메뉴 건너뛰기




Volumn 10, Issue , 2009, Pages

LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: The Daphnia pulex genome database as a key for high throughput proteomics in Daphnia

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE; PROTEOME;

EID: 65449164977     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-171     Document Type: Article
Times cited : (44)

References (48)
  • 1
    • 0034659898 scopus 로고    scopus 로고
    • Genomics, gene expression and DNA arrays
    • 10.1038/35015701 10866209
    • Lockhart DJ Winzeler EA Genomics, gene expression and DNA arrays Nature 2000, 405:827-836. 10.1038/35015701 10866209
    • (2000) Nature , vol.405 , pp. 827-836
    • Lockhart, D.J.1    Winzeler, E.A.2
  • 2
    • 0028806048 scopus 로고
    • Quantitative Monitoring of Gene-Expression Patterns with A Complementary-Dna Microarray
    • 10.1126/science.270.5235.467 7569999
    • Schena M Shalon D Davis RW Brown PO Quantitative Monitoring of Gene-Expression Patterns with A Complementary-Dna Microarray Science 1995, 270:467-470. 10.1126/science.270.5235.467 7569999
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 3
    • 0030895921 scopus 로고    scopus 로고
    • A comparison of selected mRNA and protein abundances in human liver
    • 10.1002/elps.1150180333 9150937
    • Anderson L Seilhamer J A comparison of selected mRNA and protein abundances in human liver Electrophoresis 1997, 18:533-537. 10.1002/ elps.1150180333 9150937
    • (1997) Electrophoresis , vol.18 , pp. 533-537
    • Anderson, L.1    Seilhamer, J.2
  • 4
    • 0033016717 scopus 로고    scopus 로고
    • Correlation between protein and mRNA abundance in yeast
    • 83965 10022859
    • Gygi SP Rochon Y Franza BR Aebersold R Correlation between protein and mRNA abundance in yeast Mol Cell Biol 1999, 19:1720-1730. 83965 10022859
    • (1999) Mol Cell Biol , vol.19 , pp. 1720-1730
    • Gygi, S.P.1    Rochon, Y.2    Franza, B.R.3    Aebersold, R.4
  • 5
    • 34548312349 scopus 로고    scopus 로고
    • Advancing signaling networks through proteomics
    • 10.1586/14789450.4.4.573 17705714
    • Tekirian TL Thomas SN Yang A Advancing signaling networks through proteomics Expert Rev Proteomics 2007, 4:573-583. 10.1586/ 14789450.4.4.573 17705714
    • (2007) Expert Rev Proteomics , vol.4 , pp. 573-583
    • Tekirian, T.L.1    Thomas, S.N.2    Yang, A.3
  • 8
    • 29244457242 scopus 로고    scopus 로고
    • Human liver proteome project: Plan, progress, and perspectives
    • 10.1074/mcp.R500013-MCP200 16118399
    • He F Human liver proteome project: Plan, progress, and perspectives Mol Cell Proteomics 2005, 4:1841-1848. 10.1074/mcp.R500013-MCP200 16118399
    • (2005) Mol Cell Proteomics , vol.4 , pp. 1841-1848
    • He, F.1
  • 9
    • 33747184525 scopus 로고    scopus 로고
    • C. elegans: An invaluable model organism for the proteomics studies of the cholesterol-mediated signaling pathway
    • 10.1586/14789450.3.4.439 16901202
    • Paik YK Jeong SK Lee EY Jeong PY Shim YH C. elegans: An invaluable model organism for the proteomics studies of the cholesterol-mediated signaling pathway Expert Rev Proteomics 2006, 3:439-453. 10.1586/ 14789450.3.4.439 16901202
    • (2006) Expert Rev Proteomics , vol.3 , pp. 439-453
    • Paik, Y.K.1    Jeong, S.K.2    Lee, E.Y.3    Jeong, P.Y.4    Shim, Y.H.5
  • 11
    • 33745054329 scopus 로고    scopus 로고
    • Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics
    • 10.1186/gb-2006-7-4-r35 16646984 1557991
