov 1:683-695.
141. Pleissner K-P, Eifert T, Buettner S, Schmidt F, Boehme M, Meyer TF, Kaufmann SHE, Jungblut PR (2004) Web-accessible proteome databases for microbial research. Proteomics 4:1305-1313.
142. Qi S-Y, Moir A, O'Connor CD (1996) Proteome of Salmonella typhimurium SL1344: identification of novel abundant cell envelope proteins and assignment to a two-dimensional reference map. J Bacteriol 178:5032-5038.
143. Quackenbush J (2004) Data standards for 'omic' science. Nat Biotechnol 22:613-614.
144. Rabus R (2005a) Biodegradation of hydrocarbons under anoxic conditions; in Ollivier B, Magot M (eds): Petroleum Microbiology. Washington DC, ASM Press, pp 277-299.
145. Rabus R (2005b) Functional genomics of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Appl Microbiol Biotechnol 68:580-587.
146. Rabus R, Kube M, Beck A, Widdel F, Reinhardt R (2002) Genes involved in the anaerobic degradation of ethylbenzene in a denitrifying bacterium, strain EbN1. Arch Microbiol 178:506-516.
147. Rabus R, Kube M, Heider J, Beck A, Heitmann K, Widdel F, Reinhardt R (2005) The complete genome of an aromatic-degrading denitrifying bacterium, strain EbN1. Arch Microbiol 183:27-36.
148. Rabus R, Widdel F (1995) Anaerobic degradation of ethylbenzene and other aromatic hydrocarbons by new denitrifying bacteria. Arch Microbiol 163:96-103.
149. Rabus R, Widdel F (1996) Utilization of alkylbenzenes during anaerobic growth of pure cultures of denitrifying bacteria on crude oil. Appl Environ Microbiol 62:1238-1241.
150. nd RC, Shah M, Hettich RL, Banfield JF (2005) Community proteomics of a natural microbial biofilm. Science 308:1915-1920.
151. Ramírez P, Guiliani N, Valenzuela L, Beard S, Jerez CA (2004) Differential protein expression during growth of Acidithiobacillus ferrooxidans on ferrous iron, sulfur compounds, or metal sulfides. Appl Environ Microbiol 70:4491-4498.
152. Ramnath M, Rechinger KB, Jänsch L, Hastings JW, Knøchel S, Gravesen A (2003) Development of Listeria monocytogenes EGDe partial proteome reference map and comparison with the protein profiles of food isolates. Appl Environ Microbiol 69:3368-3376.
153. Ravichandran V, Sriram RD (2005) Toward data standards for proteomics. Nat Biotechnol 23:373-376.
154. Renesto P, Azza S, Dolla A, Fourquet P, Vestris G, Gorvel J-P, Raoult D (2005) Proteome analysis of Rickettsia conorii by two-dimensional gel electrophoresis coupled with mass spectrometry. FEMS Microbiol Lett 245:231-238.
155. Rhomberg TA, Karlberg O, Mini T, Zimny-Arndt U, Wickenberg U, Röttgen M, Jungblut PR, Jenö P, Andersson SGE, Dehio C (2004) Proteomic analysis of the sarcosine-inducible outer membrane fraction of the bacterial pathogen Bartonella henselae. Proteomics 4:3021-3033.
156. Roepstorff P, Fohlman J (1984) Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed Mass Spectrom 11:601.
157. Rosen R, Sacher A, Shechter N, Becher D, Büttner K, Biran D, Hecker M, Ron EZ (2004) Two-dimensional reference map of Agrobacterium tumefaciens proteins. Proteomics 4:1061-1073.
158. Rosenkrands I, King A, Weldingh K, Moniatte M, Moertz E, Andersen P (2000) Towards the proteome of Mycobacterium tuberculosis. Electrophoresis 21:3740-3756.
159. Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3:1154-1169.
160. Sadygov RG, Cociorva D, Yates 3rd JR (2004) Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book. Nat Methods 1:195-202.
161. Sazuka T, Yamaguchi M, Ohara O (1999) Cyno2Dbase updated: linkage of 234 protein spots to corresponding genes through N-terminal microsequencing. Electrophoresis 20:2160-2171.
