-
1
-
-
55349134214
-
The interface between biomarker discovery and clinical validation: The tar pit of the protein biomarker pipeline
-
Paulovich, A. G., Whiteaker, J. R., Hoofnagle, A. N., and Wang, P. (2008) The interface between biomarker discovery and clinical validation: The tar pit of the protein biomarker pipeline. Proteomics Clin. Appl. 2, 1386-1402
-
(2008)
Proteomics Clin. Appl.
, vol.2
, pp. 1386-1402
-
-
Paulovich, A.G.1
Whiteaker, J.R.2
Hoofnagle, A.N.3
Wang, P.4
-
2
-
-
33747030845
-
Protein biomarker discovery and validation: The long and uncertain path to clinical utility
-
Rifai, N., Gillette, M. A., and Carr, S. A. (2006) Protein biomarker discovery and validation: The long and uncertain path to clinical utility. Nat. Biotechnol. 24, 971-983
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 971-983
-
-
Rifai, N.1
Gillette, M.A.2
Carr, S.A.3
-
3
-
-
27644537898
-
The roles of multiple proteomic platforms in a pipeline for new diagnostics
-
Anderson, N. L. (2005) The roles of multiple proteomic platforms in a pipeline for new diagnostics. Mol. Cell. Proteomics 4, 1441-1444
-
(2005)
Mol. Cell. Proteomics
, vol.4
, pp. 1441-1444
-
-
Anderson, N.L.1
-
4
-
-
14844292112
-
A biochemical perspective on the use of tandem mass spectrometry for newborn screening and clinical testing
-
Chace, D. H., and Kalas, T. A. (2005) A biochemical perspective on the use of tandem mass spectrometry for newborn screening and clinical testing. Clin. Biochem. 38, 296-309
-
(2005)
Clin. Biochem.
, vol.38
, pp. 296-309
-
-
Chace, D.H.1
Kalas, T.A.2
-
5
-
-
27744479716
-
The expanding role of mass spectrometry in metabolite profiling and characterization
-
DOI 10.1002/cbic.200500151
-
Want, E. J., Cravatt, B. F., and Siuzdak, G. (2005) The expanding role of mass spectrometry in metabolite profiling and characterization. Chembiochem. 6, 1941-1951 (Pubitemid 41598162)
-
(2005)
ChemBioChem
, vol.6
, Issue.11
, pp. 1941-1951
-
-
Want, E.J.1
Cravatt, B.F.2
Siuzdak, G.3
-
6
-
-
10244256354
-
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., Henderson, L. O., Turner, W. E., Smith, S. J., Hannon, W. H., Needham, L. L., and Sampson, E. J. (1996) Isotope dilution-mass spectrometric quantification of specific proteins: Model application with apolipoprotein A-I. Clin. Chem. 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
Henderson, L.O.5
Turner, W.E.6
Smith, S.J.7
Hannon, W.H.8
Needham, L.L.9
Sampson, E.J.10
-
7
-
-
0037795741
-
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
-
Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., and Gygi, S. P. (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. U.S.A. 100, 6940-6945
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 6940-6945
-
-
Gerber, S.A.1
Rush, J.2
Stemman, O.3
Kirschner, M.W.4
Gygi, S.P.5
-
8
-
-
1842528125
-
13C-labeled peptide standards
-
DOI 10.1002/pmic.200300670
-
Kuhn, E., Wu, J., Karl, J., Liao, H., Zolg, W., and Guild, B. (2004) Quantification of C-reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C-labeled peptide standards. Proteomics 4, 1175-1186 (Pubitemid 38445974)
-
(2004)
Proteomics
, vol.4
, Issue.4
, pp. 1175-1186
-
-
Kuhn, E.1
Wu, J.2
Karl, J.3
Liao, H.4
Zolg, W.5
Guild, B.6
-
9
-
-
4444301306
-
Absolute quantification of the model biomarker prostate-specific antigen in serum by LC-Ms/MS using protein cleavage and isotope dilution mass spectrometry
-
Barnidge, D. R., Goodmanson, M. K., Klee, G. G., and Muddiman, D. C. (2004) Absolute quantification of the model biomarker prostate-specific antigen in serum by LC-Ms/MS using protein cleavage and isotope dilution mass spectrometry. J. Proteome Res. 3, 644-652
-
(2004)
