메뉴 건너뛰기




Volumn 13, Issue 8, 2013, Pages 811-825

Mass spectrometric protein maps for biomarker discovery and clinical research

Author keywords

biomarker discovery; diagnostics; digital maps; mass spectrometry; proteomics; reference maps; selected reaction monitoring; SWATH MS

Indexed keywords

CLINICAL RESEARCH; MASS SPECTROMETRY; PERSONALIZED MEDICINE; PROTEOMICS; REVIEW; WORKFLOW;

EID: 84887359663     PISSN: 14737159     EISSN: 17448352     Source Type: Journal    
DOI: 10.1586/14737159.2013.845089     Document Type: Review
Times cited : (105)

References (100)
  • 2
    • 33747030845 scopus 로고    scopus 로고
    • Protein biomarker discovery and validation: The long and uncertain path to clinical utility
    • Rifai N, Gillette MA, Carr SA. Protein biomarker discovery and validation: The long and uncertain path to clinical utility. Nat. Biotechnol. 24(8), 971-983 (2006
    • (2006) Nat. Biotechnol , vol.24 , Issue.8 , pp. 971-983
    • Rifai, N.1    Gillette, M.A.2    Carr, S.A.3
  • 3
    • 41649102043 scopus 로고    scopus 로고
    • The cancer biomarker problem
    • Sawyers CL. The cancer biomarker problem. Nature 452(7187), 548-552 (2008
    • (2008) Nature , vol.452 , Issue.7187 , pp. 548-552
    • Sawyers, C.L.1
  • 4
    • 0141455186 scopus 로고    scopus 로고
    • TNM: Evolution and relation to other prognostic factors
    • Sobin LH. TNM: Evolution and relation to other prognostic factors. Semin. Surg. Oncol. 21(1), 3-7 (2003
    • (2003) Semin. Surg. Oncol , vol.21 , Issue.1 , pp. 3-7
    • Sobin, L.H.1
  • 5
    • 77954827460 scopus 로고    scopus 로고
    • The path to personalized medicine
    • Hamburg MA, Collins FS. The path to personalized medicine. N. Engl. J. Med. 363(4), 301-304 (2010
    • (2010) N. Engl. J. Med , vol.363 , Issue.4 , pp. 301-304
    • Hamburg, M.A.1    Collins, F.S.2
  • 7
    • 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(7), 710-721 (2010
    • (2010) Nat. Biotechnol , vol.28 , Issue.7 , pp. 710-721
    • Domon, B.1    Aebersold, R.2
  • 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 9(6), 555-566 (2012
    • (2012) Nat. Methods , vol.9 , Issue.6 , pp. 555-566
    • Picotti, P.1    Aebersold, R.2
  • 10
    • 84863923380 scopus 로고    scopus 로고
    • Reproducible quantification of cancer-Associated proteins in body fluids using targeted proteomics
    • Huttenhain R, Soste M, Selevsek N et al. Reproducible quantification of cancer-Associated proteins in body fluids using targeted proteomics. Sci. Transl. Med. 4(142), 142-194 (2012
    • (2012) Sci. Transl. Med , vol.4 , Issue.142 , pp. 142-194
    • Huttenhain, R.1    Soste, M.2    Selevsek, N.3
  • 11
    • 80255124868 scopus 로고    scopus 로고
    • Novel prognostic markers in the serum of patients with castration-resistant prostate cancer derived from quantitative analysis of the pten conditional knockout mouse proteome
    • Kalin M, Cima I, Schiess R et al. Novel prognostic markers in the serum of patients with castration-resistant prostate cancer derived from quantitative analysis of the pten conditional knockout mouse proteome. Eur. Urol. 60(6), 1235-1243 (2011
    • (2011) Eur. Urol , vol.60 , Issue.6 , pp. 1235-1243
    • Kalin, M.1    Cima, I.2    Schiess, R.3
  • 12
    • 79952751238 scopus 로고    scopus 로고
    • Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer
    • Cima I, Schiess R, Wild P et al. Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer. Proc. Natl Acad. Sci. USA 108(8), 3342-3347 (2011
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , Issue.8 , pp. 3342-3347
    • Cima, I.1    Schiess, R.2    Wild, P.3
  • 13
    • 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
    • Gillet LC, Navarro P, Tate S 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(6), O111 016717 (2012
    • (2012) Mol. Cell. Proteomics , vol.11 , Issue.6
    • Gillet, L.C.1    Navarro, P.2    Tate, S.3
  • 14
    • 79955595074 scopus 로고    scopus 로고
    • MProphet: Automated data processing and statistical validation for large-scale SRM experiments
    • Reiter L, Rinner O, Picotti P et al. mProphet: Automated data processing and statistical validation for large-scale SRM experiments. Nat. Methods 8(5), 430-435 (2011
    • (2011) Nat. Methods , vol.8 , Issue.5 , pp. 430-435
    • Reiter, L.1    Rinner, O.2    Picotti, P.3
  • 15
    • 84864697164 scopus 로고    scopus 로고
    • The failure of protein cancer biomarkers to reach the clinic: Why, and what can be done to address the problem?