162. Schaffer S, Weil B, Nguyen VD, Dongmann G, Günther K, Nickolaus M, Hermann T, Bott M (2001) A high-resolution reference map of cytoplasmic and membrane-associated proteins of Corynebacterium glutamicum. Electrophoresis 22:4404-4422.
163. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470.
164. Schmidt A, Kellermann J, Lottspeich F (2005a) A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5:4-15.
165. Schmid AK, Lipton MS, Mottaz H, Monroe ME, Smith RD, Lidstrom ME (2005a) Global whole-cell FTICR mass spectrometric proteomics analysis of the heat shock response in the radioresistant bacterium Deinococcus radiodurans. J Proteome Res 4:709-718.
166. Schmidt F, Donahoe S, Hagens K, Mattow J, Schaible UE, Kaufmann SHE, Aebersold R, Jungblut PR (2004) Complementary analysis of the Mycobacterium tuberculosis proteome by two-dimensional electrophoresis and isotope-coded affinity tag technology. Mol Cell Proteomics 3:24-42.
167. Schulenberg B, Arnold B, Patton WF (2003) An improved mechanically durable electrophoresis gel matrix that is fully compatible with fluorescence-based protein detection technologies. Proteomics 3:1196-1205.
168. Schürenberg M, Lübbert C, Eickhoff H, Kalkum M, Lehrach H, Nordhoff E (2000) Prestructured MALDI-MS sample supports. Anal Chem 72:3436-3442.
169. Seo JB, Kim HS, Jung GY, Nam MH, Chung JH, Kim JY, Yoo JS, Kim CW, Kwon O (2004) Psychrophilicity of Bacillus psychrosaccharolyticus: a proteomic study. Proteomics 4:3654-3659.
170. Shaw AC, Gevaert K, Demol H, Hoorelbeke B, Vandekerckhove J, Larsen MR, Roepstorff P, Holm A, Christiansen G, Birkelund S (2002) Comparative proteome analysis of Chlamydia trachomatis serovar A, D and L2. Proteomics 2:164-186.
171. Shaw J, Rowlinson R, Nickson J, Stone T, Sweet A, Williams K, Tonge R (2003) Evaluation of saturation labelling two-dimensional difference gel electrophoresis fluorescent dyes. Proteomics 3:1181-1195.
172. Shevchenko A, Chernushevich I, Ens W, Standing KG, Thomson B, Wilm M, Mann M (1997) Rapid de novo peptide sequencing by a combination of nanoelectrospray, isotopic labeling and a quadrupole/time-of-flight mass spectrometer. Rapid Commun Mass Spectrom 11:1015-1024.
173. Shevchenko A, Sunyaev S, Loboda A, Shevchenko A, Bork P, Ens W, Standing KG (2001) Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching. Anal Chem 73:1917-1926.
174. Shevchenko A, Wilm M, Vorm O, Mann M (1996) Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels. Anal Chem 68:850-858.
175. Skipp P, Robinson J, O'Connor CD, Clarke IN (2005) Shotgun proteomic analysis of Chlamydia trachomatis. Proteomics 5:1558-1573.
176. Smolka MB, Martins D, Winck FV, Santoro CE, Castellari RR, Ferrari F, Brum IJ, Galembeck E, Filho HDC, Machado MA, Marangoni S, Novello JC (2003) Proteome analysis of the plant pathogen Xylella fastidiosa reveals major cellular and extracellular proteins and a peculiar codon bias distribution. Proteomics 3:224-237.
177. Suckau D, Resemann A, Schürenberg M, Hufnagel P, Franzen J, Holle A (2003) A novel MALDI LIFT-TOF/TOF mass spectrometer for proteomics. Anal Bioanal Chem 376:952-965.
178. Taoka M, Yamauchi Y, Shinkawa T, Kaji H, Motohashi W, Nakayama H, Takahashi N, Isobe T (2004) Only a small subset of the horizontally transferred chromosomal genes in Escherichia coli are translated into proteins. Mol Cell Proteomics 3.8:780-787.
179. Tebbe A, Klein C, Bisle B, Siedler F, Scheffer B, Garcia-Rizo C, Wolfertz J, Hickmann V, Pfeiffer F, Oesterhelt D (2005) Analysis of the cytosolic proteome of Halobacterium salinarum and its implication for genome annotation. Proteomics 5:168-179.
