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Volumn 14, Issue 5, 2015, Pages 1400-1410

Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues

Author keywords

[No Author keywords available]

Indexed keywords

APOLIPOPROTEIN B100; CYTOCHROME P450; CYTOCHROME P450 2E1; GLUCURONOSYLTRANSFERASE 1A7; GLUTATHIONE TRANSFERASE; HEAT SHOCK PROTEIN 70; MULTIDRUG RESISTANCE ASSOCIATED PROTEIN 2; MULTIDRUG RESISTANCE ASSOCIATED PROTEIN 3; N ACETYL 1,4 BENZOQUINONE IMINE; PARACETAMOL; VOLTAGE DEPENDENT ANION CHANNEL 2; AMIDINOTRANSFERASE; AMMONIA LYASE; ANALGESIC AGENT; ANXA2 PROTEIN, HUMAN; FTCD PROTEIN, HUMAN; GLUTAMATE FORMIMINOTRANSFERASE; GLYCINE AMIDINOTRANSFERASE; LIPOCORTIN 2; ONCOPROTEIN; PARK7 PROTEIN, HUMAN; PEPTIDE; PEROXIREDOXIN 6; PRDX6 PROTEIN, HUMAN; PROTEIN DEGLYCASE DJ-1; PROTEOME; SIGNAL PEPTIDE; TRYPSIN; VDAC2 PROTEIN, HUMAN;

EID: 84929658087     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M114.044305     Document Type: Article
Times cited : (786)

