메뉴 건너뛰기




Volumn 14, Issue 3, 2017, Pages 251-258

A large-scale targeted proteomics assay resource based on an in vitro human proteome

Author keywords

[No Author keywords available]

Indexed keywords

6 PHOSPHOFRUCTOKINASE; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; LACTATE DEHYDROGENASE; PROTEOME; RECOMBINANT PROTEIN; TELOMERASE REVERSE TRANSCRIPTASE; TRIOSEPHOSPHATE ISOMERASE; PEPTIDE LIBRARY;

EID: 85007141026     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.4116     Document Type: Article
Times cited : (75)

References (42)
  • 1
    • 34247612307 scopus 로고    scopus 로고
    • Multiple high-throughput analyses monitor the response of E. Coli to perturbations
    • Ishii, N. et al. Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 316, 593-597 (2007).
    • (2007) Science , vol.316 , pp. 593-597
    • Ishii, N.1
  • 2
    • 0035805255 scopus 로고    scopus 로고
    • Integrated genomic and proteomic analyses of a systematically perturbed metabolic network
    • Ideker, T. et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929-934 (2001).
    • (2001) Science , vol.292 , pp. 929-934
    • Ideker, T.1
  • 3
    • 84857672615 scopus 로고    scopus 로고
    • Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism
    • Buescher, J.M. et al. Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science 335, 1099-1103 (2012).
    • (2012) Science , vol.335 , pp. 1099-1103
    • Buescher, J.M.1
  • 4
    • 66949116701 scopus 로고    scopus 로고
    • A human proteome detection and quantitation project
    • Anderson, N.L. et al. A human proteome detection and quantitation project. Mol. Cell. Proteomics 8, 883-886 (2009).
    • (2009) Mol. Cell. Proteomics , vol.8 , pp. 883-886
    • Anderson, N.L.1
  • 5
    • 38349068918 scopus 로고    scopus 로고
    • Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution
    • Keshishian, H., Addona, T., Burgess, M., Kuhn, E. & Carr, S.A. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics 6, 2212-2229 (2007).
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 2212-2229
    • Keshishian, H.1    Addona, T.2    Burgess, M.3    Kuhn, E.4    Carr, S.A.5
  • 6
    • 54049090766 scopus 로고    scopus 로고
    • Selected reaction monitoring for quantitative proteomics: A tutorial
    • Lange, V., Picotti, P., Domon, B. & Aebersold, R. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol. Syst. Biol. 4, 222 (2008).
    • (2008) Mol. Syst. Biol. , vol.4 , pp. 222
    • Lange, V.1    Picotti, P.2    Domon, B.3    Aebersold, R.4
  • 7
    • 68749094119 scopus 로고    scopus 로고
    • Full dynamic range proteome analysis of S. Cerevisiae by targeted proteomics
    • Picotti, P., Bodenmiller, B., Mueller, L.N., Domon, B. & Aebersold, R. Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 138, 795-806 (2009).
    • (2009) Cell , vol.138 , pp. 795-806
    • Picotti, P.1    Bodenmiller, B.2    Mueller, L.N.3    Domon, B.4    Aebersold, R.5
  • 8
    • 74049131716 scopus 로고    scopus 로고
    • High-throughput generation of selected reaction-monitoring assays for proteins and proteomes
    • Picotti, P. et al. High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat. Methods 7, 43-46 (2010).
    • (2010) Nat. Methods , vol.7 , pp. 43-46
    • Picotti, P.1
  • 9
    • 84895072645 scopus 로고    scopus 로고
    • Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins
    • Kennedy, J.J. et al. Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Nat. Methods 11, 149-155 (2014).
    • (2014) Nat. Methods , vol.11 , pp. 149-155
    • Kennedy, J.J.1
  • 10
    • 43049127826 scopus 로고    scopus 로고
