메뉴 건너뛰기




Volumn 7, Issue , 2017, Pages

Towards reproducible MRM based biomarker discovery using dried blood spots

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; PEPTIDE;

EID: 85016231345     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep45178     Document Type: Article
Times cited : (31)

References (41)
  • 1
    • 67650432879 scopus 로고    scopus 로고
    • The fundamental flaws of immunoassays and potential solutions using tandem mass spectrometry
    • Hoofnagle, A. N. & Wener, M. H. The fundamental flaws of immunoassays and potential solutions using tandem mass spectrometry. Journal of immunological methods 347, 3-11, doi: 10.1016/j.jim.2009.06.003 (2009).
    • (2009) Journal of Immunological Methods , vol.347 , pp. 3-11
    • Hoofnagle, A.N.1    Wener, M.H.2
  • 2
    • 84947922069 scopus 로고    scopus 로고
    • Commercialisation of biomarker tests for mental illnesses: Advances and obstacles
    • Chan, M. K., Cooper, J. D. & Bahn, S.commercialisation of Biomarker Tests for Mental Illnesses: Advances and Obstacles. Trends in biotechnology 33, 712-723, doi: 10.1016/j.tibtech.2015.09.010 (2015).
    • (2015) Trends in Biotechnology , vol.33 , pp. 712-723
    • Chan, M.K.1    Cooper, J.D.2    Bahn, S.3
  • 3
    • 84941737510 scopus 로고    scopus 로고
    • Applications of targeted proteomics in systems biology and translational medicine
    • Ebhardt, H. A., Root, A., Sander, C. & Aebersold, R. Applications of targeted proteomics in systems biology and translational medicine. Proteomics 15, 3193-3208, doi: 10.1002/pmic.201500004 (2015).
    • (2015) Proteomics , vol.15 , pp. 3193-3208
    • Ebhardt, H.A.1    Root, A.2    Sander, C.3    Aebersold, R.4
  • 4
    • 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, doi: 10.1038/nbt.1661 (2010).
    • (2010) Nat Biotechnol , vol.28 , pp. 710-721
    • Domon, B.1    Aebersold, R.2
  • 5
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteomewide protein quantification
    • Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteomewide protein quantification. Nat Biotechnol 26, 1367-1372, doi: 10.1038/nbt.1511 (2008).
    • (2008) Nat Biotechnol , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 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, doi: 10.1038/msb.2008.61 (2008).
    • (2008) Mol Syst Biol , vol.4 , pp. 222
    • Lange, V.1    Picotti, P.2    Domon, B.3    Aebersold, R.4
  • 7
    • 84894412736 scopus 로고    scopus 로고
    • Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies
    • Surinova, S. et al. Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies. Nat Protoc 8, 1602-1619, doi: 10.1038/nprot.2013.091 (2013).
    • (2013) Nat Protoc , vol.8 , pp. 1602-1619
    • Surinova, S.1
  • 8
    • 84881605158 scopus 로고    scopus 로고
    • Comparison of proteins in whole blood and dried blood spot samples by LC/MS/MS
    • Chambers, A. G., Percy, A. J., Hardie, D. B. & Borchers, C. H.comparison of proteins in whole blood and dried blood spot samples by LC/MS/MS. J Am Soc Mass Spectrom 24, 1338-1345, doi: 10.1007/s13361-013-0678-x (2013).
    • (2013) J Am Soc Mass Spectrom , vol.24 , pp. 1338-1345
    • Chambers, A.G.1    Percy, A.J.2    Hardie, D.B.3    Borchers, C.H.4
  • 9
    • 84946012492 scopus 로고    scopus 로고
    • Multiple reaction monitoring enables precise quantification of 97 proteins in dried blood spots
    • Chambers, A. G., Percy, A. J., Yang, J. & Borchers, C. H. Multiple Reaction Monitoring Enables Precise Quantification of 97 Proteins in Dried Blood Spots. Mol Cell Proteomics 14, 3094-3104, doi: 10.1074/mcp.O115.049957 (2015).
    • (2015) Mol Cell Proteomics , vol.14 , pp. 3094-3104
    • Chambers, A.G.1    Percy, A.J.2    Yang, J.3    Borchers, C.H.4
  • 10
    • 84874610996 scopus 로고    scopus 로고
    • Multiplexed quantitation of endogenous proteins in dried blood spots by multiple reaction monitoring-mass spectrometry
    • Chambers, A. G., Percy, A. J., Yang, J., Camenzind, A. G. & Borchers, C. H. Multiplexed quantitation of endogenous proteins in dried blood spots by multiple reaction monitoring-mass spectrometry. Mol Cell Proteomics 12, 781-791, doi: 10.1074/mcp.M112.022442 (2013).