J. Proteome Res.
, vol.3
, pp. 644-652
-
-
Barnidge, D.R.1
Goodmanson, M.K.2
Klee, G.G.3
Muddiman, D.C.4
-
10
-
-
33645721632
-
Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins
-
Anderson, L., and Hunter, C. L. (2006) Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Proteomics 5, 573-588
-
(2006)
Mol. Cell. Proteomics
, vol.5
, pp. 573-588
-
-
Anderson, L.1
Hunter, C.L.2
-
11
-
-
71049187147
-
Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution
-
Keshishian, H., Addona, T., Burgess, M., Mani, D. R., Shi, X., Kuhn, E., Sabatine, M. S., Gerszten, R. E., and Carr, S. A. (2009) Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics 8, 2339-2349
-
(2009)
Mol. Cell. Proteomics
, vol.8
, pp. 2339-2349
-
-
Keshishian, H.1
Addona, T.2
Burgess, M.3
Mani, D.R.4
Shi, X.5
Kuhn, E.6
Sabatine, M.S.7
Gerszten, R.E.8
Carr, S.A.9
-
12
-
-
54049090766
-
Selected reaction monitoring for quantitative proteomics: A tutorial
-
Lange, V., Picotti, P., Domon, B., and Aebersold, R. (2008) Selected reaction monitoring for quantitative proteomics: A tutorial. Mol. Syst. Biol. 4, 222
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 222
-
-
Lange, V.1
Picotti, P.2
Domon, B.3
Aebersold, R.4
-
13
-
-
61849105469
-
Mass spectrometry based targeted protein quantification: Methods and applications
-
Pan, S., Aebersold, R., Chen, R., Rush, J., Goodlett, D. R., McIntosh, M. W., Zhang, J., and Brentnall, T. A. (2009) Mass spectrometry based targeted protein quantification: Methods and applications. J. Proteome Res. 8, 787-797
-
(2009)
J. Proteome Res.
, vol.8
, pp. 787-797
-
-
Pan, S.1
Aebersold, R.2
Chen, R.3
Rush, J.4
Goodlett, D.R.5
McIntosh, M.W.6
Zhang, J.7
Brentnall, T.A.8
-
14
-
-
78649834299
-
Simultaneous quantification of apolipoprotein A-I and apolipoprotein B by liquid Chromatography-Multiple reaction Monitoring/Mass spectrometry
-
Agger, S. A., Marney, L. C., and Hoofnagle, A. N. (2010) Simultaneous quantification of apolipoprotein A-I and apolipoprotein B by liquid Chromatography-Multiple reaction Monitoring/Mass spectrometry. Clin. Chem. 56, 1804-1813
-
(2010)
Clin. Chem.