180. Tonella L, Hoogland C, Binz P-A, Appel RD, Hochstrasser DF, Sanchez J-C (2001) New perspectives in the Escherichia coli proteome investigation. Proteomics 1:409-423.
181. Turchin A, Kohane IS (2002) Gene homology resources on the World Wide Web. Physiol Genomics 11:165-177.
182. Turinsky AL, Ah-Seng AC, Gordon PMK, Stromer JN, Taschuk ML, Xu EW, Sensen CW (2004) Bioinformatics visualization and integration with open standards; the Bluejay genomic browser. In Silico Biol 5:0018.
183. Ueberle B, Frank R, Herrmann R (2002) The proteome of the bacterium Mycoplasma pneumoniae: comparing predicted open reading frames to identified gene products. Proteomics 2:754-764.
184. Ünlü M, Morgan ME, Minden JS (1997) Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18:2071-2077.
185. Venable JD, Dong M-Q, Wohlschlegel J, Dillin A, Yates 3rd JR (2004) Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat Methods 1:1-7.
186. Venter JC, Levy S, Stockwell T, Remington K, Halpern A (2003) Massive parallelism, randomness and genomic advances. Nat Gen 33:219-227.
187. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers Y-H, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74.
188. Voigt B, Schweder T, Becher D, Ehrenreich A, Gottschalk G, Feesche J, Maurer K-H, Hecker M (2004) A proteomic view of cell physiology of Bacillus licheniformis. Proteomics 4:1465-1490.
189. Vorm O, Roepstroff P, Mann M (1994) Improved resolution and very high sensitivity in MALDI TOF of matrix surfaces made by fast evaporation. Anal Chem 66:3281-3287.
190. Wagner MA, Eschenbrenner M, Horn TA, Kraycer JA, Mujer CV, Hagius S, Elzer P, DelVecchio VG (2002) Global analysis of the Brucella melitensis proteome: identification of proteins expressed in laboratory grown culture. Proteomics 2:1047-1060.
191. Wang R, Prince JT, Marcotte EM (2005) Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias. Genome Res 15:1118-1126.
192. Wang W, Sun J, Hartlep M, Deckwer W-D, Zeng A-P (2003) Combined use of proteomic analysis and enzyme activity assays for metabolic pathway analysis of glycerol fermentation by Klebsiella pneumoniae. Biotechnol Bioeng 83:525-536.
193. Wang J, Xue Y, Feng X, Li X, Wang H, Li W, Zhao C, Cheng X, Ma Y, Zhou P, Yin J, Bhatnagar A, Wang R, Liu S (2004) An analysis of the proteomic profile for Thermoanaerobacter tengcongensis under optimal culture conditions. Proteomics 4:136-150.
194. Washburn MP, Wolters D, Yates 3rd JR (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19:242-247.
195. Watt SA, Wilke A, Patschkowski T, Niehaus K (2005) Comprehensive analysis of the extracellular proteins from Xanthomonas campestris pv. campestris B100. Proteomics 5:153-167.
196. Widdel F, Rabus R (2001) Anaerobic biodegradation of saturated and aromatic hydrocarbons. Curr Opin Biotechnol 12:259-276.
197. Wilke A, Rückert C, Bartels D, Dondrup M, Goesmann A, Hüser AT, Kesphol S, Linke B, Mahne M, McHardy A, Pühler A, Meyer F (2003) Bioinformatics support for high-throughput proteomics. J Biotechnol 106:147-156.
198. Zhang W, Chait BT (2000) ProFound: an expert system for protein identification using mass spectrometric peptide mapping information. Anal Chem 72:2482-2489.
199. Zhang Y, Wang T, Chen W, Yilmaz Ö, Park Y, Jung I-Y, Hackett M, Lamont RJ (2005) Differential protein expression by Porphyromonas gingivalis in response to secreted epithelial cell components. Proteomics 5:198-211.
200. 54 in response to gentisate induction in Pseudomonas alcaligenes NCIMB 9867. Proteomics 5:1868-1876.
201. Zischka H, Weber G, Weber PJA, Posch A, Braun RJ, Bühringer D, Schneider U, Nissum M, Meitinger T, Ueffing M, Eckerskorn C (2003) Improved proteome analysis of Saccharomyces cerevisiae mitochondria by free-flow electrophoresis. Proteomics 3:906-916.