    • (2013) Mol Cell Proteomics , vol.12 , pp. 781-791
    • Chambers, A.G.1    Percy, A.J.2    Yang, J.3    Camenzind, A.G.4    Borchers, C.H.5
  • 11
    • 84880881373 scopus 로고    scopus 로고
    • Dried blood as an alternative to plasma or serum for Trypanosoma cruzi IgG detection in screening programs
    • Holguin, A. et al. Dried blood as an alternative to plasma or serum for Trypanosoma cruzi IgG detection in screening programs. Clin Vaccine Immunol 20, 1197-1202, doi: 10.1128/CVI.00221-13 (2013).
    • (2013) Clin Vaccine Immunol , vol.20 , pp. 1197-1202
    • Holguin, A.1
  • 12
    • 84912524708 scopus 로고    scopus 로고
    • The utility of dried blood spots for proteomic studies: Looking forward to looking back
    • Ignjatovic, V., Pitt, J., Monagle, P. & Craig, J. M. The utility of dried blood spots for proteomic studies: looking forward to looking back. Proteomics Clin Appl 8, 896-900, doi: 10.1002/prca.201400042 (2014).
    • (2014) Proteomics Clin Appl , vol.8 , pp. 896-900
    • Ignjatovic, V.1    Pitt, J.2    Monagle, P.3    Craig, J.M.4
  • 13
    • 78650151240 scopus 로고    scopus 로고
    • Stable-isotope dilution LC-MS for quantitative biomarker analysis
    • Ciccimaro, E. & Blair, I. A. Stable-isotope dilution LC-MS for quantitative biomarker analysis. Bioanalysis 2, 311-341, doi: 10.4155/ bio.09.185 (2010).
    • (2010) Bioanalysis , vol.2 , pp. 311-341
    • Ciccimaro, E.1    Blair, I.A.2
  • 14
    • 84864586482 scopus 로고    scopus 로고
    • Multiple reaction monitoring (MRM): Principles and application to coronary artery disease
    • Cohen Freue, G. V. & Borchers, C. H. Multiple reaction monitoring (MRM): principles and application to coronary artery disease. Circulation. Cardiovascular genetics 5, 378, doi: 10.1161/CIRCGENETICS.111.959528 (2012).
    • (2012) Circulation. Cardiovascular Genetics , vol.5 , pp. 378
    • Cohen Freue, G.V.1    Borchers, C.H.2
  • 15
    • 84899997891 scopus 로고    scopus 로고
    • PeptidePicker: A scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments
    • Mohammed, Y. et al. PeptidePicker: a scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments. J Proteomics 106, 151-161, doi: 10.1016/j.jprot.2014.04.018 (2014).
    • (2014) J Proteomics , vol.106 , pp. 151-161
    • Mohammed, Y.1
  • 16
    • 85008245572 scopus 로고    scopus 로고
    • PeptideTracker: A knowledge base for collecting and storing information on protein concentrations in biological tissues
    • Mohammed, Y. et al. PeptideTracker: A knowledge base for collecting and storing information on protein concentrations in biological tissues. Proteomics, doi: 10.1002/pmic.201600210 (2016).
    • (2016) Proteomics
    • Mohammed, Y.1
  • 17
    • 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, doi: 10.1016/j.cell.2016.06.041 (2016).
    • (2016) Cell , vol.166 , pp. 766-778
    • Kusebauch, U.1
  • 18
    • 84907958189 scopus 로고    scopus 로고
    • Using peptideAtlas, SRMAtlas, and PASSEL: Comprehensive resources for discovery and targeted proteomics
    • Kusebauch, U. et al. Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. Current protocols in bioinformatics 46, 13 25 11-28, doi: 10.1002/0471250953.bi1325s46 (2014).
    • (2014) Current Protocols in Bioinformatics , vol.46 , Issue.13-25 , pp. 11-28
    • Kusebauch, U.1
  • 19
    • 84896371874 scopus 로고    scopus 로고
    • Detection of circulating tumor DNA in early- and late-stage human malignancies
    • Bettegowda, C. et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Science translational medicine 6, 224ra224, doi: 10.1126/scitranslmed.3007094 (2014).
