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Volumn 15, Issue 2, 2016, Pages 389-399

Proteomic Biomarker Discovery in 1000 Human Plasma Samples with Mass Spectrometry

Author keywords

biomarker; blood; body fluid; clinical proteomics; mass spectrometry; obesity; tandem mass tags; TMT

Indexed keywords

ANTITHROMBIN III; BETA LACTOGLOBULIN; BIOLOGICAL MARKER; BLOOD CLOTTING FACTOR 10; C REACTIVE PROTEIN; CALGRANULIN B; COMPLEMENT COMPONENT C1R; COMPLEMENT COMPONENT C6; COMPLEMENT FACTOR I; CYCLIC AMP DEPENDENT PROTEIN KINASE ANCHORING PROTEIN; HEMOPEXIN; HERMES ANTIGEN; PROTHROMBIN; PLASMA PROTEIN; PROTEOME;

EID: 84957670863     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.5b00901     Document Type: Article
Times cited : (76)

References (41)
  • 1
    • 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 (8) 971-983 10.1038/nbt1235
    • (2006) Nat. Biotechnol. , vol.24 , Issue.8 , pp. 971-983
    • Rifai, N.1    Gillette, M.A.2    Carr, S.A.3
  • 2
    • 75749130354 scopus 로고    scopus 로고
    • The clinical plasma proteome: A survey of clinical assays for proteins in plasma and serum
    • Anderson, N. L. The clinical plasma proteome: A survey of clinical assays for proteins in plasma and serum Clin. Chem. 2010, 56 (2) 177-185 10.1373/clinchem.2009.126706
    • (2010) Clin. Chem. , vol.56 , Issue.2 , pp. 177-185
    • Anderson, N.L.1
  • 3
    • 84884572991 scopus 로고    scopus 로고
    • Proteomics of human plasma: A critical comparison of analytical workflows in terms of effort, throughput and outcome
    • Dayon, L.; Kussmann, M. Proteomics of human plasma: A critical comparison of analytical workflows in terms of effort, throughput and outcome EuPa Open Proteomics 2013, 1, 8-16 10.1016/j.euprot.2013.08.001
    • (2013) EuPa Open Proteomics , vol.1 , pp. 8-16
    • Dayon, L.1    Kussmann, M.2
  • 4
    • 84904022083 scopus 로고    scopus 로고
    • Why have so few proteomic biomarkers "survived" validation? (Sample size and independent validation considerations)
    • Hernández, B.; Parnell, A.; Pennington, S. R. Why have so few proteomic biomarkers "survived" validation? (Sample size and independent validation considerations) Proteomics 2014, 14 (13-14) 1587-1592 10.1002/pmic.201300377
    • (2014) Proteomics , vol.14 , Issue.1314 , pp. 1587-1592
    • Hernández, B.1    Parnell, A.2    Pennington, S.R.3
  • 5
    • 84969394014 scopus 로고    scopus 로고
    • Proteomic Workflows for Biomarker Identification Using Mass Spectrometry - Technical and Statistical Considerations during Initial Discovery
    • Orton, D.; Doucette, A. Proteomic Workflows for Biomarker Identification Using Mass Spectrometry - Technical and Statistical Considerations during Initial Discovery Proteomes 2013, 1 (2) 109-127 10.3390/proteomes1020109
    • (2013) Proteomes , vol.1 , Issue.2 , pp. 109-127
    • Orton, D.1    Doucette, A.2
  • 7
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold, R.; Mann, M. Mass spectrometry-based proteomics Nature 2003, 422 (6928) 198-207 10.1038/nature01511
    • (2003) Nature , vol.422 , Issue.6928 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 9
    • 33750105832 scopus 로고    scopus 로고
    • Automation, parallelism, and robotics for proteomics
    • Alterovitz, G.; Liu, J.; Chow, J.; Ramoni, M. F. Automation, parallelism, and robotics for proteomics Proteomics 2006, 6 (14) 4016-4022 10.1002/pmic.200600060