, vol.56
, pp. 1804-1813
-
-
Agger, S.A.1
Marney, L.C.2
Hoofnagle, A.N.3
-
15
-
-
68749094119
-
Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics
-
Picotti, P., Bodenmiller, B., Mueller, L. N., Domon, B., and Aebersold, R. (2009) Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 138, 795-806
-
(2009)
Cell
, vol.138
, pp. 795-806
-
-
Picotti, P.1
Bodenmiller, B.2
Mueller, L.N.3
Domon, B.4
Aebersold, R.5
-
16
-
-
67650564834
-
Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma
-
Addona, T. A., Abbatiello, S. E., Schilling, B., Skates, S. J., Mani, D. R., Bunk, D. M., Spiegelman, C. H., Zimmerman, L. J., Ham, A. J., Keshishian, H., Hall, S. C., Allen, S., Blackman, R. K., Borchers, C. H., Buck, C., Cardasis, H. L., Cusack, M. P., Dodder, N. G., Gibson, B. W., Held, J. M., Hiltke, T., Jackson, A., Johansen, E. B., Kinsinger, C. R., Li, J., Mesri, M., Neubert, T. A., Niles, R. K., Pulsipher, T. C., Ransohoff, D., Rodriguez, H., Rudnick, P. A., Smith, D., Tabb, D. L., Tegeler, T. J., Variyath, A. M., Vega-Montoto, L. J., Wahlander, A., Waldemarson, S., Wang, M., Whiteaker, J. R., Zhao, L., Anderson, N. L., Fisher, S. J., Liebler, D. C., Paulovich, A. G., Regnier, F. E., Tempst, P., and Carr, S. A. (2009) Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat. Biotechnol. 27, 633-641
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 633-641
-
-
Addona, T.A.1
Abbatiello, S.E.2
Schilling, B.3
Skates, S.J.4
Mani, D.R.5
Bunk, D.M.6
Spiegelman, C.H.7
Zimmerman, L.J.8
Ham, A.J.9
Keshishian, H.10
Hall, S.C.11
Allen, S.12
Blackman, R.K.13
Borchers, C.H.14
Buck, C.15
Cardasis, H.L.16
Cusack, M.P.17
Dodder, N.G.18
Gibson, B.W.19
Held, J.M.20
Hiltke, T.21
Jackson, A.22
Johansen, E.B.23
Kinsinger, C.R.24
Li, J.25
Mesri, M.26
Neubert, T.A.27
Niles, R.K.28
Pulsipher, T.C.29
Ransohoff, D.30
Rodriguez, H.31
Rudnick, P.A.32
Smith, D.33
Tabb, D.L.34
Tegeler, T.J.35
Variyath, A.M.36
Vega-Montoto, L.J.37
Wahlander, A.38
Waldemarson, S.39
Wang, M.40
Whiteaker, J.R.41
Zhao, L.42
Anderson, N.L.43
Fisher, S.J.44
Liebler, D.C.45
Paulovich, A.G.46
Regnier, F.E.47
Tempst, P.48
Carr, S.A.49
more..
-
17
-
-
38349068918
-
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., and Carr, S. A. (2007) Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics 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
-
18
-
-
34547800600
-
Isolation of N-linked glycopeptides from plasma
-
Zhou, Y., Aebersold, R., and Zhang, H. (2007) Isolation of N-linked glycopeptides from plasma. Anal. Chem. 79, 5826-5837
-
(2007)
Anal. Chem.
, vol.79
, pp. 5826-5837
-
-
Zhou, Y.1
Aebersold, R.2
Zhang, H.3
-
19
-
-
8844233567
-
Mass spectrometric quantitation of peptides and proteins using stable isotope standards and capture by anti-peptide antibodies (SISCAPA)
-
Anderson, N. L., Anderson, N. G., Haines, L. R., Hardie, D. B., Olafson, R. W., and Pearson, T. W. (2004) Mass spectrometric quantitation of peptides and proteins using stable isotope standards and capture by anti-peptide antibodies (SISCAPA). J. Proteome Res. 3, 235-244
-
(2004)
J. Proteome Res.
, vol.3
, 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
-
20
-
-
76649109590
-
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., and Paulovich, A. G. (2010) 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, 184-196
-
(2010)
Mol. Cell. Proteomics
, vol.9
, pp. 184-196
-
-
Whiteaker, J.R.1
Zhao, L.2
Anderson, L.3
Paulovich, A.G.4
-
21
-
-
34247116419
-
Coupling immunoaffinity techniques with MS for quantitative analysis of low-abundance protein biomarkers
-
DOI 10.1586/14789450.4.2.175
-
Ackermann, B. L., and Berna, M. J. (2007) Coupling immunoaffinity techniques with MS for quantitative analysis of low-abundance protein biomarkers. Expert Rev. Proteomics 4, 175-186 (Pubitemid 46588454)
-
(2007)
Expert Review of Proteomics
, vol.4
, Issue.2
, pp. 175-186
-
-
Ackermann, B.L.1
Berna, M.J.2
-
22
-
-
55349139657
-
Quantification of thyroglobulin, a low-abundance serum protein, by immunoaffinity peptide enrichment and tandem mass spectrometry
-
Hoofnagle, A. N., Becker, J. O., Wener, M. H., and Heinecke, J. W. (2008) Quantification of thyroglobulin, a low-abundance serum protein, by immunoaffinity peptide enrichment and tandem mass spectrometry. Clin. Chem. 54, 1796-1804
-
(2008)
Clin. Chem.