    • Diamandis EP. The failure of protein cancer biomarkers to reach the clinic: Why, and what can be done to address the problem? BMC Med. 10, 87 (2012
    • (2012) BMC Med , vol.10 , pp. 87
    • Diamandis, E.P.1
  • 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 TA, Abbatiello SE, Schilling B et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat. Biotechnol. 27(7), 633-641 (2009
    • (2009) Nat. Biotechnol , vol.27 , Issue.7 , pp. 633-641
    • Addona, T.A.1    Abbatiello, S.E.2    Schilling, B.3
  • 17
    • 84871919116 scopus 로고    scopus 로고
    • Risk stratification in prostate cancer screening
    • Roobol MJ, Carlsson SV. Risk stratification in prostate cancer screening. Nat. Rev. Urol. 10(1), 38-48 (2013
    • (2013) Nat. Rev. Urol , vol.10 , Issue.1 , pp. 38-48
    • Roobol, M.J.1    Carlsson, S.V.2
  • 18
    • 77953139647 scopus 로고    scopus 로고
    • Ovarian cancer: The duplicity of CA125 measurement
    • Karam AK, Karlan BY. Ovarian cancer: The duplicity of CA125 measurement. Nat. Rev. Clin. Oncol. 7(6), 335-339 (2010
    • (2010) Nat. Rev. Clin. Oncol , vol.7 , Issue.6 , pp. 335-339
    • Karam, A.K.1    Karlan, B.Y.2
  • 19
    • 84871264662 scopus 로고    scopus 로고
    • Trastuzumab as first-line therapy in HER2-positive metastatic breast cancer patients
    • Del Mastro L, Lambertini M, Bighin C et al. Trastuzumab as first-line therapy in HER2-positive metastatic breast cancer patients. Expert Rev. Anticancer Ther. 12(11), 1391-1405 (2012
    • (2012) Expert Rev. Anticancer Ther , vol.12 , Issue.11 , pp. 1391-1405
    • Del Mastro, L.1    Lambertini, M.2    Bighin, C.3
  • 20
    • 33645813378 scopus 로고    scopus 로고
    • Mass spectrometry and protein analysis
    • Domon B, Aebersold R. Mass spectrometry and protein analysis. Science 312(5771), 212-217 (2006
    • (2006) Science , vol.312 , Issue.5771 , pp. 212-217
    • Domon, B.1    Aebersold, R.2
  • 21
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 422(6928), 198-207 (2003
    • (2003) Nature , vol.422 , Issue.6928 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 22
    • 84864805910 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics for systems biology
    • Sabido E, Selevsek N, Aebersold R. Mass spectrometry-based proteomics for systems biology. Curr. Opin. Biotechnol. 23(4), 591-597 (2012
    • (2012) Curr. Opin. Biotechnol , vol.23 , Issue.4 , pp. 591-597
    • Sabido, E.1    Selevsek, N.2    Aebersold, R.3
  • 23
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • Elias JE, Gygi SP. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4(3), 207-214 (2007
    • (2007) Nat. Methods , vol.4 , Issue.3 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 24
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized p p b-range mass accuracies and proteome-wide protein quantification
    • Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnology 26(12), 1367-1372 (2008
    • (2008) Nat. Biotechnology , vol.26 , Issue.12 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 25
    • 76149142168 scopus 로고    scopus 로고
    • Repeatability and reproducibility in proteomic identifications by liquid chromatography-Tandem mass spectrometry
    • Tabb DL, Vega-Montoto L, Rudnick PA et al. Repeatability and reproducibility in proteomic identifications by liquid chromatography-Tandem mass spectrometry. J. Proteome Res. 9(2), 761-776 (2010
    • (2010) J. Proteome Res , vol.9 , Issue.2 , pp. 761-776
    • Tabb, D.L.1    Vega-Montoto, L.2    Rudnick, P.A.3
  • 26
    • 68349137822 scopus 로고    scopus 로고
    • Reference map for liquid chromatography-mass spectrometry-based quantitative proteomics
    • Kim YJ, Feild B, Fitzhugh W et al. Reference map for liquid chromatography-mass spectrometry-based quantitative proteomics. Anal Biochem. 393(2), 155-162 (2009
    • (2009) Anal Biochem , vol.393 , Issue.2 , pp. 155-162
    • Kim, Y.J.1    Feild, B.2    Fitzhugh, W.3
  • 27
    • 57049106891 scopus 로고    scopus 로고
    • An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures
    • Schmidt A, Gehlenborg N, Bodenmiller B et al. An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures. Mol. Cell. Proteomics 7(11), 2138-2150 (2008
    • (2008) Mol. Cell. Proteomics , vol.7 , Issue.11 , pp. 2138-2150
    • Schmidt, A.1    Gehlenborg, N.2    Bodenmiller, B.3
  • 28
    • 55049104915 scopus 로고    scopus 로고
    • Accurate inclusion mass screening: A bridge from unbiased discovery to targeted assay development for biomarker verification