References (49)
  • 1
    • 84887359663 scopus 로고    scopus 로고
    • Mass spectrometric protein maps for biomarker discovery and clinical research
    • Liu, Y., Hüttenhain, R., Collins, B., and Aebersold, R. (2013) Mass spectrometric protein maps for biomarker discovery and clinical research. Expert Rev. Mol. Diagn. 13, 811-825
    • (2013) Expert Rev. Mol. Diagn. , vol.13 , pp. 811-825
    • Liu, Y.1    Hüttenhain, R.2    Collins, B.3    Aebersold, R.4
  • 2
    • 84874232489 scopus 로고    scopus 로고
    • The coming age of complete, accurate, and ubiquitous proteomes
    • Mann, M., Kulak, N. A., Nagaraj, N., and Cox, J. (2013) The coming age of complete, accurate, and ubiquitous proteomes. Mol. Cell 49, 583-90
    • (2013) Mol. Cell , vol.49 , pp. 583-590
    • Mann, M.1    Kulak, N.A.2    Nagaraj, N.3    Cox, J.4
  • 3
    • 79953719716 scopus 로고    scopus 로고
    • More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS
    • Michalski, A., Cox, J., and Mann, M. (2011) More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J. Proteome Res. 10, 1785-93
    • (2011) J. Proteome Res. , vol.10 , pp. 1785-1793
    • Michalski, A.1    Cox, J.2    Mann, M.3
  • 5
    • 0346668199 scopus 로고    scopus 로고
    • Absolute quantification of the G protein-coupled receptor rhodopsin by LC/MS/MS using proteolysis product peptides and synthetic peptide standards
    • Barnidge, D. R., Dratz, E. A, Martin, T., Bonilla, L. E., Moran, L. B., and Lindall, A. (2003) Absolute quantification of the G protein-coupled receptor rhodopsin by LC/MS/MS using proteolysis product peptides and synthetic peptide standards. Anal. Chem. 75, 445-451
    • (2003) Anal. Chem. , vol.75 , pp. 445-451
    • Barnidge, D.R.1    Dratz, E.A.2    Martin, T.3    Bonilla, L.E.4    Moran, L.B.5    Lindall, A.6
  • 6
    • 0037795741 scopus 로고    scopus 로고
    • Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
    • Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., and Gygi, S. P. (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. U.S.A. 100, 6940-6945
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 6940-6945
    • Gerber, S.A.1    Rush, J.2    Stemman, O.3    Kirschner, M.W.4    Gygi, S.P.5
  • 7
    • 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., and Carr, S. A. (2007) Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics 6, 2212-2229
    • (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
  • 8
    • 84871983086 scopus 로고    scopus 로고
    • Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry
    • Gillette, M. A., and Carr, S. A. (2013) Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry. Nat. Methods 10, 28-34
    • (2013) Nat. Methods , vol.10 , pp. 28-34
    • Gillette, M.A.1    Carr, S.A.2
  • 9
    • 14744293536 scopus 로고    scopus 로고
    • Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra
    • Venable, J., Dong, M., and Wohlschlegel, J. (2004) Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat. Methods 1, 39-45
    • (2004) Nat. Methods , vol.1 , pp. 39-45
    • Venable, J.1    Dong, M.2    Wohlschlegel, J.3
  • 11
    • 84895071750 scopus 로고    scopus 로고
    • Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics
    • 201r
    • Distler, U., Kuharev, J., Navarro, P., and Levin, Y. (201r) Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics. Nat. Methods 11,
    • Nat. Methods , vol.11
    • Distler, U.1    Kuharev, J.2    Navarro, P.3    Levin, Y.4
  • 12
    • 84887195879 scopus 로고    scopus 로고
    • Data-independent acquisition (MSE) with ion mobility provides a systematic method for analysis of a bacteriophage structural proteome
    • Moran, D., Cross, T., Brown, L. M., Colligan, R. M., and Dunbar, D. (2014) Data-independent acquisition (MSE) with ion mobility provides a systematic method for analysis of a bacteriophage structural proteome. J. Virol. Methods 195, 9-17
    • (2014) J. Virol. Methods , vol.195 , pp. 9-17
    • Moran, D.1    Cross, T.2    Brown, L.M.3    Colligan, R.M.4    Dunbar, D.5
  • 13
    • 77957990113 scopus 로고    scopus 로고
    • Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation
    • Geiger, T., Cox, J., and Mann, M. (2010) Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation. Mol. Cell. Proteomics 9, 2252-2261
    • (2010) Mol. Cell. Proteomics , vol.9 , pp. 2252-2261
    • Geiger, T.1    Cox, J.2    Mann, M.3
  • 14
    • 79954569537 scopus 로고    scopus 로고
    • Faster, quantitative, and accurate precursor acquisition independent from ion count
    • Panchaud, A., Jung, S., Shaffer, S. A, Aitchison, J. D., and Goodlett, D. R. (2011) Faster, quantitative, and accurate precursor acquisition independent from ion count. Anal. Chem. 83, 2250-2257
    • (2011) Anal. Chem. , vol.83 , pp. 2250-2257
    • Panchaud, A.1    Jung, S.2    Shaffer, S.A.3    Aitchison, J.D.4    Goodlett, D.R.5
  • 16
    • 84857811076 scopus 로고    scopus 로고