, vol.54
, pp. 1796-1804
-
-
Hoofnagle, A.N.1
Becker, J.O.2
Wener, M.H.3
Heinecke, J.W.4
-
23
-
-
66449083773
-
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., Burgess, M., Mani, D. R., Lee, R. T., Sabatine, M. S., Gerszten, R. E., and Carr, S. A. (2009) Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry. Clin. Chem. 55, 1108-1117
-
(2009)
Clin. Chem.
, vol.55
, pp. 1108-1117
-
-
Kuhn, E.1
Addona, T.2
Keshishian, H.3
Burgess, M.4
Mani, D.R.5
Lee, R.T.6
Sabatine, M.S.7
Gerszten, R.E.8
Carr, S.A.9
-
24
-
-
77956391635
-
Online high-flow peptide immunoaffinity enrichment and nanoflow liquid Chromatography/Tandem mass spectrometry: Assay development for total salivary Pepsin/ Pepsinogen
-
Neubert, H., Gale, J., and Muirhead, D. (2010) Online high-flow peptide immunoaffinity enrichment and nanoflow liquid Chromatography/Tandem mass spectrometry: Assay development for total salivary Pepsin/ Pepsinogen. Clin. Chem. 56, 1413-1423
-
(2010)
Clin. Chem.
, vol.56
, pp. 1413-1423
-
-
Neubert, H.1
Gale, J.2
Muirhead, D.3
-
25
-
-
33846665857
-
Antibody-based enrichment of peptides on magnetic beads for mass-spectrometry-based quantification of serum biomarkers
-
Whiteaker, J. R., Zhao, L., Zhang, H. Y., Feng, L. C., Piening, B. D., Anderson, L., and Paulovich, A. G. (2007) Antibody-based enrichment of peptides on magnetic beads for mass-spectrometry-based quantification of serum biomarkers. Anal. Biochem. 362, 44-54
-
(2007)
Anal. Biochem.
, vol.362
, pp. 44-54
-
-
Whiteaker, J.R.1
Zhao, L.2
Zhang, H.Y.3
Feng, L.C.4
Piening, B.D.5
Anderson, L.6
Paulovich, A.G.7
-
26
-
-
66949116701
-
A human proteome detection and quantitation project
-
Anderson, N. L., Anderson, N. G., Pearson, T. W., Borchers, C. H., Paulovich, A. G., Patterson, S. D., Gillette, M., Aebersold, R., and Carr, S. A. (2009) A human proteome detection and quantitation project. Mol. Cell. Proteomics 8, 883-886
-
(2009)
Mol. Cell. Proteomics
, vol.8
, pp. 883-886
-
-
Anderson, N.L.1
Anderson, N.G.2
Pearson, T.W.3
Borchers, C.H.4
Paulovich, A.G.5
Patterson, S.D.6
Gillette, M.7
Aebersold, R.8
Carr, S.A.9
-
27
-
-
77951965920
-
Skyline: An open source document editor for creating and analyzing targeted proteomics experiments
-
MacLean, B., Tomazela, D. M., Shulman, N., Chambers, M., Finney, G. L., Frewen, B., Kern, R., Tabb, D. L., Liebler, D. C., and MacCoss, M. J. (2010) Skyline: An open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26, 966-968
-
(2010)
Bioinformatics
, vol.26
, pp. 966-968
-
-
MacLean, B.1
Tomazela, D.M.2
Shulman, N.3
Chambers, M.4
Finney, G.L.5
Frewen, B.6
Kern, R.7
Tabb, D.L.8
Liebler, D.C.9
MacCoss, M.J.10
-
28
-
-
85128759053
-
A list of candidate cancer biomarkers for targeted proteomics
-
Polanski, M., and Anderson, N. L. (2007) A list of candidate cancer biomarkers for targeted proteomics. Biomarker Insights 1, 1-48
-
(2007)
Biomarker Insights
, vol.1
, pp. 1-48
