메뉴 건너뛰기




Volumn 26, Issue 10, 2012, Pages 1660-1674

Minireview: Progress and challenges in proteomics data management, sharing, and integration

Author keywords

[No Author keywords available]

Indexed keywords

APOLIPOPROTEIN B MESSENGER RNA EDITING ENZYME CATALYTIC POLYPEPTIDE 1; BIOLOGICAL MARKER; BIOTIN; CALCITONIN; CELL NUCLEUS RECEPTOR; COLECALCIFEROL RECEPTOR; DNA; ESTRADIOL; ESTROGEN RECEPTOR ALPHA; G PROTEIN COUPLED RECEPTOR; GLUCAGON; INSULIN; PARATHYROID HORMONE; PROTEIN; PROTEIN SH3; PROTEOME; SORBINIL; TAMM HORSFALL GLYCOPROTEIN; THYROID HORMONE RECEPTOR ALPHA; VASOPRESSIN;

EID: 84867012851     PISSN: 08888809     EISSN: None     Source Type: Journal    
DOI: 10.1210/me.2012-1180     Document Type: Review
Times cited : (9)

References (137)
  • 1
    • 84862683358 scopus 로고    scopus 로고
    • Obesidomics: Contribution of adipose tissue secretome analysis to obesity research
    • Pardo M, Roca-Rivada A, Seoane LM, Casanueva FF 2012 Obesidomics: contribution of adipose tissue secretome analysis to obesity research. Endocrine 41:374-383
    • (2012) Endocrine , vol.41 , pp. 374-383
    • Pardo, M.1    Roca-Rivada, A.2    Seoane, L.M.3    Casanueva, F.F.4
  • 4
    • 57049093397 scopus 로고    scopus 로고
    • Much room for improvement in deposition rates of expression microarray datasets
    • Ochsner SA, Steffen DL, Stoeckert Jr CJ, McKenna NJ 2008 Much room for improvement in deposition rates of expression microarray datasets. Nat Methods 5:991
    • (2008) Nat Methods , vol.5 , pp. 991
    • Ochsner, S.A.1    Steffen, D.L.2    Stoeckert, C.J.3    McKenna, N.J.4
  • 7
    • 0031398974 scopus 로고    scopus 로고
    • Protein identification in the post-genome era: The rapid rise of proteomics
    • James P 1997 Protein identification in the post-genome era: the rapid rise of proteomics. Q Rev Biophys 30:279-331
    • (1997) Q Rev Biophys , vol.30 , pp. 279-331
    • James, P.1
  • 9
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • Schena M, Shalon D, Davis RW, Brown PO 1995 Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 10
    • 0035887145 scopus 로고    scopus 로고
    • ChinnaiyanAM2001 Profiling of cancer cells using protein microarrays: Discovery of novel radiation-regulated proteins
    • Sreekumar A, Nyati MK, Varambally S, Barrette TR, Ghosh D, Lawrence TS, ChinnaiyanAM2001 Profiling of cancer cells using protein microarrays: discovery of novel radiation-regulated proteins. Cancer Res 61:7585-7593
    • Cancer Res , vol.61 , pp. 7585-7593
    • Sreekumar, A.1    Nyati, M.K.2    Varambally, S.3    Barrette, T.R.4    Ghosh, D.5    Lawrence, T.S.6
  • 11
    • 0035221240 scopus 로고    scopus 로고
    • Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions
    • RESEARCH0004
    • Haab BB, Dunham MJ, Brown PO 2001 Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol 2:RESEARCH0004
    • (2001) Genome Biol , vol.2
    • Haab, B.B.1    Dunham, M.J.2    Brown, P.O.3
  • 14
    • 0005620475 scopus 로고    scopus 로고
    • Aptamers as therapeutic and diagnostic agents
    • Brody EN, Gold L 2000 Aptamers as therapeutic and diagnostic agents. J Biotechnol 74:5-13
    • (2000) J Biotechnol , vol.74 , pp. 5-13
    • Brody, E.N.1    Gold, L.2
  • 15
    • 0034936573 scopus 로고    scopus 로고
    • In vitro selection of nucleoprotein enzymes
    • Robertson MP, Ellington AD 2001 In vitro selection of nucleoprotein enzymes. Nat Biotechnol 19:650-655
    • (2001) Nat Biotechnol , vol.19 , pp. 650-655
    • Robertson, M.P.1    Ellington, A.D.2
  • 16
    • 80555156102 scopus 로고    scopus 로고
    • Surface plasmon resonance for proteomics
    • de Mol NJ 2012 Surface plasmon resonance for proteomics. Methods Mol Biol 800:33-53
    • (2012) Methods Mol Biol , vol.800 , pp. 33-53
    • de Mol, N.J.1
  • 18
    • 80054952604 scopus 로고    scopus 로고