    • (2006) Proteomics , vol.6 , Issue.14 , pp. 4016-4022
    • Alterovitz, G.1    Liu, J.2    Chow, J.3    Ramoni, M.F.4
  • 10
    • 33846231485 scopus 로고    scopus 로고
    • Multiplexed proteomic reactor for the processing of proteomic samples
    • Hou, W.; Ethier, M.; Smith, J. C.; Sheng, Y.; Figeys, D. Multiplexed proteomic reactor for the processing of proteomic samples Anal. Chem. 2007, 79 (1) 39-44 10.1021/ac061248v
    • (2007) Anal. Chem. , vol.79 , Issue.1 , pp. 39-44
    • Hou, W.1    Ethier, M.2    Smith, J.C.3    Sheng, Y.4    Figeys, D.5
  • 11
    • 84885400747 scopus 로고    scopus 로고
    • A high-throughput sample preparation method for cellular proteomics using 96-well filter plates
    • Switzar, L.; van Angeren, J.; Pinkse, M.; Kool, J.; Niessen, W. M. A. A high-throughput sample preparation method for cellular proteomics using 96-well filter plates Proteomics 2013, 13 (20) 2980-2983 10.1002/pmic.201300080
    • (2013) Proteomics , vol.13 , Issue.20 , pp. 2980-2983
    • Switzar, L.1    Van Angeren, J.2    Pinkse, M.3    Kool, J.4    Niessen, W.M.A.5
  • 12
    • 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, J. R.; Zhao, L.; Anderson, L.; Paulovich, A. G. 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 2010, 9 (1) 184-196 10.1074/mcp.M900254-MCP200
    • (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
  • 13
    • 84901763939 scopus 로고    scopus 로고
    • Urine sample preparation in 96-well filter plates for quantitative clinical proteomics
    • Yu, Y.; Suh, M. J.; Sikorski, P.; Kwon, K.; Nelson, K. E.; Pieper, R. Urine sample preparation in 96-well filter plates for quantitative clinical proteomics Anal. Chem. 2014, 86 (11) 5470-5477 10.1021/ac5008317
    • (2014) Anal. Chem. , vol.86 , Issue.11 , pp. 5470-5477
    • Yu, Y.1    Suh, M.J.2    Sikorski, P.3    Kwon, K.4    Nelson, K.E.5    Pieper, R.6
  • 14
    • 84895743899 scopus 로고    scopus 로고
    • Beyond antibodies: New affinity reagents to unlock the proteome
    • Lollo, B.; Steele, F.; Gold, L. Beyond antibodies: New affinity reagents to unlock the proteome Proteomics 2014, 14 (6) 638-644 10.1002/pmic.201300187
    • (2014) Proteomics , vol.14 , Issue.6 , pp. 638-644
    • Lollo, B.1    Steele, F.2    Gold, L.3
  • 15
    • 84895770914 scopus 로고    scopus 로고
    • Antibody-based proteomics and biomarker research-current status and limitations
    • Solier, C.; Langen, H. Antibody-based proteomics and biomarker research-current status and limitations Proteomics 2014, 14 (6) 774-783 10.1002/pmic.201300334
    • (2014) Proteomics , vol.14 , Issue.6 , pp. 774-783
    • Solier, C.1    Langen, H.2
  • 16
    • 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 (11) 845-867 10.1074/mcp.R200007-MCP200
    • (2002) Mol. Cell. Proteomics , vol.1 , Issue.11 , pp. 845-867
    • Anderson, N.L.1    Anderson, N.G.2
  • 17
    • 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. 2009, 3 (1) 33-44 10.1016/j.molonc.2008.12.001
    • (2009) Mol. Oncol. , vol.3 , Issue.1 , pp. 33-44
    • Schiess, R.1    Wollscheid, B.2    Aebersold, R.3
  • 18
    • 84905388250 scopus 로고    scopus 로고
    • Comprehensive and scalable highly automated MS-based proteomic workflow for clinical biomarker discovery in human plasma
    • Dayon, L.; Núñez Galindo, A.; Corthésy, J.; Cominetti, O.; Kussmann, M. Comprehensive and scalable highly automated MS-based proteomic workflow for clinical biomarker discovery in human plasma J. Proteome Res. 2014, 13 (8) 3837-3845 10.1021/pr500635f