    • PeptideAtlas: A resource for target selection for emerging targeted proteomics workfows
    • Deutsch, E.W., Lam, H. & Aebersold, R. PeptideAtlas: a resource for target selection for emerging targeted proteomics workfows. EMBO Rep. 9, 429-434 (2008).
    • (2008) EMBO Rep. , vol.9 , pp. 429-434
    • Deutsch, E.W.1    Lam, H.2    Aebersold, R.3
  • 11
    • 84901611036 scopus 로고    scopus 로고
    • Mass-spectrometry-based draft of the human proteome
    • Wilhelm, M. et al. Mass-spectrometry-based draft of the human proteome. Nature 509, 582-587 (2014).
    • (2014) Nature , vol.509 , pp. 582-587
    • Wilhelm, M.1
  • 12
    • 84901599553 scopus 로고    scopus 로고
    • A draft map of the human proteome
    • Kim, M.S. et al. A draft map of the human proteome. Nature 509, 575-581 (2014).
    • (2014) Nature , vol.509 , pp. 575-581
    • Kim, M.S.1
  • 13
    • 33846133955 scopus 로고    scopus 로고
    • Computational prediction of proteotypic peptides for quantitative proteomics
    • Mallick, P. et al. Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 25, 125-131 (2007).
    • (2007) Nat. Biotechnol. , vol.25 , pp. 125-131
    • Mallick, P.1
  • 14
    • 59849093889 scopus 로고    scopus 로고
    • Prediction of high-responding peptides for targeted protein assays by mass spectrometry
    • Fusaro, V.A., Mani, D.R., Mesirov, J.P. & Carr, S.A. Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nat. Biotechnol. 27, 190-198 (2009).
    • (2009) Nat. Biotechnol. , vol.27 , pp. 190-198
    • Fusaro, V.A.1    Mani, D.R.2    Mesirov, J.P.3    Carr, S.A.4
  • 15
    • 84871791617 scopus 로고    scopus 로고
    • Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes
    • Karlsson, C., Malmström, L., Aebersold, R. & Malmström, J. Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes. Nat. Commun. 3, 1301 (2012).
    • (2012) Nat. Commun. , vol.3 , pp. 1301
    • Karlsson, C.1    Malmström, L.2    Aebersold, R.3    Malmström, J.4
  • 16
    • 84873724658 scopus 로고    scopus 로고
    • A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis
    • Picotti, P. et al. A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature 494, 266-270 (2013).
    • (2013) Nature , vol.494 , pp. 266-270
    • Picotti, P.1
  • 17
    • 84877863368 scopus 로고    scopus 로고
    • The Mtb proteome library: A resource of assays to quantify the complete proteome of Mycobacterium tuberculosis
    • Schubert, O.T. et al. The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis. Cell Host Microbe 13, 602-612 (2013).
    • (2013) Cell Host Microbe , vol.13 , pp. 602-612
    • Schubert, O.T.1
  • 18
    • 84979649391 scopus 로고    scopus 로고
    • Human SRMAtlas: A resource of targeted assays to quantify the complete human proteome
    • Kusebauch, U. et al. Human SRMAtlas: a resource of targeted assays to quantify the complete human proteome. Cell 166, 766-778 (2016).
    • (2016) Cell , vol.166 , pp. 766-778
    • Kusebauch, U.1
  • 19
    • 80855154135 scopus 로고    scopus 로고
    • A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantifcation and multiplexed determination of protein copy numbers in cell lines
    • O111 009613
    • Zeiler, M., Straube, W.L., Lundberg, E., Uhlen, M. & Mann, M. A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantifcation and multiplexed determination of protein copy numbers in cell lines. Mol. Cell. Proteomics 11, O111 009613 (2012).
    • (2012) Mol. Cell. Proteomics , vol.11
    • Zeiler, M.1    Straube, W.L.2    Lundberg, E.3    Uhlen, M.4    Mann, M.5
  • 21
    • 57049126143 scopus 로고    scopus 로고