    • Jaffe JD, Keshishian H, Chang B, Addona TA, Gillette MA, Carr SA. Accurate inclusion mass screening: A bridge from unbiased discovery to targeted assay development for biomarker verification. Mol. Cell. Proteomics 7(10), 1952-1962 (2008
    • (2008) Mol. Cell. Proteomics , vol.7 , Issue.10 , pp. 1952-1962
    • Jaffe, J.D.1    Keshishian, H.2    Chang, B.3    Addona, T.A.4    Gillette, M.A.5    Carr, S.A.6
  • 29
    • 84869233177 scopus 로고    scopus 로고
    • Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics
    • Peterson AC, Russell JD, Bailey DJ, Westphall MS, Coon JJ. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol. Cell. Proteomics 11(11), 1475-1488 (2012
    • (2012) Mol. Cell. Proteomics , vol.11 , Issue.11 , pp. 1475-1488
    • Peterson, A.C.1    Russell, J.D.2    Bailey, D.J.3    Westphall, M.S.4    Coon, J.J.5
  • 30
    • 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
  • 32
    • 53249098366 scopus 로고    scopus 로고
    • Building consensus spectral libraries for peptide identification in proteomics
    • Lam H, Deutsch EW, Eddes JS, Eng JK, Stein SE, Aebersold R. Building consensus spectral libraries for peptide identification in proteomics. Nat. Methods 5(10), 873-875 (2008
    • (2008) Nat. Methods , vol.5 , Issue.10 , pp. 873-875
    • Lam, H.1    Deutsch, E.W.2    Eddes, J.S.3    Eng, J.K.4    Stein, S.E.5    Aebersold, R.6
  • 33
    • 77449142021 scopus 로고    scopus 로고
    • Spectral library searching for peptide identification via tandem MS
    • Lam H, Aebersold R. Spectral library searching for peptide identification via tandem MS. Methods Mol. Biol. 604, 95-103 (2010
    • (2010) Methods Mol. Biol , vol.604 , pp. 95-103
    • Lam, H.1    Aebersold, R.2
  • 34
    • 33947366516 scopus 로고    scopus 로고
    • Development and validation of a spectral library searching method for peptide identification from MS/MS
    • Lam H, Deutsch EW, Eddes JS et al Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 7(5), 655-667 (2007
    • (2007) Proteomics , vol.7 , Issue.5 , pp. 655-667
    • Lam, H.1    Deutsch, E.W.2    Eddes, J.S.3
  • 35
    • 84873724658 scopus 로고    scopus 로고
    • A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis
    • Picotti P, Clement-Ziza M, Lam H et al. A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature 494(7436), 266-270 (2013
    • (2013) Nature , vol.494 , Issue.7436 , pp. 266-270
    • Picotti, P.1    Clement-Ziza, M.2    Lam, H.3
  • 36
    • 43049127826 scopus 로고    scopus 로고
    • PeptideAtlas: A resource for target selection for emerging targeted proteomics workflows
    • Deutsch EW, Lam H, Aebersold R. PeptideAtlas: A resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 9(5), 429-434 (2008
    • (2008) EMBO Rep , vol.9 , Issue.5 , pp. 429-434
    • Deutsch, E.W.1    Lam, H.2    Aebersold, R.3
  • 37
    • 0036721834 scopus 로고    scopus 로고
    • The spot-synthesis technique synthetic peptide arrays on membrane supports-principles and applications
    • Frank R. The SPOT-synthesis technique. Synthetic peptide arrays on membrane supports-principles and applications. J. Immunol. Methods 267(1), 13-26 (2002
    • (2002) J. Immunol. Methods , vol.267 , Issue.1 , pp. 13-26
    • Frank, R.1
  • 38
    • 74049131716 scopus 로고    scopus 로고
    • High-Throughput generation of selected reaction-monitoring assays for proteins and proteomes
    • Picotti P, Rinner O, Stallmach R et al. High-Throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat. Methods 7(1), 43-46 (2010
    • (2010) Nat. Methods , vol.7 , Issue.1 , pp. 43-46
    • Picotti, P.1    Rinner, O.2    Stallmach, R.3
  • 40
    • 84871791617 scopus 로고    scopus 로고
    • Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes
    • Karlsson C, Malmstrom L, Aebersold R, Malmstrom J. Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes. Nat. Commun. 3, 1301 (2012
    • (2012) Nat. Commun , vol.3 , Issue.1301
    • Karlsson, C.1    Malmstrom, L.2    Aebersold, R.3    Malmstrom, J.4
  • 41
    • 84877863368 scopus 로고    scopus 로고
    • The mtb proteome library: A resource of assays to quantify the complete proteome of mycobacterium tuberculosis
    • Schubert OT, Mouritsen J, Ludwig C et al. The Mtb Proteome Library: A Resource of Assays to Quantify the Complete Proteome of Mycobacterium tuberculosis. Cell Host Microbe 13(5), 602-612 (2013
    • (2013) Cell Host Microbe , vol.13 , Issue.5 , pp. 602-612
    • Schubert, O.T.1    Mouritsen, J.2    Ludwig, C.3
  • 43
    • 38949210266 scopus 로고    scopus 로고
