메뉴 건너뛰기




Volumn 21, Issue 4, 2015, Pages 407-413

Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps

Author keywords

[No Author keywords available]

Indexed keywords

ION; PEPTIDE; PROTEOME;

EID: 84939991970     PISSN: 10788956     EISSN: 1546170X     Source Type: Journal    
DOI: 10.1038/nm.3807     Document Type: Article
Times cited : (308)

References (39)
  • 1
    • 0034303643 scopus 로고    scopus 로고
    • Molecular profiling of human cancer
    • Liotta, L. & Petricoin, E. Molecular profiling of human cancer. Nat. Rev. Genet. 1, 48-56 (2000).
    • (2000) Nat. Rev. Genet , vol.1 , pp. 48-56
    • Liotta, L.1    Petricoin, E.2
  • 2
    • 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
  • 3
    • 60849097255 scopus 로고    scopus 로고
    • Gene-expression signatures in breast cancer
    • Sotiriou, C. & Pusztai, L. Gene-expression signatures in breast cancer. N. Engl. J. Med. 360, 790-800 (2009).
    • (2009) N. Engl. J. Med , vol.360 , pp. 790-800
    • Sotiriou, C.1    Pusztai, L.2
  • 4
    • 58149182724 scopus 로고    scopus 로고
    • NCBI GEO: Archive for high-throughput functional genomic data
    • Barrett, T. et al. NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res. 37, D885-D890 (2009).
    • (2009) Nucleic Acids Res , vol.37 , pp. D885-D890
    • Barrett, T.1
  • 5
    • 84946040120 scopus 로고    scopus 로고
    • COSMIC: Exploring the world's knowledge of somatic mutations in human cancer
    • Forbes, S.A. et al. COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. 43, D805-D811 (2015).
    • (2015) Nucleic Acids Res , vol.43 , pp. D805-D811
    • Forbes, S.A.1
  • 6
    • 84884994218 scopus 로고    scopus 로고
    • The Cancer Genome Atlas Pan-Cancer analysis project
    • Cancer Genome Atlas Research Network
    • Cancer Genome Atlas Research Network, Weinstein, J.N. et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat. Genet. 45, 1113-1120 (2013).
    • (2013) Nat. Genet , vol.45 , pp. 1113-1120
    • Weinstein, J.N.1
  • 7
    • 20444460289 scopus 로고    scopus 로고
    • MicroRNA expression profiles classify human cancers
    • Lu, J. et al. MicroRNA expression profiles classify human cancers. Nature 435, 834-838 (2005).
    • (2005) Nature , vol.435 , pp. 834-838
    • Lu, J.1
  • 8
    • 60149091657 scopus 로고    scopus 로고
    • Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression
    • Sreekumar, A. et al. Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature 457, 910-914 (2009).
    • (2009) Nature , vol.457 , pp. 910-914
    • Sreekumar, A.1
  • 9
    • 0031822837 scopus 로고    scopus 로고
    • Tissue microarrays for high-throughput molecular profiling of tumor specimens
    • Kononen, J. et al. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat. Med. 4, 844-847 (1998).
    • (1998) Nat. Med , vol.4 , pp. 844-847
    • Kononen, J.1
  • 10
    • 17844386055 scopus 로고    scopus 로고
    • Antibody arrays in cancer research
    • Haab, B.B. Antibody arrays in cancer research. Mol. Cell Proteomics 4, 377-383 (2005).
    • (2005) Mol. Cell Proteomics , vol.4 , pp. 377-383
    • Haab, B.B.1
  • 11
    • 77954523086 scopus 로고    scopus 로고
    • Options and considerations when selecting a quantitative proteomics strategy
    • Domon, B. & Aebersold, R. Options and considerations when selecting a quantitative proteomics strategy. Nat. Biotechnol. 28, 710-721 (2010).
    • (2010) Nat. Biotechnol , vol.28 , pp. 710-721
    • Domon, B.1    Aebersold, R.2
  • 12
    • 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
    • O111016717
    • 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
  • 13
    • 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
  • 14
    • 84888858053 scopus 로고    scopus 로고
    • Quantifying protein interaction dynamics by SWATH mass spectrometry: Application to the 14-3-3 system
    • Collins, B.C. et al. Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system. Nat. Methods 10, 1246-1253 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 1246-1253
    • Collins, B.C.1
  • 16
    • 53049107743 scopus 로고    scopus 로고
    • Application of pressurized solvents for ultrafast trypsin hydrolysis in proteomics: Proteomics on the fly
    • López-Ferrer, D. et al. Application of pressurized solvents for ultrafast trypsin hydrolysis in proteomics: proteomics on the fly. J. Proteome Res. 7, 3276-3281 (2008).
    • (2008) J. Proteome Res , vol.7 , pp. 3276-3281
    • López-Ferrer, D.1
  • 17
    • 84868327851 scopus 로고    scopus 로고
    • Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion
    • Glatter, T. et al. Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion. J. Proteome Res. 11, 5145-5156 (2012).
    • (2012) J. Proteome Res , vol.11 , pp. 5145-5156
    • Glatter, T.1
  • 18
    • 84898665956 scopus 로고    scopus 로고
    • OpenSWATH: Automated, targeted analysis of mass spectrometric data generated by data-independent acquisition
    • Röst, H. et al. OpenSWATH: Automated, targeted analysis of mass spectrometric data generated by data-independent acquisition. Nat. Biotechnol. 32, 219-223 (2014).
    • (2014) Nat. Biotechnol , vol.32 , pp. 219-223
    • Röst, H.1
  • 19
    • 84907030818 scopus 로고    scopus 로고
    • ALFQ: An R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data