    • Fermin D Allen BB Blackwell TW Menon R Adamski M Xu Y Ulintz P Omenn GS States DJ Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics Genome Biol 2006, 7:R35. 10.1186/ gb-2006-7-4-r35 16646984 1557991
    • (2006) Genome Biol , vol.7
    • Fermin, D.1    Allen, B.B.2    Blackwell, T.W.3    Menon, R.4    Adamski, M.5    Xu, Y.6    Ulintz, P.7    Omenn, G.S.8    States, D.J.9
  • 12
    • 33846884410 scopus 로고    scopus 로고
    • Improving gene annotation using peptide mass spectrometry
    • 10.1101/gr.5646507 17189379 1781355
    • Tanner S Shen Z Ng J Florea L Guigo R Briggs SP Bafna V Improving gene annotation using peptide mass spectrometry Genome Res 2007, 17:231-239. 10.1101/gr.5646507 17189379 1781355
    • (2007) Genome Res , vol.17 , pp. 231-239
    • Tanner, S.1    Shen, Z.2    Ng, J.3    Florea, L.4    Guigo, R.5    Briggs, S.P.6    Bafna, V.7
  • 15
    • 0043122944 scopus 로고    scopus 로고
    • ExPASy: The proteomics server for in-depth protein knowledge and analysis
    • 10.1093/nar/gkg563 12824418 168970
    • Gasteiger E Gattiker A Hoogland C Ivanyi I Appel RD Bairoch A ExPASy: The proteomics server for in-depth protein knowledge and analysis Nucleic Acids Res 2003, 31:3784-3788. 10.1093/nar/gkg563 12824418 168970
    • (2003) Nucleic Acids Res , vol.31 , pp. 3784-3788
    • Gasteiger, E.1    Gattiker, A.2    Hoogland, C.3    Ivanyi, I.4    Appel, R.D.5    Bairoch, A.6
  • 16
    • 33644875286 scopus 로고    scopus 로고
    • The Gene Ontology (GO) project in 2006
    • 10.1093/nar/gkj021 16381878 1347384
    • The Gene Ontology (GO) project in 2006 Nucleic Acids Res 2006, 34:D322-D326. 10.1093/nar/gkj021 16381878 1347384
    • (2006) Nucleic Acids Res , vol.34
  • 17
    • 17044410094 scopus 로고    scopus 로고
    • Analysing proteomic data
    • 10.1016/j.ijpara.2005.01.013 15826646
    • Barrett J Brophy PM Hamilton JV Analysing proteomic data Int J Parasitol 2005, 35:543-553. 10.1016/j.ijpara.2005.01.013 15826646
    • (2005) Int J Parasitol , vol.35 , pp. 543-553
    • Barrett, J.1    Brophy, P.M.2    Hamilton, J.V.3
  • 19
    • 0029046847 scopus 로고
    • Electrospray mass spectrometry for protein characterization
    • 10.1016/S0968-0004(00)89019-2 7631418
    • Mann M Wilm M Electrospray mass spectrometry for protein characterization Trends Biochem Sci 1995, 20:219-224. 10.1016/ S0968-0004(00)89019-2 7631418
    • (1995) Trends Biochem Sci , vol.20 , pp. 219-224
    • Mann, M.1    Wilm, M.2
  • 20
    • 33746102929 scopus 로고    scopus 로고
    • Proteome research based on modern liquid chromatography-tandem mass spectrometry: Separation, identification and quantification
    • 10.1007/s00702-006-0509-3 16835695
    • Frohlich T Arnold GJ Proteome research based on modern liquid chromatography-tandem mass spectrometry: Separation, identification and quantification J Neural Transm 2006, 113:973-994. 10.1007/ s00702-006-0509-3 16835695
    • (2006) J Neural Transm , vol.113 , pp. 973-994
    • Frohlich, T.1    Arnold, G.J.2
  • 21
    • 14944338676 scopus 로고    scopus 로고
    • Proteomic LC-MS systems using nanoscale liquid chromatography with tandem mass spectrometry
    • 10.1016/j.chroma.2004.10.107 15844511
    • Ishihama Y Proteomic LC-MS systems using nanoscale liquid chromatography with tandem mass spectrometry J Chromatogr A 2005, 1067:73-83. 10.1016/ j.chroma.2004.10.107 15844511
    • (2005) J Chromatogr A , vol.1067 , pp. 73-83
    • Ishihama, Y.1
  • 22
    • 20544441071 scopus 로고    scopus 로고
    • Advanced nanoscale separations and mass spectrometry for sensitive high-throughput proteomics