    • Accurate peptide fragment mass analysis: Multiplexed peptide identification and quantification
    • Weisbrod, C. R., Eng, J. K., Hoopmann, M. R., Baker, T., and Bruce, J. E. (2012) Accurate peptide fragment mass analysis: Multiplexed peptide identification and quantification. J. Proteome Res. 11, 1621-1632
    • (2012) J. Proteome Res. , vol.11 , pp. 1621-1632
    • Weisbrod, C.R.1    Eng, J.K.2    Hoopmann, M.R.3    Baker, T.4    Bruce, J.E.5
  • 19
    • 84861860481 scopus 로고    scopus 로고
    • Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: A new concept for consistent and accurate proteome analysis
    • 016717
    • Gillet, L. C., Navarro, P., Tate, S., Röst, H., Selevsek, N., Reiter, L., Bonner, R., and Aebersold, R. (2012) Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell Proteomics 11(6), O111.016717
    • (2012) Mol. Cell Proteomics , vol.11 , Issue.6 , pp. O111
    • Gillet, L.C.1    Navarro, P.2    Tate, S.3    Röst, H.4    Selevsek, N.5    Reiter, L.6    Bonner, R.7    Aebersold, R.8
  • 23
    • 84887873381 scopus 로고    scopus 로고
    • Recent advances in mass spectrometry: Data independent analysis and hyper reaction monitoring
    • Law, K. P., and Lim, Y. P. (2013) Recent advances in mass spectrometry: Data independent analysis and hyper reaction monitoring. Expert Rev. Proteomics 10, 551-566
    • (2013) Expert Rev. Proteomics , vol.10 , pp. 551-566
    • Law, K.P.1    Lim, Y.P.2
  • 25
    • 84873381429 scopus 로고    scopus 로고
    • Screening for drug-induced hepatotoxicity in primary mouse hepatocytes using acetaminophen, amiodarone, and cyclosporin a as model compounds: An omics-guided approach
    • Van Summeren, A., Renes, J., Lizarraga, D., Bouwman, F. G., Noben, J.-P., van Delft, J. H. M., Kleinjans, J. C., and Mariman, E. C. (2013) Screening for drug-induced hepatotoxicity in primary mouse hepatocytes using acetaminophen, amiodarone, and cyclosporin a as model compounds: an omics-guided approach. OMICS 17, 71-83
    • (2013) OMICS , vol.17 , pp. 71-83
    • Van Summeren, A.1    Renes, J.2    Lizarraga, D.3    Bouwman, F.G.4    Noben, J.-P.5    Van Delft, J.H.M.6    Kleinjans, J.C.7    Mariman, E.C.8
  • 26
    • 79957871619 scopus 로고    scopus 로고
    • Pathophysiological relevance of proteomics investigations of drug-induced hepatotoxicity in HepG2 cells
    • author reply 431- 433
    • Jaeschke, H., McGill, M. R., and Ramachandran, A. (2011) Pathophysiological relevance of proteomics investigations of drug-induced hepatotoxicity in HepG2 cells. Toxicol. Sci. 121, 428-430; author reply 431- 433
    • (2011) Toxicol. Sci. , vol.121 , pp. 428-430
    • Jaeschke, H.1    McGill, M.R.2    Ramachandran, A.3
  • 27
    • 84872301011 scopus 로고    scopus 로고
    • Multi-cell type human liver microtissues for hepatotoxicity testing
    • Messner, S., Agarkova, I., Moritz, W., and Kelm, J. M. (2013) Multi-cell type human liver microtissues for hepatotoxicity testing. Arch. Toxicol. 87, 209-213
    • (2013) Arch. Toxicol. , vol.87 , pp. 209-213
    • Messner, S.1    Agarkova, I.2    Moritz, W.3    Kelm, J.M.4
  • 28
    • 84861800006 scopus 로고    scopus 로고
    • Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole Orbitrap mass spectrometer
    • Kelstrup, C. D., Young, C., Lavallee, R., Nielsen, M. L., and Olsen, J. V (2012) Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole Orbitrap mass spectrometer. J. Proteome Res. 11, 3487-3497
    • (2012) J. Proteome Res. , vol.11 , pp. 3487-3497
    • Kelstrup, C.D.1    Young, C.2    Lavallee, R.3    Nielsen, M.L.4    Olsen, J.V.5
  • 29
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    • Cox, J., and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367-72
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 30
    • 33947366516 scopus 로고    scopus 로고
    • Development and validation of a spectral library searching method for peptide identification from MS/MS
    • Lam, H., Deutsch, E. W., Eddes, J. S., Eng, J. K., King, N., Stein, S. E., and 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
  • 31
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang da, W., Sherman, B. T., and Lempicki, R. A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57
    • (2009) Nat. Protoc. , vol.4 , pp. 44-57
    • Huang Da, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 32
    • 84907033616 scopus 로고    scopus 로고
    • MSstats: An R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments
    • Choi, M., Chang, C.-Y., Clough, T., Broudy, D., Killeen, T., MacLean, B., and Vitek, O. (2014) MSstats: An R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. Bioinformatics 30, 2524-2526
    • (2014) Bioinformatics , vol.30 , pp. 2524-2526
    • Choi, M.1    Chang, C.-Y.2    Clough, T.3    Broudy, D.4    Killeen, T.5    MacLean, B.6    Vitek, O.7
  • 33