    • Profiling signalling pathways in formalin-fixed and paraffin-embedded breast cancer tissues reveals cross-talk between EGFR, HER2, HER3 and uPAR
    • Berg D, Wolff C, Malinowsky K, Tran K, Walch A, Bronger H, Schuster T, Höfler H, Becker KF 2012 Profiling signalling pathways in formalin-fixed and paraffin-embedded breast cancer tissues reveals cross-talk between EGFR, HER2, HER3 and uPAR. J Cell Physiol 227:204-212
    • (2012) J Cell Physiol , vol.227 , pp. 204-212
    • Berg, D.1    Wolff, C.2    Malinowsky, K.3    Tran, K.4    Walch, A.5    Bronger, H.6    Schuster, T.7    Höfler, H.8    Becker, K.F.9
  • 19
    • 33750456480 scopus 로고    scopus 로고
    • Reverse phase protein array: Validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells
    • Tibes R, Qiu Y, Lu Y, Hennessy B, Andreeff M, Mills GB, Kornblau SM 2006 Reverse phase protein array: validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells. Mol Cancer Ther 5:2512-2521
    • (2006) Mol Cancer Ther , vol.5 , pp. 2512-2521
    • Tibes, R.1    Qiu, Y.2    Lu, Y.3    Hennessy, B.4    Andreeff, M.5    Mills, G.B.6    Kornblau, S.M.7
  • 27
    • 79953701026 scopus 로고    scopus 로고
    • Cell free expression put on the spot: Advances in repeatable protein arraying from DNA (DAPA)
    • Stoevesandt O, Vetter M, Kastelic D, Palmer EA, He M, Taussig MJ 2011 Cell free expression put on the spot: advances in repeatable protein arraying from DNA (DAPA). N Biotechnol 28:282-290
    • (2011) N Biotechnol , vol.28 , pp. 282-290
    • Stoevesandt, O.1    Vetter, M.2    Kastelic, D.3    Palmer, E.A.4    He, M.5    Taussig, M.J.6
  • 28
    • 77449146554 scopus 로고    scopus 로고
    • In situ biosynthesis of peptide arrays
    • He M, Stoevesandt O 2010 In situ biosynthesis of peptide arrays. Methods Mol Biol 615:345-356
    • (2010) Methods Mol Biol , vol.615 , pp. 345-356
    • He, M.1    Stoevesandt, O.2
  • 29
    • 0035430843 scopus 로고    scopus 로고
    • Single step generation of protein arrays fromDNAby cell-free expression and in situ immobilisation (PISA method)
    • E73-E73
    • He M, Taussig MJ 2001 Single step generation of protein arrays fromDNAby cell-free expression and in situ immobilisation (PISA method). Nucleic Acids Res 29:E73-E73
    • (2001) Nucleic Acids Res , vol.29
    • He, M.1    Taussig, M.J.2
  • 30
    • 79958278798 scopus 로고    scopus 로고
    • Protein-protein interactions: An application of Tus-Ter mediated protein microarray system
    • Sitaraman K, Chatterjee DK 2011 Protein-protein interactions: an application of Tus-Ter mediated protein microarray system. Methods Mol Biol 723:185-200
    • (2011) Methods Mol Biol , vol.723 , pp. 185-200
    • Sitaraman, K.1    Chatterjee, D.K.2
  • 32
    • 84862874922 scopus 로고    scopus 로고
    • Emerging technology of in situ cell free expression protein microarrays
    • Nand A, Gautam A, Pérez JB, Merino A, Zhu J 2012 Emerging technology of in situ cell free expression protein microarrays. Protein Cell 3:84-88
    • (2012) Protein Cell , vol.3 , pp. 84-88
    • Nand, A.1    Gautam, A.2    Pérez, J.B.3    Merino, A.4    Zhu, J.5
  • 33
    • 10644230916 scopus 로고    scopus 로고
    • Current two-dimensional electrophoresis technology for proteomics
    • Görg A, Weiss W, Dunn MJ 2004 Current two-dimensional electrophoresis technology for proteomics. Proteomics 4:3665-3685
    • (2004) Proteomics , vol.4 , pp. 3665-3685
    • Görg, A.1    Weiss, W.2    Dunn, M.J.3
  • 34
    • 34248180415 scopus 로고    scopus 로고
    • Two-dimensional difference gel electrophoresis
    • Viswanathan S, Unlü M, Minden JS 2006 Two-dimensional difference gel electrophoresis. Nat Protoc 1:1351-1358
    • (2006) Nat Protoc , vol.1 , pp. 1351-1358
    • Viswanathan, S.1    Unlü, M.2    Minden, J.S.3
  • 35
    • 21244495253 scopus 로고    scopus 로고