    • 10.1586/14789450.2.3.431 16000088
    • Shen Y Smith RD Advanced nanoscale separations and mass spectrometry for sensitive high-throughput proteomics Expert Rev Proteomics 2005, 2:431-447. 10.1586/14789450.2.3.431 16000088
    • (2005) Expert Rev Proteomics , vol.2 , pp. 431-447
    • Shen, Y.1    Smith, R.D.2
  • 24
    • 35848929694 scopus 로고    scopus 로고
    • Analysis and validation of proteomic data generated by tandem mass spectrometry
    • 10.1038/nmeth1088 17901868
    • Nesvizhskii AI Vitek O Aebersold R Analysis and validation of proteomic data generated by tandem mass spectrometry Nat Methods 2007, 4:787-797. 10.1038/nmeth1088 17901868
    • (2007) Nat Methods , vol.4 , pp. 787-797
    • Nesvizhskii, A.I.1    Vitek, O.2    Aebersold, R.3
  • 25
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • 10.1002/ (SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2 10612281
    • Perkins DN Pappin DJ Creasy DM Cottrell JS Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999, 20:3551-3567. 10.1002/ (SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2 10612281
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 26
    • 27644555055 scopus 로고    scopus 로고
    • Interpretation of shotgun proteomic data: The protein inference problem
    • 10.1074/mcp.R500012-MCP200 16009968
    • Nesvizhskii AI Aebersold R Interpretation of shotgun proteomic data: The protein inference problem Mol Cell Proteomics 2005, 4:1419-1440. 10.1074/ mcp.R500012-MCP200 16009968
    • (2005) Mol Cell Proteomics , vol.4 , pp. 1419-1440
    • Nesvizhskii, A.I.1    Aebersold, R.2
  • 27
    • 33746930864 scopus 로고    scopus 로고
    • A uniform proteomics MS/MS analysis platform utilizing open XML file formats
    • 16729052 1681455
    • Keller A Eng J Zhang N Li XJ Aebersold R A uniform proteomics MS/MS analysis platform utilizing open XML file formats Mol Syst Biol 2005, 1:. 16729052 1681455
    • (2005) Mol Syst Biol , vol.1
    • Keller, A.1    Eng, J.2    Zhang, N.3    Li, X.J.4    Aebersold, R.5
  • 28
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • 10.1021/ac025747h 12403597
    • Keller A Nesvizhskii AI Kolker E Aebersold R Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search Anal Chem 2002, 74:5383-5392. 10.1021/ac025747h 12403597
    • (2002) Anal Chem , vol.74 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 29
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • 10.1021/ac0341261 14632076
    • Nesvizhskii AI Keller A Kolker E Aebersold R A statistical model for identifying proteins by tandem mass spectrometry Anal Chem 2003, 75:4646-4658. 10.1021/ac0341261 14632076
    • (2003) Anal Chem , vol.75 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 30
    • 24044513966 scopus 로고    scopus 로고
    • Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations
    • 10.1038/nmeth785 16118637
    • Elias JE Haas W Faherty BK Gygi SP Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations Nat Methods 2005, 2:667-675. 10.1038/nmeth785 16118637
    • (2005) Nat Methods , vol.2 , pp. 667-675
    • Elias, J.E.1    Haas, W.2    Faherty, B.K.3    Gygi, S.P.4
  • 31
    • 26844582863 scopus 로고    scopus 로고
    • Molecular weight assessment of proteins in total proteome profiles using 1D-PAGE and LC/MS/MS
    • 10.1186/1477-5956-3-6 15941491 1182394
    • Ahmad QR Nguyen DH Wingerd MA Church GM Steffen MA Molecular weight assessment of proteins in total proteome profiles using 1D-PAGE and LC/ MS/MS Proteome Sci 2005, 3:6. 10.1186/1477-5956-3-6 15941491 1182394
