메뉴 건너뛰기




Volumn 10, Issue 12, 2013, Pages 1239-1245

Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE 4; LUMINESPIB; MELANOMA ANTIGEN; TETRACYCLINE;

EID: 84888871108     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.2702     Document Type: Article
Times cited : (239)

References (43)
  • 2
    • 80052955256 scopus 로고    scopus 로고
    • BET bromodomain inhibition as a therapeutic strategy to target c-Myc
    • Delmore, J.E. et al. BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell 146, 904-917 (2011).
    • (2011) Cell , vol.146 , pp. 904-917
    • Delmore, J.E.1
  • 3
    • 82655179908 scopus 로고    scopus 로고
    • Disease mutations in disordered regions-Exception to the rule?
    • Vacic, V. & Iakoucheva, L.M. Disease mutations in disordered regions-exception to the rule? Mol. Biosyst. 8, 27-32 (2012).
    • (2012) Mol. Biosyst. , vol.8 , pp. 27-32
    • Vacic, V.1    Iakoucheva, L.M.2
  • 4
    • 0042830297 scopus 로고    scopus 로고
    • Molecular basis of inherited diseases: A structural perspective
    • DOI 10.1016/S0168-9525(03)00195-1
    • Steward, R.E., MacArthur, M.W., Laskowski, R.A. & Thornton, J.M. Molecular basis of inherited diseases: a structural perspective. Trends Genet. 19, 505-513 (2003). (Pubitemid 37101091)
    • (2003) Trends in Genetics , vol.19 , Issue.9 , pp. 505-513
    • Steward, R.E.1    MacArthur, M.W.2    Laskowski, R.A.3    Thornton, J.M.4
  • 5
    • 72849127628 scopus 로고    scopus 로고
    • Kinase mutations in human disease: Interpreting genotype-Phenotype relationships
    • Lahiry, P., Torkamani, A., Schork, N.J. & Hegele, R.A. Kinase mutations in human disease: interpreting genotype-phenotype relationships. Nat. Rev. Genet. 11, 60-74 (2010).
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 60-74
    • Lahiry, P.1    Torkamani, A.2    Schork, N.J.3    Hegele, R.A.4
  • 6
    • 45949108954 scopus 로고    scopus 로고
    • Protein interactions in human genetic diseases
    • Schuster-Böckler, B. & Bateman, A. Protein interactions in human genetic diseases. Genome Biol. 9, R9 (2008).
    • (2008) Genome Biol. , vol.9
    • Schuster-Böckler, B.1    Bateman, A.2
  • 7
    • 72849142731 scopus 로고    scopus 로고
    • Edgetic perturbation models of human inherited disorders
    • Zhong, Q. et al. Edgetic perturbation models of human inherited disorders. Mol. Syst. Biol. 5, 321 (2009).
    • (2009) Mol. Syst. Biol. , vol.5 , pp. 321
    • Zhong, Q.1
  • 9
  • 10
    • 84864619937 scopus 로고    scopus 로고
    • Beyond hairballs: The use of quantitative mass spectrometry data to understand protein-Protein interactions
    • Gingras, A.C. & Raught, B. Beyond hairballs: the use of quantitative mass spectrometry data to understand protein-protein interactions. FEBS Lett. 586, 2723-2731 (2012).
    • (2012) FEBS Lett. , vol.586 , pp. 2723-2731
    • Gingras, A.C.1    Raught, B.2
  • 11
    • 76149142168 scopus 로고    scopus 로고
    • Repeatability and reproducibility in proteomic identifications by liquid chromatography-Tandem mass spectrometry
    • Tabb, D.L. et al. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J. Proteome Res. 9, 761-776 (2010).
    • (2010) J. Proteome Res. , vol.9 , pp. 761-776
    • Tabb, D.L.1
  • 12
    • 84878011768 scopus 로고    scopus 로고
    • Label-Free quantitative proteomics trends for protein-Protein interactions
    • Tate, S., Larsen, B., Bonner, R. & Gingras, A.C. Label-free quantitative proteomics trends for protein-protein interactions. J. Proteomics 81, 91-101 (2013).
