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Volumn 11, Issue 2, 2014, Pages 149-155

Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

EID: 84895072645     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.2763     Document Type: Article
Times cited : (164)

References (50)
  • 1
    • 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
  • 2
    • 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
  • 3
    • 61849105469 scopus 로고    scopus 로고
    • Mass spectrometry based targeted protein quantification: Methods and applications
    • Pan, S. et al. Mass spectrometry based targeted protein quantification: Methods and applications. J. Proteome Res. 8, 787-797 (.2009
    • (2009) J. Proteome Res , vol.8 , pp. 787-797
    • Pan, S.1
  • 4
    • 84878644042 scopus 로고    scopus 로고
    • Targeted quantitation of proteins by mass spectrometry
    • Liebler, D.C. & Zimmerman, L.J. Targeted quantitation of proteins by mass spectrometry. Biochemistry 52, 3797-3806 (.2013
    • (2013) Biochemistry , vol.52 , pp. 3797-3806
    • Liebler, D.C.1    Zimmerman, L.J.2
  • 5
    • 84863923380 scopus 로고    scopus 로고
    • Reproducible quantification of cancer-Associated proteins in body fluids using targeted proteomics
    • Hüttenhain, R. et al. Reproducible quantification of cancer-Associated proteins in body fluids using targeted proteomics. Sci. Transl. Med. 4, 142ra94 (.2012
    • (2012) Sci. Transl. Med , vol.4
    • Hüttenhain, R.1
  • 6
    • 78649694616 scopus 로고    scopus 로고
    • Reconstructing the pipeline by introducing multiplexed multiple reaction monitoring mass spectrometry for cancer biomarker verification: An NCI-CPTC initiative perspective
    • Rodriguez, H. et al. Reconstructing the pipeline by introducing multiplexed multiple reaction monitoring mass spectrometry for cancer biomarker verification: An NCI-CPTC initiative perspective. Proteomics Clin. Appl. 4, 904-914 (.2010
    • (2010) Proteomics Clin. Appl , vol.4 , pp. 904-914
    • Rodriguez, H.1
  • 7
    • 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
  • 8
    • 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
  • 9
    • 79960179572 scopus 로고    scopus 로고
    • The human proteome project: Current state and future direction
    • M111.009993
    • Legrain, P. et al. The human proteome project: Current state and future direction. Mol. Cell. Proteomics 10, M111.009993 (.2011
    • (2011) Mol. Cell. Proteomics , vol.10
    • Legrain, P.1
  • 10
    • 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
  • 11
    • 84874074018 scopus 로고    scopus 로고
    • The biology/disease-driven human proteome project (.B/D-HPP): Enabling protein research for the life sciences community
    • Aebersold, R. et al. The biology/disease-driven human proteome project (.B/D-HPP): Enabling protein research for the life sciences community. J. Proteome Res. 12, 23-27 (.2013
    • (2013) J. Proteome Res , vol.12 , pp. 23-27
    • Aebersold, R.1
  • 12
    • 54049095667 scopus 로고    scopus 로고
    • A database of mass spectrometric assays for the yeast proteome
    • Picotti, P. et al. A database of mass spectrometric assays for the yeast proteome. Nat. Methods 5, 913-914 (.2008
    • (2008) Nat. Methods , vol.5 , pp. 913-914
    • Picotti, P.1
  • 13
    • 79960859298 scopus 로고    scopus 로고
    • A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer
    • Remily-Wood, E.R. et al. A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer. Proteomics Clin. Appl. 5, 383-396 (.2011
    • (2011) Proteomics Clin. Appl , vol.5 , pp. 383-396
    • Remily-Wood, E.R.1
  • 14
    • 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
  • 15
    • 84860856503 scopus 로고    scopus 로고
    • PASSEL: The PeptideAtlas SRM experiment library
    • Farrah, T. et al. PASSEL: The PeptideAtlas SRM experiment library. Proteomics 12, 1170-1175 (.2012