    • (2005) Proteome Sci , vol.3 , pp. 6
    • Ahmad, Q.R.1    Nguyen, D.H.2    Wingerd, M.A.3    Church, G.M.4    Steffen, M.A.5
  • 32
    • 41549094918 scopus 로고    scopus 로고
    • Island clustering analysis for the comparison of the membrane and the soluble protein fractions of human brain proteome
    • 10.1002/pmic.200700756 18283667
    • Kwon KH Park GW Kim JY Lee SK Lee JH Kim YH Kim SY Park YM Yoo JS Island clustering analysis for the comparison of the membrane and the soluble protein fractions of human brain proteome Proteomics 2008, 8:1149-1161. 10.1002/pmic.200700756 18283667
    • (2008) Proteomics , vol.8 , pp. 1149-1161
    • Kwon, K.H.1    Park, G.W.2    Kim, J.Y.3    Lee, S.K.4    Lee, J.H.5    Kim, Y.H.6    Kim, S.Y.7    Park, Y.M.8    Yoo, J.S.9
  • 33
    • 16244417837 scopus 로고    scopus 로고
    • Characterization of proteases in guts of Daphnia magna and their inhibition by Microcystis aeruginosa PCC 7806
    • 10.1002/tox.20123 15892063
    • Agrawal MK Zitt A Bagchi D Weckesser J Bagchi SN von Elert E Characterization of proteases in guts of Daphnia magna and their inhibition by Microcystis aeruginosa PCC 7806 Environ Toxicol 2005, 20:314-322. 10.1002/tox.20123 15892063
    • (2005) Environ Toxicol , vol.20 , pp. 314-322
    • Agrawal, M.K.1    Zitt, A.2    Bagchi, D.3    Weckesser, J.4    Bagchi, S.N.5    von Elert, E.6
  • 34
  • 35
    • 0030605480 scopus 로고    scopus 로고
    • The systematics of North American Daphnia (Crustacea: Anomopoda): A molecular phylogenetic approach
    • 10.1098/rstb.1996.0028 8730787
    • Colbourne JK Hebert PD The systematics of North American Daphnia (CrustAcea: Anomopoda): a molecular phylogenetic approach Philos Trans R Soc Lond B Biol Sci 1996, 351:349-360. 10.1098/rstb.1996.0028 8730787
    • (1996) Philos Trans R Soc Lond B Biol Sci , vol.351 , pp. 349-360
    • Colbourne, J.K.1    Hebert, P.D.2
  • 36
    • 0001792125 scopus 로고    scopus 로고
    • Inducible defenses in Cladocera: Constraints, costs and multipredator environments
    • Princeton, New Jersey: Princeton University Press Tollrian R, Harvell CD
    • Tollrian R Dodson SI Inducible defenses in Cladocera: Constraints, costs and multipredator environments The Ecology and Evolution of inducible Defenses Princeton, New Jersey: Princeton University Press Tollrian R, Harvell CD 1999:177-202.
    • (1999) The Ecology and Evolution of Inducible Defenses , pp. 177-202
    • Tollrian, R.1    Dodson, S.I.2
  • 37
    • 33750937084 scopus 로고    scopus 로고
    • Identifying exoskeleton proteins in the blue crab from an expressed sequence tag (EST) library
    • 10.1093/icb/icl022
    • Shafer TH McCartney MA Faircloth LM Identifying exoskeleton proteins in the blue crab from an expressed sequence tag (EST) library Integr Comp Biol 2006, 46:978-990. 10.1093/icb/icl022
    • (2006) Integr Comp Biol , vol.46 , pp. 978-990
    • Shafer, T.H.1    McCartney, M.A.2    Faircloth, L.M.3
  • 38
    • 0442292205 scopus 로고    scopus 로고
    • Complete mitochondrial DNA sequence of the sea-firefly, Vargula hilgendorfii (Crustacea, Ostracoda) with duplicate control regions
    • 10.1016/j.gene.2003.11.011 14960368
    • Ogoh K Ohmiya Y Complete mitochondrial DNA sequence of the sea-firefly, Vargula hilgendorfii (Crustacea, Ostracoda) with duplicate control regions Gene 2004, 327:131-139. 10.1016/j.gene.2003.11.011 14960368
    • (2004) Gene , vol.327 , pp. 131-139
    • Ogoh, K.1    Ohmiya, Y.2
  • 41
    • 0037459349 scopus 로고    scopus 로고
    • Hexapod origins: Monophyletic or paraphyletic?