    • (2014) Science Translational Medicine , vol.6 , pp. 224ra224
    • Bettegowda, C.1
  • 21
    • 0032832768 scopus 로고    scopus 로고
    • The use of the dried blood spot sample in epidemiological studies
    • Parker, S. P. & Cubitt, W. D. The use of the dried blood spot sample in epidemiological studies. Journal of clinical pathology 52, 633-639 (1999).
    • (1999) Journal of Clinical Pathology , vol.52 , pp. 633-639
    • Parker, S.P.1    Cubitt, W.D.2
  • 22
    • 79952526949 scopus 로고    scopus 로고
    • Utility of dried blood spot sampling and storage for increased stability of photosensitive compounds
    • Bowen, C. L., Hemberger, M. D., Kehler, J. R. & Evans, C. A. Utility of dried blood spot sampling and storage for increased stability of photosensitive compounds. Bioanalysis 2, 1823-1828, doi: 10.4155/bio.10.142 (2010).
    • (2010) Bioanalysis , vol.2 , pp. 1823-1828
    • Bowen, C.L.1    Hemberger, M.D.2    Kehler, J.R.3    Evans, C.A.4
  • 23
    • 0035016950 scopus 로고    scopus 로고
    • Use of filter paper for the collection and analysis of human whole blood specimens
    • Mei, J. V., Alexander, J. R., Adam, B. W. & Hannon, W. H. Use of filter paper for the collection and analysis of human whole blood specimens. The Journal of nutrition 131, 1631S-1636S (2001).
    • (2001) The Journal of Nutrition , vol.131 , pp. 1631S-1636S
    • Mei, J.V.1    Alexander, J.R.2    Adam, B.W.3    Hannon, W.H.4
  • 24
    • 75449123150 scopus 로고
    • A simple phenylalanine method for detecting phenylketonuria in large populations of newborn infants
    • Guthrie, R. & Susi, A. A Simple Phenylalanine Method for Detecting Phenylketonuria in Large Populations of Newborn Infants. Pediatrics 32, 338-343 (1963).
    • (1963) Pediatrics , vol.32 , pp. 338-343
    • Guthrie, R.1    Susi, A.2
  • 25
    • 84872582592 scopus 로고    scopus 로고
    • Dried blood spots: Analysis and applications
    • Demirev, P. A. Dried blood spots: analysis and applications. Anal Chem 85, 779-789, doi: 10.1021/ac303205m (2013).
    • (2013) Anal Chem , vol.85 , pp. 779-789
    • Demirev, P.A.1
  • 26
    • 75149186915 scopus 로고    scopus 로고
    • Dried blood spot sampling in combination with LC-MS/MS for quantitative analysis of small molecules
    • Li, W. & Tse, F. L. Dried blood spot sampling in combination with LC-MS/MS for quantitative analysis of small molecules. Biomedical chromatography: BMC 24, 49-65, doi: 10.1002/bmc.1367 (2010).
    • (2010) Biomedical Chromatography: BMC , vol.24 , pp. 49-65
    • Li, W.1    Tse, F.L.2
  • 27
    • 84868228513 scopus 로고    scopus 로고
    • Top-down proteomics and direct surface sampling of neonatal dried blood spots: Diagnosis of unknown hemoglobin variants
    • Edwards, R. L., Griffiths, P., Bunch, J. & Cooper, H. J. Top-down proteomics and direct surface sampling of neonatal dried blood spots: diagnosis of unknown hemoglobin variants. J Am Soc Mass Spectrom 23, 1921-1930, doi: 10.1007/s13361-012-0477-9 (2012).
    • (2012) J Am Soc Mass Spectrom , vol.23 , pp. 1921-1930
    • Edwards, R.L.1    Griffiths, P.2    Bunch, J.3    Cooper, H.J.4
  • 28
    • 84880831287 scopus 로고    scopus 로고
    • Dried blood spot proteomics: Surface extraction of endogenous proteins coupled with automated sample preparation and mass spectrometry analysis
    • Martin, N. J., Bunch, J. & Cooper, H. J. Dried blood spot proteomics: surface extraction of endogenous proteins coupled with automated sample preparation and mass spectrometry analysis. J Am Soc Mass Spectrom 24, 1242-1249, doi: 10.1007/s13361-013- 0658-1 (2013).
    • (2013) J Am Soc Mass Spectrom , vol.24 , pp. 1242-1249
    • Martin, N.J.1    Bunch, J.2    Cooper, H.J.3
  • 29
    • 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, doi: 10.1373/clinchem.2009.138420 (2010).