    • Human protein factory for converting the transcriptome into an in vitro-expressed proteome
    • Goshima, N. et al. Human protein factory for converting the transcriptome into an in vitro-expressed proteome. Nat. Methods 5, 1011-1017 (2008).
    • (2008) Nat. Methods , vol.5 , pp. 1011-1017
    • Goshima, N.1
  • 22
    • 80855128111 scopus 로고    scopus 로고
    • The quantitative proteome of a human cell line
    • Beck, M. et al. The quantitative proteome of a human cell line. Mol. Syst. Biol. 7, 549 (2011).
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 549
    • Beck, M.1
  • 23
    • 79956322553 scopus 로고    scopus 로고
    • Global quantifcation of mammalian gene expression control
    • Schwanhäusser, B. et al. Global quantifcation of mammalian gene expression control. Nature 473, 337-342 (2011).
    • (2011) Nature , vol.473 , pp. 337-342
    • Schwanhäusser, B.1
  • 24
    • 84929586811 scopus 로고    scopus 로고
    • Large-scale interlaboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma
    • Abbatiello, S.E. et al. Large-scale interlaboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma. Mol. Cell. Proteomics 14, 2357-2374 (2015).
    • (2015) Mol. Cell. Proteomics , vol.14 , pp. 2357-2374
    • Abbatiello, S.E.1
  • 25
    • 77951965920 scopus 로고    scopus 로고
    • Skyline: An open source document editor for creating and analyzing targeted proteomics experiments
    • MacLean, B. et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26, 966-968 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 966-968
    • MacLean, B.1
  • 26
    • 53049096977 scopus 로고    scopus 로고
    • Multiple reaction monitoring of mTRAQ-labeled peptides enables absolute quantifcation of endogenous levels of a potential cancer marker in cancerous and normal endometrial tissues
    • DeSouza, L.V. et al. Multiple reaction monitoring of mTRAQ-labeled peptides enables absolute quantifcation of endogenous levels of a potential cancer marker in cancerous and normal endometrial tissues. J. Proteome Res. 7, 3525-3534 (2008).
    • (2008) J. Proteome Res. , vol.7 , pp. 3525-3534
    • DeSouza, L.V.1
  • 27
    • 78149369733 scopus 로고    scopus 로고
    • Comparative analysis of human SRC-family kinase substrate specifcity in vitro
    • Takeda, H. et al. Comparative analysis of human SRC-family kinase substrate specifcity in vitro. J. Proteome Res. 9, 5982-5993 (2010).
    • (2010) J. Proteome Res. , vol.9 , pp. 5982-5993
    • Takeda, H.1
  • 28
    • 80855128254 scopus 로고    scopus 로고
    • Deep proteome and transcriptome mapping of a human cancer cell line
    • Nagaraj, N. et al. Deep proteome and transcriptome mapping of a human cancer cell line. Mol. Syst. Biol. 7, 548 (2011).
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 548
    • Nagaraj, N.1
  • 29
    • 84868028972 scopus 로고    scopus 로고
    • Quantitative analysis of fssion yeast transcriptomes and proteomes in proliferating and quiescent cells
    • Marguerat, S. et al. Quantitative analysis of fssion yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell 151, 671-683 (2012).
    • (2012) Cell , vol.151 , pp. 671-683
    • Marguerat, S.1
  • 30
    • 84994893513 scopus 로고    scopus 로고
    • Direct and absolute quantifcation of over 1800 yeast proteins via selected reaction monitoring
    • Lawless, C. et al. Direct and absolute quantifcation of over 1800 yeast proteins via selected reaction monitoring. Mol. Cell. Proteomics 15, 1309-1322 (2016).
    • (2016) Mol. Cell. Proteomics , vol.15 , pp. 1309-1322
    • Lawless, C.1
  • 31
    • 84964931417 scopus 로고    scopus 로고