    • (2013) J. Proteomics , vol.81 , pp. 91-101
    • Tate, S.1    Larsen, B.2    Bonner, R.3    Gingras, A.C.4
  • 13
    • 79960245388 scopus 로고    scopus 로고
    • Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor
    • Bisson, N. et al. Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor. Nat. Biotechnol. 29, 653-658 (2011).
    • (2011) Nat. Biotechnol. , vol.29 , pp. 653-658
    • Bisson, N.1
  • 14
    • 84880441014 scopus 로고    scopus 로고
    • Temporal regulation of EGF signalling networks by the scaffold protein Shc1
    • Zheng, Y. et al. Temporal regulation of EGF signalling networks by the scaffold protein Shc1. Nature 499, 166-171 (2013).
    • (2013) Nature , vol.499 , pp. 166-171
    • Zheng, Y.1
  • 15
    • 84861990380 scopus 로고    scopus 로고
    • Selected reaction monitoring-Based proteomics: Workflows, potential, pitfalls and future directions
    • Picotti, P. & Aebersold, R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat. Methods 9, 555-566 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 555-566
    • Picotti, P.1    Aebersold, R.2
  • 16
    • 67650564834 scopus 로고    scopus 로고
    • Multi-Site assessment of the precision and reproducibility of multiple reaction monitoring-Based measurements of proteins in plasma
    • Addona, T.A. et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat. Biotechnol. 27, 633-641 (2009).
    • (2009) Nat. Biotechnol. , vol.27 , pp. 633-641
    • Addona, T.A.1
  • 17
    • 14744293536 scopus 로고    scopus 로고
    • Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra
    • Venable, J.D., Dong, M.Q., Wohlschlegel, J., Dillin, A. & Yates, J.R. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat. Methods 1, 39-45 (2004).
    • (2004) Nat. Methods , vol.1 , pp. 39-45
    • Venable, J.D.1    Dong, M.Q.2    Wohlschlegel, J.3    Dillin, A.4    Yates, J.R.5
  • 18
    • 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
    • O111.016717
    • Gillet, L.C. et al. 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, O111.016717 (2012).
    • (2012) Mol. Cell. Proteomics , vol.11
    • Gillet, L.C.1
  • 19
    • 84876337044 scopus 로고    scopus 로고
    • Quantitative measurements of N-Linked glycoproteins in human plasma by SWATH-MS
    • Liu, Y. et al. Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS. Proteomics 13, 1247-1256 (2013).
    • (2013) Proteomics , vol.13 , pp. 1247-1256
    • Liu, Y.1
  • 20
    • 84888858053 scopus 로고    scopus 로고
    • Quantifying protein interaction dynamics by SWATH mass spectrometry: Application to the 14-3-3 system
    • doi:10.1038/nmeth.2703 (27 October)
    • Collins, B.C. et al. Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system. Nat. Methods doi:10.1038/nmeth.2703 (27 October 2013).
    • (2013) Nat. Methods
    • Collins, B.C.1
  • 21
    • 79959958529 scopus 로고    scopus 로고
    • Performance characteristics of a new hybrid quadrupole time-Of-Flight tandem mass spectrometer (TripleTOF 5600)
    • Andrews, G.L., Simons, B.L., Young, J.B., Hawkridge, A.M. & Muddiman, D.C. Performance characteristics of a new hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600). Anal. Chem. 83, 5442-5446 (2011).
    • (2011) Anal. Chem. , vol.83 , pp. 5442-5446
    • Andrews, G.L.1    Simons, B.L.2    Young, J.B.3    Hawkridge, A.M.4    Muddiman, D.C.5
  • 22
    • 84866401301 scopus 로고    scopus 로고
    • Mass spectrometry approaches to study mammalian kinase and phosphatase associated proteins
    • Kean, M.J., Couzens, A.L. & Gingras, A.C. Mass spectrometry approaches to study mammalian kinase and phosphatase associated proteins. Methods 57, 400-408 (2012).