    • Human proteinpedia enables sharing of human protein data
    • Mathivanan S, Ahmed M, Ahn NG et al. Human Proteinpedia enables sharing of human protein data. Nat. Biotechnol. 26(2), 164-167 (2008
    • (2008) Nat. Biotechnol , vol.26 , Issue.2 , pp. 164-167
    • Mathivanan, S.1    Ahmed, M.2    Ahn, N.G.3
  • 44
    • 11144320641 scopus 로고    scopus 로고
    • Open source system for analyzing, validating, and storing protein identification data
    • Craig R, Cortens JP, Beavis RC. Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res. 3(6), 1234-1242 (2004
    • (2004) J. Proteome Res , vol.3 , Issue.6 , pp. 1234-1242
    • Craig, R.1    Cortens, J.P.2    Beavis, R.C.3
  • 45
    • 38549117407 scopus 로고    scopus 로고
    • Pride: New developments and new datasets
    • Database issue
    • Jones P, Cote RG, Cho SY et al. PRIDE: New developments and new datasets. Nucleic Acids Res. 36(Database issue), D878-D883 (2008
    • (2008) Nucleic Acids Res , vol.36
    • Jones, P.1    Cote, R.G.2    Cho, S.Y.3
  • 46
    • 84860856503 scopus 로고    scopus 로고
    • Passel: The pepti deatlas srm experiment library
    • Farrah T, Deutsch EW, Kreisberg R et al. PASSEL: The Pepti deAtlas SRM experiment library. Proteomics 12(8), 1170-1175 (2012
    • (2012) Proteomics , vol.12 , Issue.8 , pp. 1170-1175
    • Farrah, T.1    Deutsch, E.W.2    Kreisberg, R.3
  • 47
    • 33846548168 scopus 로고    scopus 로고
    • Mass spectrometric detection of tissue proteins in plasma
    • Zhang H, Liu AY, Loriaux P et al. Mass spectrometric detection of tissue proteins in plasma. Mol. Cell. Proteomics 6(1), 64-71 (2007
    • (2007) Mol. Cell. Proteomics , vol.6 , Issue.1 , pp. 64-71
    • Zhang, H.1    Liu, A.Y.2    Loriaux, P.3
  • 48
    • 0001644020 scopus 로고    scopus 로고
    • The human plasma proteome: History, character, and diagnostic prospects
    • Anderson NL, Anderson NG. The human plasma proteome: History, character, and diagnostic prospects. Mol. Cell. Proteomics 1(11), 845-867 (2002
    • (2002) Mol. Cell. Proteomics , vol.1 , Issue.11 , pp. 845-867
    • Anderson, N.L.1    Anderson, N.G.2
  • 49
    • 33644864034 scopus 로고    scopus 로고
    • Challenges in deriving high-confidence protein identifications from data gathered by a hupo plasma proteome collaborative study
    • States DJ, Omenn GS, Blackwell TW et al. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat. Biotechnol 24(3), 333-338 (2006
    • (2006) Nat. Biotechnol , vol.24 , Issue.3 , pp. 333-338
    • States, D.J.1    Omenn, G.S.2    Blackwell, T.W.3
  • 50
    • 79959499115 scopus 로고    scopus 로고
    • A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas
    • Farrah T, Deutsch EW, Omenn GS et al. A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol. Cell. Proteomics 10(9), M110 006353 (2011
    • (2011) Mol. Cell. Proteomics , vol.10 , Issue.9
    • Farrah, T.1    Deutsch, E.W.2    Omenn, G.S.3
  • 51
    • 33845921119 scopus 로고    scopus 로고
    • ProteomeBinders: Planning a European resource of affinity reagents for analysis of the human proteome
    • Taussig MJ, Stoevesandt O, Borrebaeck CA et al. ProteomeBinders: Planning a European resource of affinity reagents for analysis of the human proteome. Nat. Methods 4(1), 13-17 (2007
    • (2007) Nat. Methods , vol.4 , Issue.1 , pp. 13-17
    • Taussig, M.J.1    Stoevesandt, O.2    Borrebaeck, C.A.3
  • 52
    • 78650642557 scopus 로고    scopus 로고
    • Defining the transcriptome and proteome in three functionally different human cell lines
    • Lundberg E, Fagerberg L, Klevebring D et al. Defining the transcriptome and proteome in three functionally different human cell lines. Mol. Syst. Biol. 6, 450 (2010
    • (2010) Mol. Syst. Biol , vol.6 , pp. 450
    • Lundberg, E.1    Fagerberg, L.2    Klevebring, D.3
  • 53
    • 84874232489 scopus 로고    scopus 로고
    • The coming age of complete, accurate, and ubiquitous proteomes
    • Mann M, Kulak NA, Nagaraj N, Cox J. The coming age of complete, accurate, and ubiquitous proteomes. Mol. Cell 49(4), 583-590 (2013
    • (2013) Mol. Cell , vol.49 , Issue.4 , pp. 583-590
    • Mann, M.1    Kulak, N.A.2    Nagaraj, N.3    Cox, J.4
  • 54
    • 80855128254 scopus 로고    scopus 로고
    • Deep proteome and transcriptome mapping of a human cancer cell line
    • Nagaraj N, Wisniewski JR, Geiger T et al. Deep proteome and transcriptome mapping of a human cancer cell line. Mol. Syst. Biol. 7, 548 (2011
    • (2011) Mol. Syst. Biol , vol.7 , pp. 548