    • 10.1126/science.1078607 12649480
    • Nardi F Spinsanti G Boore JL Carapelli A Dallai R Frati F Hexapod origins: Monophyletic or paraphyletic? Science 2003, 299:1887-1889. 10.1126/science.1078607 12649480
    • (2003) Science , vol.299 , pp. 1887-1889
    • Nardi, F.1    Spinsanti, G.2    Boore, J.L.3    Carapelli, A.4    Dallai, R.5    Frati, F.6
  • 42
    • 0035855865 scopus 로고    scopus 로고
    • Arthropod phylogeny based on eight molecular loci and morphology
    • 10.1038/35093097 11557979
    • Giribet G Edgecombe GD Wheeler WC Arthropod phylogeny based on eight molecular loci and morphology Nature 2001, 413:157-161. 10.1038/35093097 11557979
    • (2001) Nature , vol.413 , pp. 157-161
    • Giribet, G.1    Edgecombe, G.D.2    Wheeler, W.C.3
  • 43
    • 1942501957 scopus 로고    scopus 로고
    • The colonization of land by animals: Molecular phylogeny and divergence times among arthropods
    • 10.1186/1741-7007-2-1 14731304 333434
    • Pisani D Poling LL Lyons-Weiler M Hedges SB The colonization of land by animals: Molecular phylogeny and divergence times among arthropods BMC Biol 2004, 2:1. 10.1186/1741-7007-2-1 14731304 333434
    • (2004) BMC Biol , vol.2 , pp. 1
    • Pisani, D.1    Poling, L.L.2    Lyons-Weiler, M.3    Hedges, S.B.4
  • 44
    • 24144454626 scopus 로고    scopus 로고
    • Pax3/7 genes reveal conservation and divergence in the arthropod segmentation hierarchy
    • 10.1016/j.ydbio.2005.06.014 16083872
    • Davis GK D'Alessio JA Patel NH Pax3/7 genes reveal conservation and divergence in the arthropod segmentation hierarchy Dev Biol 2005, 285:169-184. 10.1016/j.ydbio.2005.06.014 16083872
    • (2005) Dev Biol , vol.285 , pp. 169-184
    • Davis, G.K.1    D'Alessio, J.A.2    Patel, N.H.3
  • 45
    • 34547828023 scopus 로고    scopus 로고
    • Sampling Daphnia's expressed genes: Preservation, expansion and invention of crustacean genes with reference to insect genomes
    • 10.1186/1471-2164-8-217 17612412 1940262
    • Colbourne JK Eads BD Shaw J Bohuski E Bauer DJ Andrews J Sampling Daphnia's expressed genes: Preservation, expansion and invention of crustacean genes with reference to insect genomes BMC Genomics 2007, 8:217. 10.1186/1471-2164-8-217 17612412 1940262
    • (2007) BMC Genomics , vol.8 , pp. 217
    • Colbourne, J.K.1    Eads, B.D.2    Shaw, J.3    Bohuski, E.4    Bauer, D.J.5    Andrews, J.6
  • 46
    • 34547153650 scopus 로고    scopus 로고
    • Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing
    • 10.1002/pmic.200700003 17623296
    • Waridel P Frank A Thomas H Surendranath V Sunyaev S Pevzner P Shevchenko A Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing Proteomics 2007, 7:2318-2329. 10.1002/pmic.200700003 17623296
    • (2007) Proteomics , vol.7 , pp. 2318-2329
    • Waridel, P.1    Frank, A.2    Thomas, H.3    Surendranath, V.4    Sunyaev, S.5    Pevzner, P.6    Shevchenko, A.7
  • 47
    • 8644224901 scopus 로고    scopus 로고
    • An acoustic microscopy technique reveals hidden morphological defenses in Daphnia
    • 10.1073/pnas.0404860101 15520396 528736
    • Laforsch C Ngwa W Grill W Tollrian R An acoustic microscopy technique reveals hidden morphological defenses in Daphnia Proc Natl Acad Sci USA 2004, 101:15911-15914. 10.1073/pnas.0404860101 15520396 528736
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 15911-15914
    • Laforsch, C.1    Ngwa, W.2    Grill, W.3    Tollrian, R.4
  • 48
    • 0034041516 scopus 로고    scopus 로고
    • Density-dependent effects of prey defences
    • 10.1007/s004420051026
    • Jeschke JM Tollrian R Density-dependent effects of prey defences Oecologia 2000, 123:391-396. 10.1007/s004420051026
    • (2000) Oecologia , vol.123 , pp. 391-396
    • Jeschke, J.M.1    Tollrian, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.