    • (2012) Methods , vol.57 , pp. 400-408
    • Kean, M.J.1    Couzens, A.L.2    Gingras, A.C.3
  • 23
    • 0032834055 scopus 로고    scopus 로고
    • EIF4 initiation factors: Effectors of mRNA recruitment to ribosomes and regulators of translation
    • DOI 10.1146/annurev.biochem.68.1.913
    • Gingras, A.C., Raught, B. & Sonenberg, N. eIF4 initiation factors: effectors of mRNA recruitment to ribosomes and regulators of translation. Annu. Rev. Biochem. 68, 913-963 (1999). (Pubitemid 29449212)
    • (1999) Annual Review of Biochemistry , vol.68 , pp. 913-963
    • Gingras, A.-C.1    Raught, B.2    Sonenberg, N.3
  • 24
    • 0037216626 scopus 로고    scopus 로고
    • The transformation suppressor Pdcd4 is a novel eukaryotic translation initiation factor 4A binding protein that inhibits translation
    • Yang, H.S. et al. The transformation suppressor Pdcd4 is a novel eukaryotic translation initiation factor 4A binding protein that inhibits translation. Mol. Cell. Biol. 23, 26-37 (2003).
    • (2003) Mol. Cell. Biol. , vol.23 , pp. 26-37
    • Yang, H.S.1
  • 26
    • 0028978274 scopus 로고
    • A p16INK4a-Insensitive CDK4 mutant targeted by cytolytic T lymphocytes in a human melanoma
    • Wölfel, T. et al. A p16INK4a-insensitive CDK4 mutant targeted by cytolytic T lymphocytes in a human melanoma. Science 269, 1281-1284 (1995).
    • (1995) Science , vol.269 , pp. 1281-1284
    • Wölfel, T.1
  • 28
    • 0027769876 scopus 로고
    • A new regulatory motif in cell-cycle control causing specific inhibition of cyclin D/CDK4
    • DOI 10.1038/366704a0
    • Serrano, M., Hannon, G.J. & Beach, D. A new regulatory motif in cell-cycle control causing specific inhibition of cyclin D/CDK4. Nature 366, 704-707 (1993). (Pubitemid 24036021)
    • (1993) Nature , vol.366 , Issue.6456 , pp. 704-707
    • Serrano, M.1    Hannon, G.J.2    Beach, D.3
  • 30
    • 22244485706 scopus 로고    scopus 로고
    • Epidermal growth factor receptors harboring kinase domain mutations associate with the heat shock protein 90 chaperone and are destabilized following exposure to geldanamycins
    • DOI 10.1158/0008-5472.CAN-05-0933
    • Shimamura, T., Lowell, A.M., Engelman, J.A. & Shapiro, G.I. Epidermal growth factor receptors harboring kinase domain mutations associate with the heat shock protein 90 chaperone and are destabilized following exposure to geldanamycins. Cancer Res. 65, 6401-6408 (2005). (Pubitemid 40994428)
    • (2005) Cancer Research , vol.65 , Issue.14 , pp. 6401-6408
    • Shimamura, T.1    Lowell, A.M.2    Engelman, J.A.3    Shapiro, G.I.4
  • 32
    • 84865695733 scopus 로고    scopus 로고
    • Quantitative analysis of Hsp90-Client interactions reveals principles of substrate recognition
    • Taipale, M. et al. Quantitative analysis of Hsp90-client interactions reveals principles of substrate recognition. Cell 150, 987-1001 (2012).
    • (2012) Cell , vol.150 , pp. 987-1001
    • Taipale, M.1
  • 33
    • 74249116634 scopus 로고    scopus 로고
    • Strategies for stalling malignancy: Targeting cancer's addiction to Hsp90
    • Prodromou, C. Strategies for stalling malignancy: targeting cancer's addiction to Hsp90. Curr. Top. Med. Chem. 9, 1352-1368 (2009).
    • (2009) Curr. Top. Med. Chem. , vol.9 , pp. 1352-1368
    • Prodromou, C.1
  • 34
    • 38349157746 scopus 로고    scopus 로고
    • 4,5-Diarylisoxazole hsp90 chaperone inhibitors: Potential therapeutic agents for the treatment of cancer
    • Brough, P.A. et al. 4,5-Diarylisoxazole Hsp90 chaperone inhibitors: potential therapeutic agents for the treatment of cancer. J. Med. Chem. 51, 196-218 (2008).