    • Rosenberger, G., Ludwig, C., Rost, H.L., Aebersold, R. & Malmstrom, L. aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data. Bioinformatics 30, 2511-2513 (2014).
    • (2014) Bioinformatics , vol.30 , pp. 2511-2513
    • Rosenberger, G.1    Ludwig, C.2    Rost, H.L.3    Aebersold, R.4    Malmstrom, L.5
  • 20
    • 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
  • 21
    • 80052264424 scopus 로고    scopus 로고
    • Current pathology keys of renal cell carcinoma
    • Algaba, F. et al. Current pathology keys of renal cell carcinoma. Eur. Urol. 60, 634-643 (2011).
    • (2011) Eur. Urol , vol.60 , pp. 634-643
    • Algaba, F.1
  • 22
    • 84900393064 scopus 로고    scopus 로고
    • Renal tumors: Diagnostic and prognostic biomarkers
    • Tan, P.H. et al. Renal tumors: diagnostic and prognostic biomarkers. Am. J. Surg. Pathol. 37, 1518-1531 (2013).
    • (2013) Am. J. Surg. Pathol , vol.37 , pp. 1518-1531
    • Tan, P.H.1
  • 24
    • 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
  • 25
    • 84872685287 scopus 로고    scopus 로고
    • Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma
    • Wi͆niewski, J.R. et al. Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma. Mol. Syst. Biol. 8, 611 (2012).
    • (2012) Mol. Syst. Biol , vol.8 , pp. 611
    • Wis̈niewski, J.R.1
  • 26
    • 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
  • 27
    • 84887433583 scopus 로고    scopus 로고
    • Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories
    • 't Hoen, P.A. et al. Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat. Biotechnol. 31, 1015-1022 (2013).
    • (2013) Nat. Biotechnol , vol.31 , pp. 1015-1022
    • T'Hoen, P.A.1
  • 28
    • 84880384052 scopus 로고    scopus 로고
    • Targeted proteomics reveals strain-specific changes in the mouse insulin and central metabolic pathways after a sustained high-fat diet
    • Sabidó, E. et al. Targeted proteomics reveals strain-specific changes in the mouse insulin and central metabolic pathways after a sustained high-fat diet. Mol. Syst. Biol. 16, 681 (2013).
    • (2013) Mol. Syst. Biol , vol.16 , pp. 681
    • Sabidó, E.1
  • 29
    • 84860869167 scopus 로고    scopus 로고
    • Using iRT, a normalized retention time for more targeted measurement of peptides
    • Escher, C. et al. Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics 12, 1111-1121 (2012).
    • (2012) Proteomics , vol.12 , pp. 1111-1121
    • Escher, C.1
  • 30
    • 84857966803 scopus 로고    scopus 로고
    • Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography
    • M111014126
    • Leitner, A. et al. Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography. Mol. Cell. Proteomics 11, M111.014126 (2012).
    • (2012) Mol. Cell. Proteomics , vol.11
    • Leitner, A.1
  • 31
    • 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
  • 32
    • 7044246160 scopus 로고    scopus 로고
    • Open mass spectrometry search algorithm
    • Geer, L.Y. et al. Open mass spectrometry search algorithm. J. Proteome Res. 3, 958-964 (2004).
    • (2004) J. Proteome Res , vol.3 , pp. 958-964
    • Geer, L.Y.1
  • 33
    • 77949676526 scopus 로고    scopus 로고
    • A guided tour of the Trans-Proteomic Pipeline
    • Deutsch, E.W. et al. A guided tour of the Trans-Proteomic Pipeline. Proteomics 10, 1150-1159 (2010).
    • (2010) Proteomics , vol.10 , pp. 1150-1159
    • Deutsch, E.W.1
  • 34
    • 84922875582 scopus 로고    scopus 로고
    • IPortal: The Swiss Grid Proteomics Portal: Requirements and new features based on experience and usability considerations
    • Kunszt, P. et al. iPortal: the Swiss Grid Proteomics Portal: requirements and new features based on experience and usability considerations. Concurrency and Computation: Practice and Experience 27, 433-445 (2015).
    • (2015) Concurrency and Computation: Practice and Experience , vol.27 , pp. 433-445
    • Kunszt, P.1
  • 35
    • 54949129419 scopus 로고    scopus 로고
    • ProteoWizard: Open source software for rapid proteomics tools development
    • Kessner, D., Chambers, M., Burke, R., Agus, D. & Mallick, P. ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 24, 2534-2536 (2008).
    • (2008) Bioinformatics , vol.24 , pp. 2534-2536
    • Kessner, D.1    Chambers, M.2    Burke, R.3    Agus, D.4    Mallick, P.5
  • 36
    • 42249108173 scopus 로고    scopus 로고
    • OpenMS: An open-source software framework for mass spectrometry
    • Sturm, M. et al. OpenMS: an open-source software framework for mass spectrometry. BMC Bioinformatics 9, 163 (2008).
    • (2008) BMC Bioinformatics , vol.9 , pp. 163
    • Sturm, M.1
  • 37
    • 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 , pp. D1063-D1069
    • Vizcaíno, J.A.1
  • 38
    • 11244346557 scopus 로고    scopus 로고
    • Variance stabilization applied to microarray data calibration and to the quantification of differential expression
    • Huber, W., von Heydebreck, A., Sultmann, H., Poustka, A. & Vingron, M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18 (suppl. 1), S96-S104 (2002).
    • (2002) Bioinformatics , vol.18 , pp. S96-S104
    • Huber, W.1    Von Heydebreck, A.2    Sultmann, H.3    Poustka, A.4    Vingron, M.5
  • 39
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • 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).
    • (2003) Bioinformatics , vol.19 , 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.