    • The development of the DIGE system: 2D fluorescence difference gel analysis technology
    • 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
    • (2005) Anal Bioanal Chem , vol.382 , pp. 669-678
    • Marouga, R.1    David, S.2    Hawkins, E.3
  • 36
    • 0037253267 scopus 로고    scopus 로고
    • A novel experimental design for comparative twodimensional gel analysis: Two-dimensional difference gel electrophoresis incorporating a pooled internal standard
    • Alban A, David SO, Bjorkesten L, Andersson C, Sloge E, Lewis S, Currie I 2003 A novel experimental design for comparative twodimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 3:36-44
    • (2003) Proteomics , vol.3 , pp. 36-44
    • Alban, A.1    David, S.O.2    Bjorkesten, L.3    Andersson, C.4    Sloge, E.5    Lewis, S.6    Currie, I.7
  • 38
    • 29544444603 scopus 로고    scopus 로고
    • Efficient enrichment of intact phosphorylated proteins by modified immobilized metal-affinity chromatography
    • Dubrovska A, Souchelnytskyi S 2005 Efficient enrichment of intact phosphorylated proteins by modified immobilized metal-affinity chromatography. Proteomics 5:4678-4683
    • (2005) Proteomics , vol.5 , pp. 4678-4683
    • Dubrovska, A.1    Souchelnytskyi, S.2
  • 39
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold R, Mann M 2003 Mass spectrometry-based proteomics. Nature 422:198-207
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 41
    • 66749171697 scopus 로고    scopus 로고
    • Statistical design of quantitative mass spectrometry-based proteomic experiments
    • Oberg AL, Vitek O 2009 Statistical design of quantitative mass spectrometry-based proteomic experiments. J Proteome Res 8:2144-2156
    • (2009) J Proteome Res , vol.8 , pp. 2144-2156
    • Oberg, A.L.1    Vitek, O.2
  • 42
    • 34250372908 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture for quantitative proteomics
    • Ong SE, Mann M 2007 Stable isotope labeling by amino acids in cell culture for quantitative proteomics. Methods Mol Biol 359: 37-52
    • (2007) Methods Mol Biol , vol.359 , pp. 37-52
    • Ong, S.E.1    Mann, M.2
  • 43
    • 33746408762 scopus 로고    scopus 로고
    • The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry. II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the application of statistical tools for data analysis and interpretation
    • von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD 2003 The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry. II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the application of statistical tools for data analysis and interpretation. Mol Cell Proteomics 2:428-442
    • (2003) Mol Cell Proteomics , vol.2 , pp. 428-442
    • von Haller, P.D.1    Yi, E.2    Donohoe, S.3    Vaughn, K.4    Keller, A.5    Nesvizhskii, A.I.6    Eng, J.7    Li, X.J.8    Goodlett, D.R.9    Aebersold, R.10    Watts, J.D.11
  • 44
    • 33746432742 scopus 로고    scopus 로고
    • The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry. I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT and tandem mass spectrometry to proteins copurifying with T cell lipid rafts
    • von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD 2003 The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry. I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT and tandem mass spectrometry to proteins copurifying with T cell lipid rafts. Mol Cell Proteomics 2:426-427
    • (2003) Mol Cell Proteomics , vol.2 , pp. 426-427
    • von Haller, P.D.1    Yi, E.2    Donohoe, S.3    Vaughn, K.4    Keller, A.5    Nesvizhskii, A.I.6    Eng, J.7    Li, X.J.8    Goodlett, D.R.9    Aebersold, R.10    Watts, J.D.11
  • 45
    • 33646269941 scopus 로고    scopus 로고
    • A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies
    • Zieske LR 2006 A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies. J Exp Bot 57: 1501-1508