    • (2014) J. Proteome Res. , vol.13 , Issue.8 , pp. 3837-3845
    • Dayon, L.1    Núñez Galindo, A.2    Corthésy, J.3    Cominetti, O.4    Kussmann, M.5
  • 22
    • 0031599142 scopus 로고    scopus 로고
    • Mersenne Twister: A 623-dimensionally equidistributed uniform pseudo-random number generator
    • Matsumoto, M.; Nishimura, T. Mersenne Twister: a 623-dimensionally equidistributed uniform pseudo-random number generator ACM Trans. Model. Comput. Simul. 1998, 8 (1) 3-30 10.1145/272991.272995
    • (1998) ACM Trans. Model. Comput. Simul. , vol.8 , Issue.1 , pp. 3-30
    • Matsumoto, M.1    Nishimura, T.2
  • 23
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins, D. N.; Pappin, D. J. C.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999, 20 (18) 3551-3567 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2
    • (1999) Electrophoresis , vol.20 , Issue.18 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.C.2    Creasy, D.M.3    Cottrell, J.S.4
  • 24
    • 79957523606 scopus 로고    scopus 로고
    • A large, consistent plasma proteomics data set from prospectively collected breast cancer patient and healthy volunteer samples
    • Riley, C. P.; Zhang, X.; Nakshatri, H.; Schneider, B.; Regnier, F. E.; Adamec, J.; Buck, C. A large, consistent plasma proteomics data set from prospectively collected breast cancer patient and healthy volunteer samples J. Transl. Med. 2011, 9, 80 10.1186/1479-5876-9-80
    • (2011) J. Transl. Med. , vol.9 , pp. 80
    • Riley, C.P.1    Zhang, X.2    Nakshatri, H.3    Schneider, B.4    Regnier, F.E.5    Adamec, J.6    Buck, C.7
  • 28
    • 42349105213 scopus 로고    scopus 로고
    • Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags
    • Dayon, L.; Hainard, A.; Licker, V.; Turck, N.; Kuhn, K.; Hochstrasser, D. F.; Burkhard, P. R.; Sanchez, J. C. Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags Anal. Chem. 2008, 80 (8) 2921-2931 10.1021/ac702422x
    • (2008) Anal. Chem. , vol.80 , Issue.8 , pp. 2921-2931
    • Dayon, L.1    Hainard, A.2    Licker, V.3    Turck, N.4    Kuhn, K.5    Hochstrasser, D.F.6    Burkhard, P.R.7    Sanchez, J.C.8
  • 31
    • 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, L. C.; Navarro, P.; Tate, S.; Röst, H.; Selevsek, N.; Reiter, L.; Bonner, R.; Aebersold, R. 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 2012, 11 (6), O111.016717 10.1074/mcp.O111.016717
    • (2012) Mol. Cell. Proteomics , vol.11 , Issue.6 , pp. O111016717
    • Gillet, L.C.1    Navarro, P.2    Tate, S.3    Röst, H.4    Selevsek, N.5    Reiter, L.6    Bonner, R.7    Aebersold, R.8
  • 32
    • 0019450757 scopus 로고
    • Circulating levels of pregnancy zone protein: Normal range and the influence of age and gender
    • Folkersen, J.; Teisner, B.; Grunnet, N.; Grudzinskas, J. G.; Westergaard, J. G.; Hindersson, P. Circulating levels of pregnancy zone protein: Normal range and the influence of age and gender Clin. Chim. Acta 1981, 110 (2-3) 139-145 10.1016/0009-8981(81)90343-0
    • (1981) Clin. Chim. Acta , vol.110 , Issue.23 , pp. 139-145
    • Folkersen, J.1    Teisner, B.2    Grunnet, N.3    Grudzinskas, J.G.4    Westergaard, J.G.5    Hindersson, P.6
  • 33
    • 0022341006 scopus 로고
    • Characterization of human pregnancy zone protein. Comparison with human α2-macroglobulin