    • A strategy for absolute proteome quantifcation with mass spectrometry by hierarchical use of peptide-concatenated standards
    • Kito, K., Okada, M., Ishibashi, Y., Okada, S. & Ito, T. A strategy for absolute proteome quantifcation with mass spectrometry by hierarchical use of peptide-concatenated standards. Proteomics 16, 1457-1473 (2016).
    • (2016) Proteomics , vol.16 , pp. 1457-1473
    • Kito, K.1    Okada, M.2    Ishibashi, Y.3    Okada, S.4    Ito, T.5
  • 32
    • 0033614998 scopus 로고    scopus 로고
    • Creation of human tumour cells with defned genetic elements
    • Hahn, W.C. et al. Creation of human tumour cells with defned genetic elements. Nature 400, 464-468 (1999).
    • (1999) Nature , vol.400 , pp. 464-468
    • Hahn, W.C.1
  • 33
    • 0344823945 scopus 로고    scopus 로고
    • Refractory nature of normal human diploid fbroblasts with respect to oncogene-mediated transformation
    • Akagi, T., Sasai, K. & Hanafusa, H. Refractory nature of normal human diploid fbroblasts with respect to oncogene-mediated transformation. Proc. Natl. Acad. Sci. USA 100, 13567-13572 (2003).
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 13567-13572
    • Akagi, T.1    Sasai, K.2    Hanafusa, H.3
  • 35
    • 79551600149 scopus 로고    scopus 로고
    • Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics
    • Costenoble, R. et al. Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics. Mol. Syst. Biol. 7, 464 (2011).
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 464
    • Costenoble, R.1
  • 36
    • 84880384052 scopus 로고    scopus 로고
    • Targeted proteomics reveals strain-specifc changes in the mouse insulin and central metabolic pathways after a sustained high-fat diet
    • Sabidó, E. et al. Targeted proteomics reveals strain-specifc changes in the mouse insulin and central metabolic pathways after a sustained high-fat diet. Mol. Syst. Biol. 9, 681 (2013).
    • (2013) Mol. Syst. Biol. , vol.9 , pp. 681
    • Sabidó, E.1
  • 37
    • 84921826349 scopus 로고    scopus 로고
    • A sentinel protein assay for simultaneously quantifying cellular processes
    • Soste, M. et al. A sentinel protein assay for simultaneously quantifying cellular processes. Nat. Methods 11, 1045-1048 (2014).
    • (2014) Nat. Methods , vol.11 , pp. 1045-1048
    • Soste, M.1
  • 38
    • 58149191255 scopus 로고    scopus 로고
    • Human Gene and Protein Database (HGPD): A novel database presenting a large quantity of experiment-based results in human proteomics
    • Maruyama, Y. et al. Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics. Nucleic Acids Res. 37, D762-D766 (2009).
    • (2009) Nucleic Acids Res. , vol.37 , pp. D762-D766
    • Maruyama, Y.1
  • 39
    • 84862233435 scopus 로고    scopus 로고
    • HGPD: Human Gene and Protein Database 2012 update
    • Maruyama, Y. et al. HGPD: Human Gene and Protein Database, 2012 update. Nucleic Acids Res. 40, D924-D929 (2012).
    • (2012) Nucleic Acids Res. , vol.40 , pp. D924-D929
    • Maruyama, Y.1
  • 41
    • 0021355340 scopus 로고
    • A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids
    • Wessel, D. & Flügge, U.I. A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal. Biochem. 138, 141-143 (1984).
    • (1984) Anal. Biochem. , vol.138 , pp. 141-143
    • Wessel, D.1    Flügge, U.I.2
  • 42
    • 0042424602 scopus 로고    scopus 로고
    • Statistical signifcance for genomewide studies
    • Storey, J.D. & Tibshirani, R. Statistical signifcance for genomewide studies. Proc. Natl. Acad. Sci. USA 100, 9440-9445 (2003).
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.