    • (2008) J. Med. Chem. , vol.51 , pp. 196-218
    • Brough, P.A.1
  • 35
    • 77953916528 scopus 로고    scopus 로고
    • HSP90 at the hub of protein homeostasis: Emerging mechanistic insights
    • Taipale, M., Jarosz, D.F. & Lindquist, S. HSP90 at the hub of protein homeostasis: emerging mechanistic insights. Nat. Rev. Mol. Cell Biol. 11, 515-528 (2010).
    • (2010) Nat. Rev. Mol. Cell Biol. , vol.11 , pp. 515-528
    • Taipale, M.1    Jarosz, D.F.2    Lindquist, S.3
  • 36
    • 28244444919 scopus 로고    scopus 로고
    • Activated B-RAF is an Hsp90 client protein that is targeted by the anticancer drug 17-Allylamino-17-Demethoxygeldanamycin
    • da Rocha Dias, S. et al. Activated B-RAF is an Hsp90 client protein that is targeted by the anticancer drug 17-allylamino-17-demethoxygeldanamycin. Cancer Res. 65, 10686-10691 (2005).
    • (2005) Cancer Res. , vol.65 , pp. 10686-10691
    • Da Rocha-Dias, S.1
  • 37
    • 77957947158 scopus 로고    scopus 로고
    • ProHits: Integrated software for mass spectrometry-Based interaction proteomics
    • Liu, G. et al. ProHits: integrated software for mass spectrometry-based interaction proteomics. Nat. Biotechnol. 28, 1015-1017 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , pp. 1015-1017
    • Liu, G.1
  • 38
    • 84881475940 scopus 로고    scopus 로고
    • The CRA Pome: A contaminant repository for affinity purification-Mass spectrometry data
    • Mellacheruvu, D. et al. The CRA Pome: a contaminant repository for affinity purification-mass spectrometry data. Nat. Methods 10, 730-736 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 730-736
    • Mellacheruvu, D.1
  • 39
    • 79959735636 scopus 로고    scopus 로고
    • A cost-Benefit analysis of multidimensional fractionation of affinity purification-Mass spectrometry samples
    • Dunham, W.H. et al. A cost-benefit analysis of multidimensional fractionation of affinity purification-mass spectrometry samples. Proteomics 11, 2603-2612 (2011).
    • (2011) Proteomics , vol.11 , pp. 2603-2612
    • Dunham, W.H.1
  • 40
    • 34250215269 scopus 로고    scopus 로고
    • CIF-1, a shared subunit of the COP9/signalosome and eukaryotic initiation factor 3 complexes, regulates MEL-26 levels in the Caenorhabditis elegans embryo
    • DOI 10.1128/MCB.01724-06
    • Luke-Glaser, S. et al. CIF-1, a shared subunit of the COP9/signalosome and eukaryotic initiation factor 3 complexes, regulates MEL-26 levels in the Caenorhabditis elegans embryo. Mol. Cell. Biol. 27, 4526-4540 (2007). (Pubitemid 46906574)
    • (2007) Molecular and Cellular Biology , vol.27 , Issue.12 , pp. 4526-4540
    • Luke-Glaser, S.1    Roy, M.2    Larsen, B.3    Le Bihan, T.4    Metalnikov, P.5    Tyers, M.6    Peter, M.7    Pintard, L.8
  • 42
    • 79955595074 scopus 로고    scopus 로고
    • MProphet: Automated data processing and statistical validation for large-Scale SRM experiments
    • Reiter, L. et al. mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat. Methods 8, 430-435 (2011).
    • (2011) Nat. Methods , vol.8 , pp. 430-435
    • Reiter, L.1
  • 43
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • DOI 10.1093/bioinformatics/19.2.185
    • Bolstad, B.M., Irizarry, R.A., Astrand, M. & Speed, T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185-193 (2003). (Pubitemid 36181903)
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.