메뉴 건너뛰기




Volumn 9, Issue 3-4, 2015, Pages 423-431

Recent advances in targeted proteomics for clinical applications

Author keywords

Biomarker; High resolution and accurate mass; Parallel reaction monitoring; Quadrupole orbitrap; SRM; Targeted proteomics

Indexed keywords

BIOLOGICAL MARKER; LACTATE DEHYDROGENASE; OSTEOPONTIN;

EID: 84928054762     PISSN: 18628346     EISSN: 18628354     Source Type: Journal    
DOI: 10.1002/prca.201400136     Document Type: Note
Times cited : (55)

References (37)
  • 1
    • 0001644020 scopus 로고    scopus 로고
    • The human plasma proteome: history, character, and diagnostic prospects
    • Anderson, N. L., Anderson, N. G., The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics 2002, 1, 845-867.
    • (2002) Mol. Cell. Proteomics , vol.1 , pp. 845-867
    • Anderson, N.L.1    Anderson, N.G.2
  • 2
    • 84906716279 scopus 로고    scopus 로고
    • Mass spectrometry based biomarker discovery, verification, and validation-quality assurance and control of protein biomarker assays
    • Parker, C. E., Borchers, C. H., Mass spectrometry based biomarker discovery, verification, and validation-quality assurance and control of protein biomarker assays. Mol. Oncol. 2014, 8, 840-858.
    • (2014) Mol. Oncol. , vol.8 , pp. 840-858
    • Parker, C.E.1    Borchers, C.H.2
  • 3
    • 84895555123 scopus 로고    scopus 로고
    • Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach
    • Carr, S. A., Abbatiello, S. E., Ackermann, B. L., Borchers, C. et al., Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol. Cell. Proteomics 2014, 13, 907-917.
    • (2014) Mol. Cell. Proteomics , vol.13 , pp. 907-917
    • Carr, S.A.1    Abbatiello, S.E.2    Ackermann, B.L.3    Borchers, C.4
  • 4
    • 33747030845 scopus 로고    scopus 로고
    • Protein biomarker discovery and validation: the long and uncertain path to clinical utility
    • Rifai, N., Gillette, M. A., Carr, S. A., Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol. 2006, 24, 971-983.
    • (2006) Nat. Biotechnol. , vol.24 , pp. 971-983
    • Rifai, N.1    Gillette, M.A.2    Carr, S.A.3
  • 5
    • 77951757994 scopus 로고    scopus 로고
    • Multiplex assays for biomarker research and clinical application: translational science coming of age
    • Fu, Q., Schoenhoff, F. S., Savage, W. J., Zhang, P., Van Eyk, J. E., Multiplex assays for biomarker research and clinical application: translational science coming of age. Proteom. Clin. Appl. 2010, 4, 271-284.
    • (2010) Proteom. Clin. Appl. , vol.4 , pp. 271-284
    • Fu, Q.1    Schoenhoff, F.S.2    Savage, W.J.3    Zhang, P.4    Van Eyk, J.E.5
  • 6
    • 84891109918 scopus 로고    scopus 로고
    • Cross-reactivity in antibody microarrays and multiplexed sandwich assays: shedding light on the dark side of multiplexing
    • Juncker, D., Bergeron, S., Laforte, V., Li, H., Cross-reactivity in antibody microarrays and multiplexed sandwich assays: shedding light on the dark side of multiplexing. Curr. Opin. Chem. Biol. 2014, 18, 29-37.
    • (2014) Curr. Opin. Chem. Biol. , vol.18 , pp. 29-37
    • Juncker, D.1    Bergeron, S.2    Laforte, V.3    Li, H.4
  • 7
    • 79952540456 scopus 로고    scopus 로고
    • Selected reaction monitoring applied to proteomics
    • Gallien, S., Duriez, E., Domon, B., Selected reaction monitoring applied to proteomics. J. Mass Spectrom. 2011, 46, 298-312.
    • (2011) J. Mass Spectrom. , vol.46 , pp. 298-312
    • Gallien, S.1    Duriez, E.2    Domon, B.3
  • 8
    • 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 2012, 9, 555-566.
    • (2012) Nat. Methods , vol.9 , pp. 555-566
    • Picotti, P.1    Aebersold, R.2