    • (2010) Clin Chem , vol.56 , pp. 291-305
    • Abbatiello, S.E.1    Mani, D.R.2    Keshishian, H.3    Carr, S.A.4
  • 31
    • 71049137289 scopus 로고    scopus 로고
    • Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma
    • Kuzyk, M. A. et al. Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma. Mol Cell Proteomics 8, 1860-1877, doi: 10.1074/mcp.M800540-MCP200 (2009).
    • (2009) Mol Cell Proteomics , vol.8 , pp. 1860-1877
    • Kuzyk, M.A.1
  • 32
    • 78649834299 scopus 로고    scopus 로고
    • Simultaneous quantification of apolipoprotein A-I and apolipoprotein B by liquidchromatography- multiple- reaction-monitoring mass spectrometry
    • Agger, S. A., Marney, L. C. & Hoofnagle, A. N. Simultaneous quantification of apolipoprotein A-I and apolipoprotein B by liquidchromatography- multiple- reaction-monitoring mass spectrometry. Clin Chem 56, 1804-1813, doi: 10.1373/clinchem.2010.152264 (2010).
    • (2010) Clin Chem , vol.56 , pp. 1804-1813
    • Agger, S.A.1    Marney, L.C.2    Hoofnagle, A.N.3
  • 33
    • 84883189721 scopus 로고    scopus 로고
    • Development of MRM-based assays for the absolute quantitation of plasma proteins
    • Kuzyk, M. A., Parker, C. E., Domanski, D. & Borchers, C. H. Development of MRM-based assays for the absolute quantitation of plasma proteins. Methods Mol Biol 1023, 53-82, doi: 10.1007/978-1-4614-7209-4-4 (2013).
    • (2013) Methods Mol Biol , vol.1023 , pp. 53-82
    • Kuzyk, M.A.1    Parker, C.E.2    Domanski, D.3    Borchers, C.H.4
  • 34
    • 68549102013 scopus 로고    scopus 로고
    • Proteome maps of the main human peripheral blood constituents
    • Haudek, V. J. et al. Proteome maps of the main human peripheral blood constituents. J Proteome Res 8, 3834-3843, doi: 10.1021/ pr801085g (2009).
    • (2009) J Proteome Res , vol.8 , pp. 3834-3843
    • Haudek, V.J.1
  • 35
    • 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, doi: 10.1093/bioinformatics/btq054 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 966-968
    • MacLean, B.1
  • 36
    • 84952712991 scopus 로고    scopus 로고
    • A language and environment for statistical computing
    • R Core Team.:, Vienna, Austria.
    • R Core Team.: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria., https://www.R-project.org/ (2015).
    • (2015) R Foundation for Statistical Computing
  • 37
    • 0036376993 scopus 로고    scopus 로고
    • Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments
    • Dudoit, S., Yang, Y. H., Callow, M. J. & Speed, T. P. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Stat Sinica 12, 111-139 (2002).
    • (2002) Stat Sinica , vol.12 , pp. 111-139
    • Dudoit, S.1    Yang, Y.H.2    Callow, M.J.3    Speed, T.P.4
  • 38
    • 85016244082 scopus 로고
    • Controlling the false discovery rate - A practical and powerful approach to multiple testing
    • Benjamini, Y. & Hochberg, Y. Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. J Roy Stat Soc B Met 57, 289-300 (1995).
    • (1995) J Roy Stat Soc B Met , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 39
    • 84903893560 scopus 로고    scopus 로고
    • Head-to-head randomised, crossover study of oral versus subcutaneous methotrexate in patients with rheumatoid arthritis: Drug-exposure limitations of oral methotrexate at doses> /= 15 mg may be overcome with subcutaneous administration. Ann
    • Schiff, M. H., Jaffe, J. S. & Freundlich, B. Head-to-head, randomised, crossover study of oral versus subcutaneous methotrexate in patients with rheumatoid arthritis: drug-exposure limitations of oral methotrexate at doses> /= 15 mg may be overcome with subcutaneous administration. Ann Rheum Dis 73, 1549-1551, doi: 10.1136/annrheumdis-2014-205228 (2014).
    • (2014) Rheum Dis , vol.73 , pp. 1549-1551
    • Schiff, M.H.1    Jaffe, J.S.2    Freundlich, B.3
  • 40
    • 84908219488 scopus 로고
    • Statistical methods for assessing agreement between two methods of clinical measurement
    • Bland, J. M. & Altman, D. G. Statistical methods for assessing agreement between two methods of clinical measurement. Lancet 1, 307-310 (1986).
    • (1986) Lancet , vol.1 , pp. 307-310
    • Bland, J.M.1    Altman, D.G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.