    • (2006) J Exp Bot , vol.57 , pp. 1501-1508
    • Zieske, L.R.1
  • 46
    • 77954366021 scopus 로고    scopus 로고
    • Quantitative analysis of mTRAQ-labeled proteome using full MS scans
    • Kang UB, Yeom J, Kim H, Lee C 2010 Quantitative analysis of mTRAQ-labeled proteome using full MS scans. J Proteome Res 9:3750-3758
    • (2010) J Proteome Res , vol.9 , pp. 3750-3758
    • Kang, U.B.1    Yeom, J.2    Kim, H.3    Lee, C.4
  • 47
    • 0024438708 scopus 로고
    • Electrospray ionization for mass spectrometry of large biomolecules
    • Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM 1989 Electrospray ionization for mass spectrometry of large biomolecules. Science 246:64-71
    • (1989) Science , vol.246 , pp. 64-71
    • Fenn, J.B.1    Mann, M.2    Meng, C.K.3    Wong, S.F.4    Whitehouse, C.M.5
  • 48
    • 84984042980 scopus 로고
    • Protein and polymer analysis up to m/z 100,000 by laser ionization time-offlight mass spectrometry
    • Tanaka K, Ido Y, Akita S, Yoshida Y, Yoshida T 1988 Protein and polymer analysis up to m/z 100,000 by laser ionization time-offlight mass spectrometry. Rapid Commun Mass Spectrom 2:151
    • (1988) Rapid Commun Mass Spectrom , vol.2 , pp. 151
    • Tanaka, K.1    Ido, Y.2    Akita, S.3    Yoshida, Y.4    Yoshida, T.5
  • 49
    • 33845379876 scopus 로고
    • Influence of the wavelength in high irradiance ultraviolet laser desorption mass spectrometry of organic molecules
    • Karas M, Bachmann, D., and Hillenkamp, F 1985 Influence of the wavelength in high irradiance ultraviolet laser desorption mass spectrometry of organic molecules. Anal Chem 57:2935-2939
    • (1985) Anal Chem , vol.57 , pp. 2935-2939
    • Karas, M.1    Bachmann, D.2    Hillenkamp, F.3
  • 50
    • 0029758906 scopus 로고    scopus 로고
    • Ligand induction of a transcriptionally active thyroid hormone receptor coactivator complex
    • Fondell JD, Ge H, Roeder RG 1996 Ligand induction of a transcriptionally active thyroid hormone receptor coactivator complex. Proc Natl Acad Sci USA 93:8329-8333
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 8329-8333
    • Fondell, J.D.1    Ge, H.2    Roeder, R.G.3
  • 51
    • 0032525781 scopus 로고    scopus 로고
    • A novel protein complex that interacts with the vitamin D3 receptor in a ligand-dependent manner and enhances VDR transactivation in a cell-free system
    • Rachez C, Suldan Z, Ward J, Chang CP, Burakov D, Erdjument-Bromage H, Tempst P, Freedman LP 1998 A novel protein complex that interacts with the vitamin D3 receptor in a ligand-dependent manner and enhances VDR transactivation in a cell-free system. Genes Dev 12:1787-1800
    • (1998) Genes Dev , vol.12 , pp. 1787-1800
    • Rachez, C.1    Suldan, Z.2    Ward, J.3    Chang, C.P.4    Burakov, D.5    Erdjument-Bromage, H.6    Tempst, P.7    Freedman, L.P.8
  • 52
    • 78650360165 scopus 로고    scopus 로고
    • Identification of proteins associated with ligand-activated estrogen receptor _ in human breast cancer cell nuclei by tandem affinity purification and nano LC-MS/M
    • Tarallo R, Bamundo A, Nassa G, Nola E, Paris O, Ambrosino C, Facchiano A, Baumann M, Nyman TA, Weisz A 2011 Identification of proteins associated with ligand-activated estrogen receptor _ in human breast cancer cell nuclei by tandem affinity purification and nano LC-MS/MS. Proteomics 11:172-179
    • (2011) Proteomic , vol.1 , pp. 172-179
    • Tarallo, R.1    Bamundo, A.2    Nassa, G.3    Nola, E.4    Paris, O.5    Ambrosino, C.6    Facchiano, A.7    Baumann, M.8    Nyman, T.A.9    Weisz, A.10
  • 56
    • 76749140070 scopus 로고    scopus 로고
    • A comparison of proteomic profiles changes during 17_-estradiol treatment in human prostate cancer PC-3 cell line