    • Nagaraj, N.1    Wisniewski, J.R.2    Geiger, T.3
  • 55
    • 80855128111 scopus 로고    scopus 로고
    • The quantitative proteome of a human cell line
    • Beck M, Schmidt A, Malmstroem J 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    Schmidt, A.2    Malmstroem, J.3
  • 56
  • 57
    • 84887323583 scopus 로고    scopus 로고
    • Contribution of antibody-based protein profiling to the human chromosome-centric proteome project (c-hpp
    • Fagerberg L, Oksvold P, Skogs M et al. Contribution of antibody-based protein profiling to the human Chromosome-centric Proteome Project (C-HPP). J. Proteome Res. (2012
    • (2012) J. Proteome Res
    • Fagerberg, L.1    Oksvold, P.2    Skogs, M.3
  • 58
    • 84874093356 scopus 로고    scopus 로고
    • The state of the human proteome in 2012 as viewed through PeptideAtlas
    • Farrah T, Deutsch EW, Hoopmann MR et al. The state of the human proteome in 2012 as viewed through PeptideAtlas. J. Proteome Res. 12(1), 162-171 (2013
    • (2013) J. Proteome Res , vol.12 , Issue.1 , pp. 162-171
    • Farrah, T.1    Deutsch, E.W.2    Hoopmann, M.R.3
  • 59
    • 85128759053 scopus 로고    scopus 로고
    • A list of candidate cancer biomarkers for targeted proteomics
    • Polanski M, Anderson NL. A list of candidate cancer biomarkers for targeted proteomics. Biomarker insights 1, 1-48 (2007
    • (2007) Biomarker insights , vol.1 , pp. 1-48
    • Polanski, M.1    Anderson, N.L.2
  • 60
    • 64349089985 scopus 로고    scopus 로고
    • Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins
    • Wollscheid B, Bausch-Fluck D, Henderson C et al. Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nat. Biotechnol. 27(4), 378-386 (2009
    • (2009) Nat. Biotechnol , vol.27 , Issue.4 , pp. 378-386
    • Wollscheid, B.1    Bausch-Fluck, D.2    Henderson, C.3
  • 61
    • 0036462601 scopus 로고    scopus 로고
    • Protein N-glycosylation along the secretory pathway: Relationship to organelle topography and function, protein quality control, and cell interactions
    • Roth J. Protein N-glycosylation along the secretory pathway: Relationship to organelle topography and function, protein quality control, and cell interactions. Chem. Rev. 102(2), 285-303 (2002
    • (2002) Chem. Rev , vol.102 , Issue.2 , pp. 285-303
    • Roth, J.1
  • 62
    • 59149084542 scopus 로고    scopus 로고
    • Targeted proteomic strategy for clinical biomarker discovery
    • Schiess R, Wollscheid B, Aebersold R. Targeted proteomic strategy for clinical biomarker discovery. Mol. Oncol. 3(1), 33-44 (2009
    • (2009) Mol. Oncol , vol.3 , Issue.1 , pp. 33-44
    • Schiess, R.1    Wollscheid, B.2    Aebersold, R.3
  • 63
    • 0038699625 scopus 로고    scopus 로고
    • Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry
    • Zhang H, Li XJ, Martin DB, Aebersold R. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat. Biotechnol. 21(6), 660-666 (2003
    • (2003) Nat. Biotechnol , vol.21 , Issue.6 , pp. 660-666
    • Zhang, H.1    Li, X.J.2    Martin, D.B.3    Aebersold, R.4
  • 64
    • 77953240454 scopus 로고    scopus 로고
    • Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints
    • Zielinska DF, Gnad F, Wisniewski JR, Mann M. Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints. Cell 141(5), 897-907 (2010
    • (2010) Cell , vol.141 , Issue.5 , pp. 897-907
    • Zielinska, D.F.1    Gnad, F.2    Wisniewski, J.R.3    Mann, M.4
  • 65
    • 80052805542 scopus 로고    scopus 로고
    • Quantitative glycoproteomic analysis of optimal cutting temperature-embedded frozen tissues identifying glycoproteins associated with aggressive prostate cancer
    • Tian Y, Bova GS, Zhang H. Quantitative glycoproteomic analysis of optimal cutting temperature-embedded frozen tissues identifying glycoproteins associated with aggressive prostate cancer. Anal Chem. 83(18), 7013-7019 (2011
    • (2011) Anal Chem , vol.83 , Issue.18 , pp. 7013-7019
    • Tian, Y.1    Bova, G.S.2    Zhang, H.3
  • 66
    • 84855188603 scopus 로고    scopus 로고
    • Development of glycoprotein capture-based label-free method for the high-Throughput screening of differential glycoproteins in hepatocellular carcinoma
    • Chen R, Tan Y, Wang M et al. Development of glycoprotein capture-based label-free method for the high-Throughput screening of differential glycoproteins in hepatocellular carcinoma. Mol. Cell. Proteomics 10(7), M110 006445 (2011
    • (2011) Mol. Cell. Proteomics , vol.10 , Issue.7
    • Chen, R.1    Tan, Y.2    Wang, M.3
  • 67
    • 78649861704 scopus 로고    scopus 로고