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y., and Hochberg, Y. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. 57, 289-300 http://www.jstor.org/stable/2346101
    • (1995) J. R. Stat. Soc. , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 34
    • 0023710206 scopus 로고
    • Comparing the areas under two or more correlated receiver operating characteristic curves: A nonparametric approach
    • DeLong, E. R., DeLong, D. M., and Clarke-Pearson, D. L. (1988) Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach. Biometrics 44, 837-845
    • (1988) Biometrics , vol.44 , pp. 837-845
    • DeLong, E.R.1    DeLong, D.M.2    Clarke-Pearson, D.L.3
  • 35
    • 77449146854 scopus 로고    scopus 로고
    • Target-decoy search strategy for mass spectrometry-based proteomics
    • Elias, J. E., and Gygi, S. P. (2010) Target-decoy search strategy for mass spectrometry-based proteomics. Methods Mol. Biol. 604, 55-71
    • (2010) Methods Mol. Biol. , vol.604 , pp. 55-71
    • Elias, J.E.1    Gygi, S.P.2
  • 36
    • 66749171697 scopus 로고    scopus 로고
    • Statistical design of quantitative mass spectrometry-based proteomic experiments
    • Oberg, A. L., and 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
  • 38
    • 32344442813 scopus 로고    scopus 로고
    • Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics research articles
    • Callister, S. J., Barry, R. C., Adkins, J. N., Johnson, E. T., Qian, W., Webb-Robertson, B. J., Smith, R. D., and Lipton, M. S. (2006) Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics research articles. J. Proteome Res. 5, 277-286
    • (2006) J. Proteome Res. , vol.5 , pp. 277-286
    • Callister, S.J.1    Barry, R.C.2    Adkins, J.N.3    Johnson, E.T.4    Qian, W.5    Webb-Robertson, B.J.6    Smith, R.D.7    Lipton, M.S.8
  • 39
    • 84883295568 scopus 로고    scopus 로고
    • Metabolism and disposition of acetaminophen: Recent advances in relation to hepatotoxicity and diagnosis
    • McGill, M. R., and Jaeschke, H. (2013) Metabolism and disposition of acetaminophen: Recent advances in relation to hepatotoxicity and diagnosis. Pharm. Res. 30, 2174-2187
    • (2013) Pharm. Res. , vol.30 , pp. 2174-2187
    • McGill, M.R.1    Jaeschke, H.2
  • 40
    • 13844319935 scopus 로고    scopus 로고
    • Drug bioactivation, covalent binding to target proteins and toxicity relevance
    • Zhou, S., Chan, E., Duan, W., Huang, M., and Chen, Y.-Z. (2005) Drug bioactivation, covalent binding to target proteins and toxicity relevance. Drug Metab. Rev. 37, 41-213
    • (2005) Drug Metab. Rev. , vol.37 , pp. 41-213
    • Zhou, S.1    Chan, E.2    Duan, W.3    Huang, M.4    Chen, Y.-Z.5
  • 41
    • 25144489068 scopus 로고    scopus 로고
    • Review overview of cell death signaling pathways
    • Jin, Z., and El-Deiry, W. S. (2005) Review overview of cell death signaling pathways. Cancer Biol. Ther. 4, 139-163
    • (2005) Cancer Biol. Ther. , vol.4 , pp. 139-163
    • Jin, Z.1    El-Deiry, W.S.2
  • 42
    • 84878053091 scopus 로고    scopus 로고
    • Normalization and missing value imputation for label-free LC-MS analysis
    • Karpievitch, Y. V., Dabney, A. R., and Smith, R. D. (2012) Normalization and missing value imputation for label-free LC-MS analysis. BMC Bioinformatics 13(Suppl 16), S5
    • (2012) BMC Bioinformatics , vol.13 , pp. S5
    • Karpievitch, Y.V.1    Dabney, A.R.2    Smith, R.D.3
  • 44
    • 84907197082 scopus 로고    scopus 로고
    • Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ
    • Cox, J., Hein, M. Y., Luber, C. A., Paron, I., Nagaraj, N., and Mann, M. (2014) Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol. Cell. Proteomics 13, 2513-26
    • (2014) Mol. Cell. Proteomics , vol.13 , pp. 2513-12256
    • Cox, J.1    Hein, M.Y.2    Luber, C.A.3    Paron, I.4    Nagaraj, N.5    Mann, M.6
  • 48
    • 84929660702 scopus 로고    scopus 로고
    • Mitochondrial translocation of GSK-3beta, a trigger of mitochondrial permeability transition, is mediated by its N-terminal domain and promoted by interaction with VDAC2
    • Tanno, M., Miura, T., Miki, T., Kuno, A., Ishikawa, S., Yano, T., and Kouzu, H. (2014) Mitochondrial translocation of GSK-3beta, a trigger of mitochondrial permeability transition, is mediated by its N-terminal domain and promoted by interaction with VDAC2. Cardiovasc. Res. S 3, 2014
    • (2014) Cardiovasc. Res. S , vol.3 , pp. 2014
    • Tanno, M.1    Miura, T.2    Miki, T.3    Kuno, A.4    Ishikawa, S.5    Yano, T.6    Kouzu, H.7
  • 49
    • 84904016840 scopus 로고    scopus 로고
    • Dynamic reciprocity: The role of annexin A2 in tissue integrity
    • Hitchcock, J. K., Katz, A. A. and Schäfer, G. (2014) Dynamic reciprocity: the role of annexin A2 in tissue integrity. J. Cell Commun. Signal. 8, 125-133
    • (2014) J. Cell Commun. Signal. , vol.8 , pp. 125-133
    • Hitchcock, J.K.1    Katz, A.A.2    Schäfer, G.3


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