    • Chen J, Huang P, Kaku H, Zhang K, Watanabe M, Saika T, Nasu Y, Kumon H 2009 A comparison of proteomic profiles changes during 17_-estradiol treatment in human prostate cancer PC-3 cell line. Cancer Genomics Proteomics 6:331-335
    • (2009) Cancer Genomics Proteomics , vol.6 , pp. 331-335
    • Chen, J.1    Huang, P.2    Kaku, H.3    Zhang, K.4    Watanabe, M.5    Saika, T.6    Nasu, Y.7    Kumon, H.8
  • 57
    • 38449089795 scopus 로고    scopus 로고
    • Estradiol in vivo regulation of brain mitochondrial proteome
    • Nilsen J, Irwin RW, Gallaher TK, Brinton RD 2007 Estradiol in vivo regulation of brain mitochondrial proteome. J Neurosci 27: 14069-14077
    • (2007) J Neurosci , vol.27 , pp. 14069-14077
    • Nilsen, J.1    Irwin, R.W.2    Gallaher, T.K.3    Brinton, R.D.4
  • 60
    • 0025817801 scopus 로고
    • Dopamine activation of an orphan of the steroid receptor superfamily
    • Power RF, Lydon JP, Conneely OM, O'Malley BW 1991 Dopamine activation of an orphan of the steroid receptor superfamily. Science 252:1546-1548
    • (1991) Science , vol.252 , pp. 1546-1548
    • Power, R.F.1    Lydon, J.P.2    Conneely, O.M.3    O'Malley, B.W.4
  • 61
    • 0025043196 scopus 로고
    • Hormonal regulation and identification of chicken progesterone receptor phosphorylation sites
    • Denner LA, Schrader WT, O'Malley BW, Weigel NL 1990 Hormonal regulation and identification of chicken progesterone receptor phosphorylation sites. J Biol Chem 265:16548-16555
    • (1990) J Biol Chem , vol.265 , pp. 16548-16555
    • Denner, L.A.1    Schrader, W.T.2    O'Malley, B.W.3    Weigel, N.L.4
  • 64
    • 79952384301 scopus 로고    scopus 로고
    • Quantitative phosphoproteomics studies using stable isotope dimethyl labeling coupled with IMAC-HILIC-nanoLC-MS/MS for estrogen-induced transcriptional regulation
    • Wu CJ, Chen YW, Tai JH, Chen SH 2011 Quantitative phosphoproteomics studies using stable isotope dimethyl labeling coupled with IMAC-HILIC-nanoLC-MS/MS for estrogen-induced transcriptional regulation. J Proteome Res 10:1088-1097
    • (2011) J Proteome Res , vol.10 , pp. 1088-1097
    • Wu, C.J.1    Chen, Y.W.2    Tai, J.H.3    Chen, S.H.4
  • 66
    • 70350443849 scopus 로고    scopus 로고
    • Proteomic analysis of phosphorylated nuclear proteins underscores novel roles for rapid actions of retinoic acid in the regulation of mRNA splicing and translation
    • Laserna EJ, Valero ML, Sanz L, del Pino MM, Calvete JJ, Barettino D 2009 Proteomic analysis of phosphorylated nuclear proteins underscores novel roles for rapid actions of retinoic acid in the regulation of mRNA splicing and translation. Mol Endocrinol 23:1799-1814
    • (2009) Mol Endocrinol , vol.23 , pp. 1799-1814
    • Laserna, E.J.1    Valero, M.L.2    Sanz, L.3    del Pino, M.M.4    Calvete, J.J.5    Barettino, D.6
  • 67
    • 3242793327 scopus 로고    scopus 로고
    • Historical review: A brief history and personal retrospective of seven-transmembrane receptors
    • Lefkowitz RJ 2004 Historical review: a brief history and personal retrospective of seven-transmembrane receptors. Trends Pharmacol Sci 25:413-422
    • (2004) Trends Pharmacol Sci , vol.25 , pp. 413-422
    • Lefkowitz, R.J.1
  • 68
    • 56749170664 scopus 로고    scopus 로고
    • Proteomic identification and functional validation of activins and bone morphogenetic protein 11 as candidate novel muscle mass regulators
    • Souza TA, Chen X, Guo Y, Sava P, Zhang J, Hill JJ, Yaworsky PJ, Qiu Y 2008 Proteomic identification and functional validation of activins and bone morphogenetic protein 11 as candidate novel muscle mass regulators. Mol Endocrinol 22:2689-2702
    • (2008) Mol Endocrinol , vol.22 , pp. 2689-2702
    • Souza, T.A.1    Chen, X.2    Guo, Y.3    Sava, P.4    Zhang, J.5    Hill, J.J.6    Yaworsky, P.J.7    Qiu, Y.8
  • 72
    • 15744364422 scopus 로고    scopus 로고
    • Identification of parathyroid hormone-regulated proteins in mouse bone marrow cells by proteomics