  • 9
    • 84871420249 scopus 로고    scopus 로고
    • Considerations on selected reaction monitoring experiments: implications for the selectivity and accuracy of measurements
    • Domon, B., Considerations on selected reaction monitoring experiments: implications for the selectivity and accuracy of measurements. Proteom. Clin. Appl. 2012, 6, 609-614.
    • (2012) Proteom. Clin. Appl. , vol.6 , pp. 609-614
    • Domon, B.1
  • 10
    • 35348863892 scopus 로고    scopus 로고
    • High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites
    • Stahl-Zeng, J., Lange, V., Ossola, R., Eckhardt, K. et al., High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol. Cell. Proteomics 2007, 6, 1809-1817.
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 1809-1817
    • Stahl-Zeng, J.1    Lange, V.2    Ossola, R.3    Eckhardt, K.4
  • 11
    • 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 2007, 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
  • 12
    • 84870656540 scopus 로고    scopus 로고
    • Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer
    • Gallien, S., Duriez, E., Crone, C., Kellmann, M. et al., Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer. Mol. Cell. Proteomics 2012, 11, 1709-1723.
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. 1709-1723
    • Gallien, S.1    Duriez, E.2    Crone, C.3    Kellmann, M.4
  • 13
    • 84869233177 scopus 로고    scopus 로고
    • Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics
    • Peterson, A. C., Russell, J. D., Bailey, D. J., Westphall, M. S., Coon, J. J., Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol. Cell. Proteomics 2012, 11, 1475-1488.
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. 1475-1488
    • Peterson, A.C.1    Russell, J.D.2    Bailey, D.J.3    Westphall, M.S.4    Coon, J.J.5
  • 14
    • 67449097825 scopus 로고    scopus 로고
    • SISCAPA peptide enrichment on magnetic beads using an in-line bead trap device
    • Anderson, N. L., Jackson, A., Smith, D., Hardie, D. et al., SISCAPA peptide enrichment on magnetic beads using an in-line bead trap device. Mol. Cell. Proteomics 2009, 8, 995-1005.
    • (2009) Mol. Cell. Proteomics , vol.8 , pp. 995-1005
    • Anderson, N.L.1    Jackson, A.2    Smith, D.3    Hardie, D.4
  • 15
    • 55049086987 scopus 로고    scopus 로고
    • Use of an immunoaffinity-mass spectrometry-based approach for the quantification of protein biomarkers from serum samples of lung cancer patients
    • Nicol, G. R., Han, M., Kim, J., Birse, C. E. et al., Use of an immunoaffinity-mass spectrometry-based approach for the quantification of protein biomarkers from serum samples of lung cancer patients. Mol. Cell. Proteomics 2008, 7, 1974-1982.
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 1974-1982
    • Nicol, G.R.1    Han, M.2    Kim, J.3    Birse, C.E.4
  • 16
    • 84902168242 scopus 로고    scopus 로고
    • An automated, high-throughput method for targeted quantification of intact insulin and its therapeutic analogs in human serum or plasma coupling mass spectrometric immunoassay with high resolution and accurate mass detection (MSIA-HR/AM)
    • Peterman, S., Niederkofler, E. E., Phillips, D. A., Krastins, B. et al., An automated, high-throughput method for targeted quantification of intact insulin and its therapeutic analogs in human serum or plasma coupling mass spectrometric immunoassay with high resolution and accurate mass detection (MSIA-HR/AM). Proteomics 2014, 14, 1445-1456.
    • (2014) Proteomics , vol.14 , pp. 1445-1456
    • Peterman, S.1    Niederkofler, E.E.2    Phillips, D.A.3    Krastins, B.4