    • Sand, O.; Folkersen, J.; Westergaard, J. G.; Sottrup-Jensen, L. Characterization of human pregnancy zone protein. Comparison with human α2-macroglobulin J. Biol. Chem. 1985, 260 (29) 15723-15735
    • (1985) J. Biol. Chem. , vol.260 , Issue.29 , pp. 15723-15735
    • Sand, O.1    Folkersen, J.2    Westergaard, J.G.3    Sottrup-Jensen, L.4
  • 35
    • 0033821406 scopus 로고    scopus 로고
    • Sex hormone-binding globulin concentration: Differences among commercially available methods
    • Bukowski, C.; Grigg, M. A.; Longcope, C. Sex hormone-binding globulin concentration: Differences among commercially available methods Clin. Chem. 2000, 46 (9) 1415-1416
    • (2000) Clin. Chem. , vol.46 , Issue.9 , pp. 1415-1416
    • Bukowski, C.1    Grigg, M.A.2    Longcope, C.3
  • 36
    • 0023737154 scopus 로고
    • Evaluation of an immunoassay for plasma sex hormone-binding globulin: Comparison with steroid-binding assay under physiological and pathological conditions
    • Cunningham, S. K.; McKenna, T. J. Evaluation of an immunoassay for plasma sex hormone-binding globulin: Comparison with steroid-binding assay under physiological and pathological conditions Ann. Clin. Biochem. 1988, 25 (4) 360-366 10.1177/000456328802500406
    • (1988) Ann. Clin. Biochem. , vol.25 , Issue.4 , pp. 360-366
    • Cunningham, S.K.1    McKenna, T.J.2
  • 38
    • 0034474076 scopus 로고    scopus 로고
    • Sex steroid hormones, sex hormone-binding globulin, and obesity in men and women
    • Tchernof, A.; Després, J. P. Sex steroid hormones, sex hormone-binding globulin, and obesity in men and women Horm. Metab. Res. 2000, 32 (11-12) 526-536 10.1055/s-2007-978681
    • (2000) Horm. Metab. Res. , vol.32 , Issue.1112 , pp. 526-536
    • Tchernof, A.1    Després, J.P.2
  • 39
    • 84155172877 scopus 로고    scopus 로고
    • Effects of weight loss and long-term weight maintenance with diets varying in protein and glycemic index on cardiovascular risk factors: The diet, obesity, and genes (diogenes) study: A randomized, controlled trial
    • Gögebakan, O.; Kohl, A.; Osterhoff, M. A.; Van Baak, M. A.; Jebb, S. A.; Papadaki, A.; Martinez, J. A.; Handjieva-Darlenska, T.; Hlavaty, P.; Weickert, M. O.; Holst, C.; Saris, W. H. M.; Astrup, A.; Pfeiffer, A. F. H. Effects of weight loss and long-term weight maintenance with diets varying in protein and glycemic index on cardiovascular risk factors: The diet, obesity, and genes (diogenes) study: A randomized, controlled trial Circulation 2011, 124 (25) 2829-2838 10.1161/CIRCULATIONAHA.111.033274
    • (2011) Circulation , vol.124 , Issue.25 , pp. 2829-2838
    • Gögebakan, O.1    Kohl, A.2    Osterhoff, M.A.3    Van Baak, M.A.4    Jebb, S.A.5    Papadaki, A.6    Martinez, J.A.7    Handjieva-Darlenska, T.8    Hlavaty, P.9    Weickert, M.O.10    Holst, C.11    Saris, W.H.M.12    Astrup, A.13    Pfeiffer, A.F.H.14
  • 40
    • 0033537013 scopus 로고    scopus 로고
    • Elevated C-reactive protein levels in overweight and obese adults
    • Visser, M.; Bouter, L. M.; McQuillan, G. M.; Wener, M. H.; Harris, T. B. Elevated C-reactive protein levels in overweight and obese adults J. Am. Med. Assoc. 1999, 282 (22) 2131-2135 10.1001/jama.282.22.2131
    • (1999) J. Am. Med. Assoc. , vol.282 , Issue.22 , pp. 2131-2135
    • Visser, M.1    Bouter, L.M.2    McQuillan, G.M.3    Wener, M.H.4    Harris, T.B.5


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