    • Kim SH, Jun S, Jang HS, Lim SK 2005 Identification of parathyroid hormone-regulated proteins in mouse bone marrow cells by proteomics. Biochem Biophys Res Commun 330:423-429
    • (2005) Biochem Biophys Res Commun , vol.330 , pp. 423-429
    • Kim, S.H.1    Jun, S.2    Jang, H.S.3    Lim, S.K.4
  • 73
    • 79961014854 scopus 로고    scopus 로고
    • Large-scale phosphosite quantification in tissues by a spike-in SILAC method
    • Monetti M, Nagaraj N, Sharma K, Mann M 2011 Large-scale phosphosite quantification in tissues by a spike-in SILAC method. Nat Methods 8:655-658
    • (2011) Nat Methods , vol.8 , pp. 655-658
    • Monetti, M.1    Nagaraj, N.2    Sharma, K.3    Mann, M.4
  • 75
    • 77957272228 scopus 로고    scopus 로고
    • Quantitative phosphoproteomic analysis reveals cAMP/vasopressin-dependent signaling pathways in native renal thick ascending limb cells
    • Gunaratne R, Braucht DW, Rinschen MM, Chou CL, Hoffert JD, Pisitkun T, Knepper MA 2010 Quantitative phosphoproteomic analysis reveals cAMP/vasopressin-dependent signaling pathways in native renal thick ascending limb cells. Proc Natl Acad Sci USA 107:15653-15658
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 15653-15658
    • Gunaratne, R.1    Braucht, D.W.2    Rinschen, M.M.3    Chou, C.L.4    Hoffert, J.D.5    Pisitkun, T.6    Knepper, M.A.7
  • 78
    • 84855302577 scopus 로고    scopus 로고
    • Comparison of tear proteins between healthy and early diabetic retinopathy patients
    • Kim HJ, Kim PK, Yoo HS, Kim CW 2012 Comparison of tear proteins between healthy and early diabetic retinopathy patients. Clin Biochem 45:60-67
    • (2012) Clin Biochem , vol.45 , pp. 60-67
    • Kim, H.J.1    Kim, P.K.2    Yoo, H.S.3    Kim, C.W.4
  • 80
    • 80052772366 scopus 로고    scopus 로고
    • Characterization of human myotubes from type 2 diabetic and nondiabetic subjects using complementary quantitative mass spectrometric methods
    • M110.006650
    • Thingholm TE, Bak S, Beck-Nielsen H, Jensen ON, Gaster M 2011 Characterization of human myotubes from type 2 diabetic and nondiabetic subjects using complementary quantitative mass spectrometric methods. Mol Cell Proteomics 10:M110.006650
    • (2011) Mol Cell Proteomics , vol.10
    • Thingholm, T.E.1    Bak, S.2    Beck-Nielsen, H.3    Jensen, O.N.4    Gaster, M.5
  • 81
    • 84855185323 scopus 로고    scopus 로고
    • Targeted proteomics of isolated glomeruli from the kidneys of diabetic rats: Sorbin and SH3 domain containing 2 is a novel protein associated with diabetic nephropathy
    • Nakatani S, Kakehashi A, Ishimura E, Yamano S, Mori K, Wei M, Inaba M, Wanibuchi H 2011 Targeted proteomics of isolated glomeruli from the kidneys of diabetic rats: sorbin and SH3 domain containing 2 is a novel protein associated with diabetic nephropathy. Exp Diabetes Res 2011:9793
    • (2011) Exp Diabetes Res , vol.9793 , pp. 2011
    • Nakatani, S.1    Kakehashi, A.2    Ishimura, E.3    Yamano, S.4    Mori, K.5    Wei, M.6    Inaba, M.7    Wanibuchi, H.8
  • 85
    • 67049146471 scopus 로고    scopus 로고
    • Getting started in computational mass spectrometry-based proteomics
    • Vitek O 2009 Getting started in computational mass spectrometry-based proteomics. PLoS Comput Biol 5:e1000366
    • (2009) PLoS Comput Biol , vol.5
    • Vitek, O.1
  • 86
    • 41349096900 scopus 로고    scopus 로고
    • Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
    • Deutsch EW, Lam H, Aebersold R 2008 Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiol Genomics 33:18-25
    • (2008) Physiol Genomics , vol.33 , pp. 18-25
    • Deutsch, E.W.1    Lam, H.2    Aebersold, R.3
  • 87
    • 35848929694 scopus 로고    scopus 로고
    • Analysis and validation of proteomic data generated by tandem mass spectrometry