    • Lung cancer serum biomarker discovery using glycoprotein capture and liquid chromatography mass spectrometry
    • Zeng X, Hood BL, Sun M et al. Lung cancer serum biomarker discovery using glycoprotein capture and liquid chromatography mass spectrometry. J. Proteome Res. 9(12), 6440-6449 (2010
    • (2010) J. Proteome Res , vol.9 , Issue.12 , pp. 6440-6449
    • Zeng, X.1    Hood, B.L.2    Sun, M.3
  • 68
    • 84875969679 scopus 로고    scopus 로고
    • N-Glycoprotein SRMAtlas: A resource of mass-spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications
    • Huttenhain R, Surinova S, Ossola R et al. N-Glycoprotein SRMAtlas: A resource of mass-spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications. Mol. Cell. Proteomics 12(4), 1005-1016 (2013
    • (2013) Mol. Cell. Proteomics , vol.12 , Issue.4 , pp. 1005-1016
    • Huttenhain, R.1    Surinova, S.2    Ossola, R.3
  • 69
    • 84863393526 scopus 로고    scopus 로고
    • Ultra high resolution linear ion trap orbitrap mass spectrometer (orbitrap elite) facilitates top down lc ms/ms and versatile peptide fragmentation modes
    • Michalski A, Damoc E, Lange O et al. Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes. Mol. Cell. Proteomics 11(3), O111 013698 (2012
    • (2012) Mol. Cell. Proteomics , vol.11 , Issue.3
    • Michalski, A.1    Damoc, E.2    Lange, O.3
  • 70
    • 84863700845 scopus 로고    scopus 로고
    • In-house construction of a UHPLC system enabling the identification of over 4000 protein groups in a single analysis
    • Cristobal A, Hennrich ML, Giansanti P, Goerdayal SS, Heck AJ, Mohammed S. In-house construction of a UHPLC system enabling the identification of over 4000 protein groups in a single analysis. Analyst 137(15), 3541-3548 (2012
    • (2012) Analyst , vol.137 , Issue.15 , pp. 3541-3548
    • Cristobal, A.1    Hennrich, M.L.2    Giansanti, P.3    Goerdayal, S.S.4    Heck, A.J.5    Mohammed, S.6
  • 71
    • 33845902530 scopus 로고    scopus 로고
    • Overcoming the dynamic range problem in mass spectrometry-based shotgun proteomics
    • Wu L, Han DK. Overcoming the dynamic range problem in mass spectrometry-based shotgun proteomics. Expert Rev. Proteomics 3(6), 611-619 (2006
    • (2006) Expert Rev. Proteomics , vol.3 , Issue.6 , pp. 611-619
    • Wu, L.1    Han, D.K.2
  • 72
    • 70549084975 scopus 로고    scopus 로고
    • Directed mass spectrometry: Towards hypothesis-driven proteomics
    • Schmidt A, Claassen M, Aebersold R. Directed mass spectrometry: Towards hypothesis-driven proteomics. Curr. Opin. Chem. Biol. 13(5-6), 510-517 (2009
    • (2009) Curr. Opin. Chem. Biol , vol.13 , Issue.5-6 , pp. 510-517
    • Schmidt, A.1    Claassen, M.2    Aebersold, R.3
  • 73
    • 84867421373 scopus 로고    scopus 로고
    • Shotgun and targeted proteomics reveal that pre-surgery serum levels of LRG1 SAA, and C4BP may refine prognosis of resected squamous cell lung cancer
    • Liu YS, Luo XY, Li QR et al. Shotgun and targeted proteomics reveal that pre-surgery serum levels of LRG1, SAA, and C4BP may refine prognosis of resected squamous cell lung cancer. J. Mol. Cell Biol. 4(5), 344-347 (2012
    • (2012) J. Mol. Cell Biol , vol.4 , Issue.5 , pp. 344-347
    • Liu, Y.S.1    Luo, X.Y.2    Li, Q.R.3
  • 74
    • 71049137289 scopus 로고    scopus 로고
    • Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma
    • Kuzyk MA, Smith D, Yang J et al. Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma. Mol. Cellular Proteomics 8(8), 1860-1877 (2009
    • (2009) Mol. Cellular Proteomics , vol.8 , Issue.8 , pp. 1860-1877
    • Kuzyk, M.A.1    Smith, D.2    Yang, J.3
  • 76
    • 70549113220 scopus 로고    scopus 로고
    • Perspectives of targeted mass spectrometry for protein biomarker verification
    • Huttenhain R, Malmstrom J, Picotti P, Aebersold R. Perspectives of targeted mass spectrometry for protein biomarker verification. Current Opin. Chem. Biol. 13(5-6), 518-525 (2009
    • (2009) Current Opin. Chem. Biol , vol.13 , Issue.5-6 , pp. 518-525
    • Huttenhain, R.1    Malmstrom, J.2    Picotti, P.3    Aebersold, R.4
  • 77
    • 35348863892 scopus 로고    scopus 로고
    • High sensitivity detection of plasma proteins by multiple reaction monitoring of Nglycosites
    • Stahl-Zeng J, Lange V, Ossola R et al. High sensitivity detection of plasma proteins by multiple reaction monitoring of Nglycosites. Mol. Cell. Proteomics 6(10), 1809-1817 (2007
    • (2007) Mol. Cell. Proteomics , vol.6 , Issue.10 , pp. 1809-1817
    • Stahl-Zeng, J.1    Lange, V.2    Ossola, R.3