  • 17
    • 23044507211 scopus 로고    scopus 로고
    • Quantitative MS for proteomics: teaching a new dog old tricks
    • MacCoss, M. J., Matthews, D. E., Quantitative MS for proteomics: teaching a new dog old tricks. Anal. Chem. 2005, 77, 294A-302A.
    • (2005) Anal. Chem. , vol.77 , pp. 294A-302A
    • MacCoss, M.J.1    Matthews, D.E.2
  • 18
    • 10244256354 scopus 로고    scopus 로고
    • Isotope dilution-mass spectrometric quantification of specific proteins: model application with apolipoprotein A-I
    • Barr, J. R., Maggio, V. L., Patterson, D. G., Jr., Cooper, G. R. et al., Isotope dilution-mass spectrometric quantification of specific proteins: model application with apolipoprotein A-I. Clin. Chem. 1996, 42, 1676-1682.
    • (1996) Clin. Chem. , vol.42 , pp. 1676-1682
    • Barr, J.R.1    Maggio, V.L.2    Patterson Jr, D.G.3    Cooper, G.R.4
  • 19
    • 84903542932 scopus 로고    scopus 로고
    • CPTAC Assay Portal: a repository of targeted proteomic assays
    • Whiteaker, J. R., Halusa, G. N., Hoofnagle, A. N., Sharma, V. et al., CPTAC Assay Portal: a repository of targeted proteomic assays. Nat. Methods 2014, 11, 703-704.
    • (2014) Nat. Methods , vol.11 , pp. 703-704
    • Whiteaker, J.R.1    Halusa, G.N.2    Hoofnagle, A.N.3    Sharma, V.4
  • 20
    • 54049095667 scopus 로고    scopus 로고
    • A database of mass spectrometric assays for the yeast proteome
    • Picotti, P., Lam, H., Campbell, D., Deutsch, E. W. et al., A database of mass spectrometric assays for the yeast proteome. Nat. Methods 2008, 5, 913-914.
    • (2008) Nat. Methods , vol.5 , pp. 913-914
    • Picotti, P.1    Lam, H.2    Campbell, D.3    Deutsch, E.W.4
  • 21
    • 43049127826 scopus 로고    scopus 로고
    • PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
    • Deutsch, E. W., Lam, H., Aebersold, R., PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 2008, 9, 429-434.
    • (2008) EMBO Rep. , vol.9 , pp. 429-434
    • Deutsch, E.W.1    Lam, H.2    Aebersold, R.3
  • 22
    • 33644875983 scopus 로고    scopus 로고
    • PRIDE: a public repository of protein and peptide identifications for the proteomics community
    • Jones, P., Cote, R. G., Martens, L., Quinn, A. F. et al., PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucl. Acids Res. 2006, 34, D659-D663.
    • (2006) Nucl. Acids Res. , vol.34 , pp. D659-D663
    • Jones, P.1    Cote, R.G.2    Martens, L.3    Quinn, A.F.4
  • 23
    • 11144320641 scopus 로고    scopus 로고
    • Open source system for analyzing, validating, and storing protein identification data
    • Craig, R., Cortens, J. P., Beavis, R. C., Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res. 2004, 3, 1234-1242.
    • (2004) J. Proteome Res. , vol.3 , pp. 1234-1242
    • Craig, R.1    Cortens, J.P.2    Beavis, R.C.3
  • 24
    • 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. 2010, 56, 291-305.
    • (2010) Clin. Chem. , vol.56 , pp. 291-305
    • Abbatiello, S.E.1    Mani, D.R.2    Keshishian, H.3    Carr, S.A.4
  • 25
    • 84877813399 scopus 로고    scopus 로고
    • Selectivity of LC-MS/MS analysis: implication for proteomics experiments
    • Gallien, S., Duriez, E., Demeure, K., Domon, B., Selectivity of LC-MS/MS analysis: implication for proteomics experiments. J. Proteomics 2013, 81, 148-158.
    • (2013) J. Proteomics , vol.81 , pp. 148-158
    • Gallien, S.1    Duriez, E.2    Demeure, K.3    Domon, B.4
  • 26
    • 77951965920 scopus 로고    scopus 로고
    • Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
    • MacLean, B., Tomazela, D. M., Shulman, N., Chambers, M. et al., Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 2010, 26, 966-968.