    • Nesvizhskii AI, Vitek O, Aebersold R 2007 Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods 4:787-797
    • (2007) Nat Methods , vol.4 , pp. 787-797
    • Nesvizhskii, A.I.1    Vitek, O.2    Aebersold, R.3
  • 88
    • 17844394177 scopus 로고    scopus 로고
    • Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry
    • Listgarten J, Emili A 2005 Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics 4:419-434
    • (2005) Mol Cell Proteomics , vol.4 , pp. 419-434
    • Listgarten, J.1    Emili, A.2
  • 90
    • 33947366516 scopus 로고    scopus 로고
    • Development and validation of a spectral library searching method for peptide identification from MS/MS
    • Lam H, Deutsch EW, Eddes JS, Eng JK, King N, Stein SE, Aebersold R 2007 Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 7:655-667
    • (2007) Proteomics , vol.7 , pp. 655-667
    • Lam, H.1    Deutsch, E.W.2    Eddes, J.S.3    Eng, J.K.4    King, N.5    Stein, S.E.6    Aebersold, R.7
  • 93
    • 79961230601 scopus 로고    scopus 로고
    • The International Proteomics Tutorial Programme: Reaching out to the next generation proteome scientists
    • James P, Marko-Varga GA 2011 The International Proteomics Tutorial Programme: reaching out to the next generation proteome scientists. J Proteome Res 10:3311-3312
    • (2011) J Proteome Res , vol.10 , pp. 3311-3312
    • James, P.1    Marko-Varga, G.A.2
  • 95
    • 84863036408 scopus 로고    scopus 로고
    • Translational proteomics in neurodegenerative diseases-16th HUPO
    • BPP workshop September 5 Geneva, Switzerland
    • Gröttrup B, Böckmann M, Stephan C, Marcus K, Grinberg LT, Meyer HE, Park YM 2012 Translational proteomics in neurodegenerative diseases-16th HUPO BPP workshop September 5, 2011 Geneva, Switzerland. Proteomics 12:356-358
    • (2011) Proteomics , vol.12 , pp. 356-358
    • Gröttrup, B.1    Böckmann, M.2    Stephan, C.3    Marcus, K.4    Grinberg, L.T.5    Meyer, H.E.6    Park, Y.M.7
  • 101
    • 42049114671 scopus 로고    scopus 로고
    • The HUPO proteomics standards initiative: Easing communication and minimizing data loss in a changing world
    • Orchard S, Hermjakob H 2008 The HUPO proteomics standards initiative: easing communication and minimizing data loss in a changing world. Brief Bioinform 9:166-173
    • (2008) Brief Bioinform , vol.9 , pp. 166-173
    • Orchard, S.1    Hermjakob, H.2
  • 106
    • 43049127826 scopus 로고    scopus 로고
    • PeptideAtlas: A resource for target selection for emerging targeted proteomics workflows
    • Deutsch EW, Lam H, Aebersold R 2008 PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep 9:429-434
    • (2008) EMBO Rep , vol.9 , pp. 429-434
    • Deutsch, E.W.1    Lam, H.2    Aebersold, R.3
  • 107
    • 77449100000 scopus 로고    scopus 로고
    • Using the PRIDE proteomics identifications database for knowledge discovery and data analysis
    • Jones P, Martens L 2010 Using the PRIDE proteomics identifications database for knowledge discovery and data analysis. Methods Mol Biol 604:297-307
    • (2010) Methods Mol Biol , vol.604 , pp. 297-307
    • Jones, P.1    Martens, L.2
  • 109
    • 79952196987 scopus 로고    scopus 로고
    • Data management and data integration in the HUPO plasma proteome project
    • Omenn GS 2011 Data management and data integration in the HUPO plasma proteome project. Methods Mol Biol 696:247-257
    • (2011) Methods Mol Biol , vol.696 , pp. 247-257
    • Omenn, G.S.1
  • 110
    • 3042735127 scopus 로고    scopus 로고
    • The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data
    • Carr S, Aebersold R, Baldwin M, Burlingame A, Clauser K, Nesvizhskii A 2004 The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol Cell Proteomics 3:531-533
    • (2004) Mol Cell Proteomics , vol.3 , pp. 531-533
    • Carr, S.1    Aebersold, R.2    Baldwin, M.3    Burlingame, A.4    Clauser, K.5    Nesvizhskii, A.6