    • (2012) Proteomics , vol.12 , pp. 1170-1175
    • Farrah, T.1
  • 16
    • 75749126208 scopus 로고    scopus 로고
    • Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry
    • Abbatiello, S.E., Mani, D.R., Keshishian, H. & Carr, S.A. Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry. Clin. Chem. 56, 291-305 (.2010
    • (2010) Clin. Chem , vol.56 , pp. 291-305
    • Abbatiello, S.E.1    Mani, D.R.2    Keshishian, H.3    Carr, S.A.4
  • 17
    • 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
  • 18
    • 84859880168 scopus 로고    scopus 로고
    • Protein significance analysis in selected reaction monitoring (.SRM) measurements
    • M111.014662
    • Chang, C.Y. et al. Protein significance analysis in selected reaction monitoring (.SRM) measurements. Mol. Cell. Proteomics 11, M111.014662 (.2012
    • (2012) Mol. Cell. Proteomics , vol.11
    • Chang, C.Y.1
  • 19
    • 84877028141 scopus 로고    scopus 로고
    • Comprehensive molecular portraits of human breast tumours
    • The Cancer Genome Atlas Network
    • The Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 490, 61-70 (.2012
    • (2012) Nature , vol.490 , pp. 61-70
  • 20
    • 36248962105 scopus 로고    scopus 로고
    • The genomic landscapes of human breast and colorectal cancers
    • Wood, L.D. et al. The genomic landscapes of human breast and colorectal cancers. Science 318, 1108-1113 (.2007
    • (2007) Science , vol.318 , pp. 1108-1113
    • Wood, L.D.1
  • 21
    • 84861527388 scopus 로고    scopus 로고
    • The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
    • Curtis, C. et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 486, 346-352 (.2012
    • (2012) Nature , vol.486 , pp. 346-352
    • Curtis, C.1
  • 22
    • 67650252530 scopus 로고    scopus 로고
    • Molecular profiling of breast cancer cell lines defines relevant tumor models and provides a resource for cancer gene discovery
    • Kao, J. et al. Molecular profiling of breast cancer cell lines defines relevant tumor models and provides a resource for cancer gene discovery. PLoS ONE 4, e6146 (.2009
    • (2009) PLoS ONE , vol.4
    • Kao, J.1
  • 23
    • 33845209913 scopus 로고    scopus 로고
    • A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes
    • Neve, R.M. et al. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell 10, 515-527 (.2006
    • (2006) Cancer Cell , vol.10 , pp. 515-527
    • Neve, R.M.1
  • 24
    • 79960015997 scopus 로고    scopus 로고
    • Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies
    • Lehmann, B.D. et al. Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. J. Clin. Invest. 121, 2750-2767 (.2011
    • (2011) J. Clin. Invest , vol.121 , pp. 2750-2767
    • Lehmann, B.D.1
  • 25
    • 33644843376 scopus 로고    scopus 로고
    • Functional proteomics approach to investigate the biological activities of cDNAs implicated in breast cancer
    • Witt, A.E. et al. Functional proteomics approach to investigate the biological activities of cDNAs implicated in breast cancer. J. Proteome Res. 5, 599-610 (.2006
    • (2006) J. Proteome Res , vol.5 , pp. 599-610
    • Witt, A.E.1
  • 26
    • 0345822598 scopus 로고    scopus 로고
    • The positive false discovery rate: A Bayesian interpretation and the q-value
    • Storey, J.D. The positive false discovery rate: A Bayesian interpretation and the q-value. Ann. Stat. 31, 2013-2035 (.2003
    • (2003) Ann. Stat , vol.31 , pp. 2013-2035
    • Storey, J.D.1
  • 27
    • 33847348449 scopus 로고    scopus 로고
    • A gene-expression signature to predict survival in breast cancer across independent data sets
    • Naderi, A. et al. A gene-expression signature to predict survival in breast cancer across independent data sets. Oncogene 26, 1507-1516 (.2007
    • (2007) Oncogene , vol.26 , pp. 1507-1516
    • Naderi, A.1