    • (2010) Bioinformatics , vol.26 , pp. 966-968
    • MacLean, B.1    Tomazela, D.M.2    Shulman, N.3    Chambers, M.4
  • 27
    • 84875604405 scopus 로고    scopus 로고
    • Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics
    • Mani, D. R., Abbatiello, S. E., Carr, S. A., Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics. BMC Bioinformatics 2012, 13 Suppl 16, S9.
    • (2012) BMC Bioinformatics , vol.13 , pp. S9
    • Mani, D.R.1    Abbatiello, S.E.2    Carr, S.A.3
  • 28
    • 79955595074 scopus 로고    scopus 로고
    • mProphet: automated data processing and statistical validation for large-scale SRM experiments
    • Reiter, L., Rinner, O., Picotti, P., Huttenhain, R. et al., mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat. Methods 2011, 8, 430-435.
    • (2011) Nat. Methods , vol.8 , pp. 430-435
    • Reiter, L.1    Rinner, O.2    Picotti, P.3    Huttenhain, R.4
  • 29
    • 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. et al., MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. Bioinformatics 2014, 30, 2524-2526.
    • (2014) Bioinformatics , vol.30 , pp. 2524-2526
    • Choi, M.1    Chang, C.Y.2    Clough, T.3    Broudy, D.4
  • 31
    • 70649087115 scopus 로고    scopus 로고
    • Multiple reaction monitoring cubed for protein quantification at the low nanogram/milliliter level in nondepleted human serum
    • Fortin, T., Salvador, A., Charrier, J. P., Lenz, C. et al., Multiple reaction monitoring cubed for protein quantification at the low nanogram/milliliter level in nondepleted human serum. Anal. Chem. 2009, 81, 9343-9352.
    • (2009) Anal. Chem. , vol.81 , pp. 9343-9352
    • Fortin, T.1    Salvador, A.2    Charrier, J.P.3    Lenz, C.4
  • 32
    • 67650901565 scopus 로고    scopus 로고
    • Validated quantitation method for a peptide in rat serum using liquid chromatography/high-field asymmetric waveform ion mobility spectrometry
    • Klaassen, T., Szwandt, S., Kapron, J. T., Roemer, A., Validated quantitation method for a peptide in rat serum using liquid chromatography/high-field asymmetric waveform ion mobility spectrometry. Rapid Commun. Mass Spectrom. 2009, 23, 2301-2306.
    • (2009) Rapid Commun. Mass Spectrom. , vol.23 , pp. 2301-2306
    • Klaassen, T.1    Szwandt, S.2    Kapron, J.T.3    Roemer, A.4
  • 33
    • 84896954847 scopus 로고    scopus 로고
    • Technical considerations for large-scale parallel reaction monitoring analysis
    • Gallien, S., Bourmaud, A., Kim, S. Y., Domon, B., Technical considerations for large-scale parallel reaction monitoring analysis. J. Proteomics 2014, 100, 147-159.
    • (2014) J. Proteomics , vol.100 , pp. 147-159
    • Gallien, S.1    Bourmaud, A.2    Kim, S.Y.3    Domon, B.4
  • 34
    • 84975901444 scopus 로고    scopus 로고
    • Eyers, C. E., Gaskell, S. J. (Eds.), Royal Society of Chemistry, London, UK.
    • Bourmaud, A., Gallien, S., Domon, B., in: Eyers, C. E., Gaskell, S. J. (Eds.), Quantitative Proteomics, Royal Society of Chemistry, London, UK 2014, pp. 26-47.
    • (2014) Quantitative Proteomics , pp. 26-47
    • Bourmaud, A.1    Gallien, S.2    Domon, B.3
  • 35
    • 84860866702 scopus 로고    scopus 로고
    • Highly multiplexed targeted proteomics using precise control of peptide retention time
    • Gallien, S., Peterman, S., Kiyonami, R., Souady, J. et al., Highly multiplexed targeted proteomics using precise control of peptide retention time. Proteomics 2012, 12, 1122-1133.
    • (2012) Proteomics , vol.12 , pp. 1122-1133
    • Gallien, S.1    Peterman, S.2    Kiyonami, R.3    Souady, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.