  • 78
    • 79952308635 scopus 로고    scopus 로고
    • Systematic quantification of peptides/proteins in urine using selected reaction monitoring
    • Selevsek N, Matondo M, Sanchez Carbayo M, Aebersold R, Domon B. Systematic quantification of peptides/proteins in urine using selected reaction monitoring. Proteomics 11(6), 1135-1147 (2011
    • (2011) Proteomics , vol.11 , Issue.6 , pp. 1135-1147
    • Selevsek, N.1    Matondo, M.2    Sanchez Carbayo, M.3    Aebersold, R.4    Domon, B.5
  • 79
    • 84860856325 scopus 로고    scopus 로고
    • Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate
    • Ebhardt HA, Sabido E, Huttenhain R, Collins B, Aebersold R. Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate. Proteomics 12(8), 1185-1193 (2012
    • (2012) Proteomics , vol.12 , Issue.8 , pp. 1185-1193
    • Ebhardt, H.A.1    Sabido, E.2    Huttenhain, R.3    Collins, B.4    Aebersold, R.5
  • 80
    • 8844233567 scopus 로고    scopus 로고
    • Mass spectrometric quantitation of peptides and proteins using stable isotope standards and capture by anti-peptide a ntibodies (siscapa
    • Anderson NL, Anderson NG, Haines LR, Hardie DB, Olafson RW, Pearson TW. Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide A ntibodies (SISCAPA). J. Proteome Res. 3(2), 235-244 (2004
    • (2004) J. Proteome Res , vol.3 , Issue.2 , pp. 235-244
    • Anderson, N.L.1    Anderson, N.G.2    Haines, L.R.3    Hardie, D.B.4    Olafson, R.W.5    Pearson, T.W.6
  • 81
    • 76649109590 scopus 로고    scopus 로고
    • An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers
    • Whiteaker JR, Zhao L, Anderson L, Paulovich AG. An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers. Mol. Cell. Proteomics 9(1), 184-196 (2010
    • (2010) Mol. Cell. Proteomics , vol.9 , Issue.1 , pp. 184-196
    • Whiteaker, J.R.1    Zhao, L.2    Anderson, L.3    Paulovich, A.G.4
  • 82
    • 66449083773 scopus 로고    scopus 로고
    • Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry
    • Kuhn E, Addona T, Keshishian H et al. Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry. Clin. Chem. 55(6), 1108-1117 (2009
    • (2009) Clin. Chem , vol.55 , Issue.6 , pp. 1108-1117
    • Kuhn, E.1    Addona, T.2    Keshishian, H.3
  • 83
    • 84860880032 scopus 로고    scopus 로고
    • Interlaboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma
    • Kuhn E, Whiteaker JR, Mani DR et al. Interlaboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma. Mol. Cell. Proteomics 11(6), M111 013854 (2012
    • (2012) Mol. Cell. Proteomics , vol.11 , Issue.6
    • Kuhn, E.1    Whiteaker, J.R.2    Mani, D.R.3
  • 84
    • 84876337044 scopus 로고    scopus 로고
    • Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS
    • Liu Y, Huttenhain R, Surinova S et al Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS. Proteomics 13(8), 1247-1256 (2013
    • (2013) Proteomics , vol.13 , Issue.8 , pp. 1247-1256
    • Liu, Y.1    Huttenhain, R.2    Surinova, S.3
  • 85
    • 79952284442 scopus 로고    scopus 로고
    • Mutant proteins as cancer-specific biomarkers
    • Wang Q, Chaerkady R, Wu J et al. Mutant proteins as cancer-specific biomarkers. Proc. Natl Acad. Sci. USA 108(6), 2444-2449 (2011
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , Issue.6 , pp. 2444-2449
    • Wang, Q.1    Chaerkady, R.2    Wu, J.3
  • 86
    • 77957755656 scopus 로고    scopus 로고
    • Secretome proteomics for discovery of cancer biomarkers
    • Makridakis M, Vlahou A. Secretome proteomics for discovery of cancer biomarkers. J. Proteomics 73(12), 2291-2305 (2010
    • (2010) J. Proteomics , vol.73 , Issue.12 , pp. 2291-2305
    • Makridakis, M.1    Vlahou, A.2
  • 87
    • 79952242850 scopus 로고    scopus 로고
    • A high-quality secretome of A549 cells aided the discovery of C4b-binding protein as a novel serum biomarker for non-small cell lung cancer
    • Luo X, Liu Y, Wang R, Hu H, Zeng R, Chen H. A high-quality secretome of A549 cells aided the discovery of C4b-binding protein as a novel serum biomarker for non-small cell lung cancer. J. Proteomics 74(4), 528-538 (2011
    • (2011) J. Proteomics , vol.74 , Issue.4 , pp. 528-538
    • Luo, X.1    Liu, Y.2    Wang, R.3    Hu, H.4    Zeng, R.5    Chen, H.6
  • 88
    • 84871269094 scopus 로고    scopus 로고
    • Integrative proteomics and tissue microarray profiling indicate the association between overexpressed serum proteins and non-small cell lung cancer