  • 28
    • 58149350355 scopus 로고    scopus 로고
    • Relapse-free survival in breast cancer patients is associated with a gene expression signature characteristic for inflammatory breast cancer
    • Van Laere, S. et al. Relapse-free survival in breast cancer patients is associated with a gene expression signature characteristic for inflammatory breast cancer. Clin. Cancer Res. 14, 7452-7460 (.2008
    • (2008) Clin. Cancer Res , vol.14 , pp. 7452-7460
    • Van Laere, S.1
  • 29
    • 84878238535 scopus 로고    scopus 로고
    • Prognostic significance in breast cancer of a gene signature capturing stromal PDGF signaling
    • Frings, O. et al. Prognostic significance in breast cancer of a gene signature capturing stromal PDGF signaling. Am. J. Pathol. 182, 2037-2047 (.2013
    • (2013) Am. J. Pathol , vol.182 , pp. 2037-2047
    • Frings, O.1
  • 31
    • 18244409687 scopus 로고    scopus 로고
    • Gene expression profiling predicts clinical outcome of breast cancer
    • van t Veer, L.J. et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 415, 530-536 (.2002
    • (2002) Nature , vol.415 , pp. 530-536
    • Van T Veer, L.J.1
  • 32
    • 34247145491 scopus 로고    scopus 로고
    • Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade
    • Loi, S. et al. Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade. J. Clin. Oncol. 25, 1239-1246 (.2007
    • (2007) J. Clin. Oncol , vol.25 , pp. 1239-1246
    • Loi, S.1
  • 33
    • 62449131093 scopus 로고    scopus 로고
    • Supervised risk predictor of breast cancer based on intrinsic subtypes
    • Parker, J.S. et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. J. Clin. Oncol. 27, 1160-1167 (.2009
    • (2009) J. Clin. Oncol , vol.27 , pp. 1160-1167
    • Parker, J.S.1
  • 34
    • 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
  • 35
    • 35348863892 scopus 로고    scopus 로고
    • High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites
    • Stahl-Zeng, J. et al. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol. Cell. Proteomics 6, 1809-1817 (.2007
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 1809-1817
    • Stahl-Zeng, J.1
  • 36
    • 84863611387 scopus 로고    scopus 로고
    • GeLC-MRM quantitation of mutant KRAS oncoprotein in complex biological samples
    • Halvey, P.J., Ferrone, C.R. & Liebler, D.C. GeLC-MRM quantitation of mutant KRAS oncoprotein in complex biological samples. J. Proteome Res. 11, 3908-3913 (.2012
    • (2012) J. Proteome Res , vol.11 , pp. 3908-3913
    • Halvey, P.J.1    Ferrone, C.R.2    Liebler, D.C.3
  • 37
    • 84872510161 scopus 로고    scopus 로고
    • Mass-linked immuno-selective assays in targeted proteomics
    • Madian, A.G., Rochelle, N.S. & Regnier, F.E. Mass-linked immuno-selective assays in targeted proteomics. Anal. Chem. 85, 737-748 (.2013
    • (2013) Anal. Chem , vol.85 , pp. 737-748
    • Madian, A.G.1    Rochelle, N.S.2    Regnier, F.E.3
  • 38
    • 85058721573 scopus 로고    scopus 로고
    • Peptide immunoaffinity enrichment coupled with mass spectrometry for peptide and protein quantification
    • Whiteaker, J.R. & Paulovich, A.G. Peptide immunoaffinity enrichment coupled with mass spectrometry for peptide and protein quantification. Clin. Lab. Med. 31, 385-396 (.2011
    • (2011) Clin. Lab. Med , vol.31 , pp. 385-396
    • Whiteaker, J.R.1    Paulovich, A.G.2
  • 39
    • 77956389484 scopus 로고    scopus 로고
    • Hybrid immunoaffinity-mass spectrometric methods for efficient protein biomarker verification in pharmaceutical development
    • Ackermann, B.L. Hybrid immunoaffinity-mass spectrometric methods for efficient protein biomarker verification in pharmaceutical development. Bioanalysis 1, 265-268 (.2009
    • (2009) Bioanalysis , vol.1 , pp. 265-268
    • Ackermann, B.L.1
  • 40
    • 79953305842 scopus 로고    scopus 로고
    • Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry
    • Whiteaker, J.R. et al. Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry. Mol. Cell. Proteomics 10, M110.005645 (.2011
    • (2011) Mol. Cell. Proteomics , vol.10
    • Whiteaker, J.R.1
  • 41
    • 8844233567 scopus 로고    scopus 로고
    • Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (.SISCAPA
    • Anderson, N.L. et al. Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (.SISCAPA). J. Proteome Res. 3, 235-244 (.2004
    • (2004) J. Proteome Res , vol.3 , pp. 235-244
    • Anderson, N.L.1
  • 42
    • 33744814477 scopus 로고    scopus 로고
    • Gene expression and benefit of chemotherapy in women with node-negative, estrogen receptor-positive breast cancer
    • Paik, S. et al. Gene expression and benefit of chemotherapy in women with node-negative, estrogen receptor-positive breast cancer. J. Clin. Oncol. 24, 3726-3734 (.2006
    • (2006) J. Clin. Oncol , vol.24 , pp. 3726-3734
    • Paik, S.1
  • 43
    • 78649885451 scopus 로고    scopus 로고
    • Platform for establishing interlaboratory reproducibility of selected reaction monitoring-based mass spectrometry peptide assays
    • Prakash, A. et al. Platform for establishing interlaboratory reproducibility of selected reaction monitoring-based mass spectrometry peptide assays. J. Proteome Res. 9, 6678-6688 (.2010
    • (2010) J. Proteome Res , vol.9 , pp. 6678-6688
    • Prakash, A.1
  • 44
    • 84864583363 scopus 로고    scopus 로고
    • Interlaboratory reproducibility of selective reaction monitoring assays using multiple upfront analyte enrichment strategies
    • Prakash, A. et al. Interlaboratory reproducibility of selective reaction monitoring assays using multiple upfront analyte enrichment strategies. J. Proteome Res. 11, 3986-3995 (.2012
    • (2012) J. Proteome Res , vol.11 , pp. 3986-3995
    • Prakash, A.1
  • 45
    • 33750979860 scopus 로고    scopus 로고
    • General framework for developing and evaluating database scoring algorithms using the TANDEM search engine
    • MacLean, B., Eng, J.K., Beavis, R.C. & McIntosh, M. General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics 22, 2830-2832 (.2006
    • (2006) Bioinformatics , vol.22 , pp. 2830-2832
    • MacLean, B.1    Eng, J.K.2    Beavis, R.C.3    McIntosh, M.4
  • 46
    • 84874762979 scopus 로고    scopus 로고
    • The PRoteomics IDEntifications (.PRIDE) database and associated tools: Status in 2013
    • Vizcaíno, J.A. et al. The PRoteomics IDEntifications (.PRIDE) database and associated tools: Status in 2013. Nucleic Acids Res. 41, D1063-D1069 (.2013
    • (2013) Nucleic Acids Res , vol.41
    • Vizcaíno, J.A.1
  • 47
    • 74049132731 scopus 로고    scopus 로고
    • Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis
    • Griffin, N.M. et al. Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis. Nat. Biotechnol. 28, 83-89 (.2010
    • (2010) Nat. Biotechnol , vol.28 , pp. 83-89
    • Griffin, N.M.1
  • 48
    • 33751208935 scopus 로고    scopus 로고
    • Sequence-specific retention calculator. Algorithm for peptide retention prediction in ion-pair RP-HPLC: Application to 300-And 100-Å pore size C18 sorbents
    • Krokhin, O.V. Sequence-specific retention calculator. Algorithm for peptide retention prediction in ion-pair RP-HPLC: Application to 300-And 100-Å pore size C18 sorbents. Anal. Chem. 78, 7785-7795 (.2006
    • (2006) Anal. Chem , vol.78 , pp. 7785-7795
    • Krokhin, O.V.1
  • 50
    • 37249032736 scopus 로고    scopus 로고
    • Spatial smoothing and hot spot detection for CGH data using the fused lasso
    • Tibshirani, R. & Wang, P. Spatial smoothing and hot spot detection for CGH data using the fused lasso. Biostatistics 9, 18-29 (.2008
    • (2008) Biostatistics , vol.9 , pp. 18-29
    • Tibshirani, R.1    Wang, P.2


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