  • 115
    • 33644527950 scopus 로고    scopus 로고
    • The model organism as a system: Integrating 'omics' data sets
    • Joyce AR, Palsson BØ 2006 The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol 7:198-210
    • (2006) Nat Rev Mol Cell Biol , vol.7 , pp. 198-210
    • Joyce, A.R.1    Palsson, B.O.2
  • 118
    • 75549085083 scopus 로고    scopus 로고
    • Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology
    • Prasad TS, Kandasamy K, Pandey A 2009 Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology. Methods Mol Biol 577:67-79
    • (2009) Methods Mol Biol , vol.577 , pp. 67-79
    • Prasad, T.S.1    Kandasamy, K.2    Pandey, A.3
  • 123
    • 84860833500 scopus 로고    scopus 로고
    • Reorganizing the protein space at the Universal Protein Resource (UniProt)
    • UniProt Consortium
    • UniProt Consortium 2012 Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 40:D71-D75
    • (2012) Nucleic Acids Res , vol.40
  • 126
    • 84861168275 scopus 로고    scopus 로고
    • OCAP: An open comprehensive analysis pipeline for iTRAQ
    • Wang P, Yang P, Yang JY 2012 OCAP: an open comprehensive analysis pipeline for iTRAQ. Bioinformatics 28:1404-1405
    • (2012) Bioinformatics , vol.28 , pp. 1404-1405
    • Wang, P.1    Yang, P.2    Yang, J.Y.3
  • 127
    • 77957190045 scopus 로고    scopus 로고
    • Integrated data management and validation platform for phosphorylated tandem mass spectrometry data
    • Lahesmaa-Korpinen AM, Carlson SM, White FM, Hautaniemi S 2010 Integrated data management and validation platform for phosphorylated tandem mass spectrometry data. Proteomics 10: 3515-3524
    • (2010) Proteomics , vol.10 , pp. 3515-3524
    • Lahesmaa-Korpinen, A.M.1    Carlson, S.M.2    White, F.M.3    Hautaniemi, S.4
  • 129
    • 33746930864 scopus 로고    scopus 로고
    • Aebersold R2005 A uniform proteomics MS/MS analysis platform utilizing open XML file formats
    • Keller A, Eng J, Zhang N, Li XJ, Aebersold R2005 A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol 1:2005.0017
    • (2005) Mol Syst Biol , vol.1 , pp. 0017
    • Keller, A.1    Eng, J.2    Zhang, N.3    Li, X.J.4
  • 131
    • 0033434080 scopus 로고    scopus 로고
    • Probabilitybased protein identification by searching sequence databases using mass spectrometry data
    • Perkins DN, Pappin DJ, Creasy DM, Cottrell JS 1999 Probabilitybased protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551-3567
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 134
    • 0036808207 scopus 로고    scopus 로고
    • ProbID: A probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data
    • Zhang N, Aebersold R, Schwikowski B 2002 ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics 2:1406-1412
    • (2002) Proteomics , vol.2 , pp. 1406-1412
    • Zhang, N.1    Aebersold, R.2    Schwikowski, B.3
  • 135
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng JK, McCormack AL, Yates 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
    • (1994) J Am Soc Mass Spectrom , vol.5 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates, J.R.3
  • 136
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: Matching proteins with tandem mass spectra
    • Craig R, Beavis RC 2004 TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20:1466-1467
    • (2004) Bioinformatics , vol.20 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 137
    • 84855166719 scopus 로고    scopus 로고
    • MR-Tandem: Parallel XTandem using Hadoop MapReduce on Amazon Web Services
    • Pratt B, Howbert JJ, Tasman NI, Nilsson EJ 2012 MR-Tandem: parallel XTandem using Hadoop MapReduce on Amazon Web Services. Bioinformatics 28:136-137
    • (2012) Bioinformatics , vol.28 , pp. 136-137
    • Pratt, B.1    Howbert, J.J.2    Tasman, N.I.3    Nilsson, E.J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.