    • Liu Y, Luo X, Hu H et al. Integrative proteomics and tissue microarray profiling indicate the association between overexpressed serum proteins and non-small cell lung cancer. PloS one 7(12), e51748 (2012
    • (2012) PloS one , vol.7 , Issue.12
    • Liu, Y.1    Luo, X.2    Hu, H.3
  • 90
    • 79960214321 scopus 로고    scopus 로고
    • A targeted proteomics-based pipeline for verification of biomarkers in plasma
    • Whiteaker JR, Lin C, Kennedy J et al. A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat. Biotechnol. 29(7), 625-634 (2011
    • (2011) Nat. Biotechnol , vol.29 , Issue.7 , pp. 625-634
    • Whiteaker, J.R.1    Lin, C.2    Kennedy, J.3
  • 91
    • 79960269601 scopus 로고    scopus 로고
    • A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease
    • Addona TA, Shi X, Keshishian H et al. A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease. Nat. Biotechnol. 29(7), 635-643 (2011
    • (2011) Nat. Biotechnol , vol.29 , Issue.7 , pp. 635-643
    • Addona, T.A.1    Shi, X.2    Keshishian, H.3
  • 92
    • 79960262137 scopus 로고    scopus 로고
    • Streamlining biomarker discovery
    • Latterich M, Schnitzer JE. Streamlining biomarker discovery. Nat. Biotechnol. 29(7), 600-602 (2011
    • (2011) Nat. Biotechnol , vol.29 , Issue.7 , pp. 600-602
    • Latterich, M.1    Schnitzer, J.E.2
  • 93
    • 77952226764 scopus 로고    scopus 로고
    • Super-SILAC mix for quantitative proteomics of human tumor tissue
    • Geiger T, Cox J, Ostasiewicz P, Wisniewski JR, Mann M. Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat. Methods 7(5), 383-385 (2010
    • (2010) Nat. Methods , vol.7 , Issue.5 , pp. 383-385
    • Geiger, T.1    Cox, J.2    Ostasiewicz, P.3    Wisniewski, J.R.4    Mann, M.5
  • 94
    • 79955765660 scopus 로고    scopus 로고
    • A bioinformatics workflow for variant peptide detection in shotgun proteomics
    • Li J, Su Z, Ma ZQ et al. A bioinformatics workflow for variant peptide detection in shotgun proteomics. Mol. Cell. Proteomics 10(5), M110 006536 (2011
    • (2011) Mol. Cell. Proteomics , vol.10 , Issue.5
    • Li, J.1    Su, Z.2    Ma, Z.Q.3
  • 95
    • 84881094423 scopus 로고    scopus 로고
    • Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq
    • Sheynkman GM, Shortreed MR, Frey BL, Smith LM. Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq. Mol. Cell. Proteomics 12(8), 2341-2353 (2013
    • (2013) Mol. Cell. Proteomics , vol.12 , Issue.8 , pp. 2341-2353
    • Sheynkman, G.M.1    Shortreed, M.R.2    Frey, B.L.3    Smith, L.M.4
  • 96
    • 77954378942 scopus 로고    scopus 로고
    • Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry
    • Ostasiewicz P, Zielinska DF, Mann M, Wisniewski Jr. Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry. J. Proteome Res. 9(7), 3688-3700 (2010
    • (2010) J. Proteome Res , vol.9 , Issue.7 , pp. 3688-3700
    • Ostasiewicz, P.1    Zielinska, D.F.2    Mann, M.3    Wisniewski, J.R.4
  • 97
    • 84861442569 scopus 로고    scopus 로고
    • Label-free mass spectrometry-based proteomics for biomarker discovery and validation
    • Pham TV, Piersma SR, Oudgenoeg G, Jimenez CR. Label-free mass spectrometry-based proteomics for biomarker discovery and validation. Expert Rev. Molecular Diagn. 12(4), 343-359 (2012
    • (2012) Expert Rev. Molecular Diagn , vol.12 , Issue.4 , pp. 343-359
    • Pham, T.V.1    Piersma, S.R.2    Oudgenoeg, G.3    Jimenez, C.R.4
  • 98
    • 0036583926 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    • Ong SE, Blagoev B, Kratchmarova I et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1(5), 376-386 (2002
    • (2002) Mol. Cell. Proteomics , vol.1 , Issue.5 , pp. 376-386
    • Ong, S.E.1    Blagoev, B.2    Kratchmarova, I.3
  • 99
    • 19944432197 scopus 로고    scopus 로고
    • Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
    • Ross PL, Huang YN, Marchese JN et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3(12), 1154-1169 (2004
    • (2004) Mol. Cell. Proteomics , vol.3 , Issue.12 , pp. 1154-1169
    • Ross, P.L.1    Huang, Y.N.2    Marchese, J.N.3
  • 100
    • 33745777632 scopus 로고    scopus 로고
    • UPLC/MS(E); a new approach for generating molecular fragment information for biomarker structure elucidation
    • Plumb RS, Johnson KA, Rainville P et al. UPLC/MS(E); a new approach for generating molecular fragment information for biomarker structure elucidation. Rapid Commun. Mass Spectrom. 20(13), 1989-1994 (2006
    • (2006) Rapid Commun. Mass Spectrom , vol.20 , Issue.13 , pp. 1989-1994
    • Plumb, R.S.1    Johnson, K.A.2    Rainville, P.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.