-
-
Polanski, M.1
Anderson, N.L.2
-
29
-
-
59849093889
-
Prediction of high-responding peptides for targeted protein assays by mass spectrometry
-
Fusaro, V. A., Mani, D. R., Mesirov, J. P., and Carr, S. A. (2009) Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nat. Biotechnol. 27, 190-198
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 190-198
-
-
Fusaro, V.A.1
Mani, D.R.2
Mesirov, J.P.3
Carr, S.A.4
-
30
-
-
11144246404
-
Benchmarking B cell epitope prediction: Underperformance of existing methods
-
Blythe, M. J., and Flower, D. R. (2005) Benchmarking B cell epitope prediction: Underperformance of existing methods. Protein Sci. 14, 246-248
-
(2005)
Protein Sci.
, vol.14
, pp. 246-248
-
-
Blythe, M.J.1
Flower, D.R.2
-
31
-
-
0242611620
-
Characterizing degradation products of peptides containing N-terminal cys residues by (offline high-performance liquid chromatography)/matrix-assisted laser desorption/ionization quadrupole time-of-flight measurements
-
Krokhin, O. V., Ens, W., and Standing, K. G. (2003) Characterizing degradation products of peptides containing N-terminal cys residues by (offline high-performance liquid chromatography)/matrix-assisted laser desorption/ionization quadrupole time-of-flight measurements. Rapid Commun. Mass Spectrom. 17, 2528-2534
-
(2003)
Rapid Commun. Mass Spectrom.
, vol.17
, pp. 2528-2534
-
-
Krokhin, O.V.1
Ens, W.2
Standing, K.G.3
-
32
-
-
79953299836
-
-
manuscript in preparation
-
Pearson, T. W., Pope, M., Razavi, M., Soste, M., Brown, T., Eyford, B. A., Jackson, A., Dufield, D., Neubert, H., VanBogelen, R., and Anderson, N. L. (manuscript in preparation) Antibodies for peptide enrichment in immunoproteomics.
-
Antibodies for Peptide Enrichment in Immunoproteomics
-
-
Pearson, T.W.1
Pope, M.2
Razavi, M.3
Soste, M.4
Brown, T.5
Eyford, B.A.6
Jackson, A.7
Dufield, D.8
Neubert, H.9
VanBogelen, R.10
Anderson, N.L.11
-
33
-
-
77649273179
-
Automated screening of monoclonal antibodies for SISCAPA assays using a magnetic bead processor and liquid chromatography-selected reaction monitoring-mass spectrometry
-
Schoenherr, R. M., Zhao, L., Whiteaker, J. R., Feng, L. C., Li, L., Liu, L., Liu, X., and Paulovich, A. G. (2010) Automated screening of monoclonal antibodies for SISCAPA assays using a magnetic bead processor and liquid chromatography-selected reaction monitoring-mass spectrometry. J. Immunol. Methods 353, 49-61
-
(2010)
J. Immunol. Methods
, vol.353
, pp. 49-61
-
-
Schoenherr, R.M.1
Zhao, L.2
Whiteaker, J.R.3
Feng, L.C.4
Li, L.5
Liu, L.6
Liu, X.7
Paulovich, A.G.8
-
34
-
-
59249094196
-
Anti-peptide antibody screening: Selection of high affinity monoclonal reagents by a refined surface plasmon resonance technique
-
Pope, M. E., Soste, M. V., Eyford, B. A., Anderson, N. L., and Pearson, T. W. (2009) Anti-peptide antibody screening: Selection of high affinity monoclonal reagents by a refined surface plasmon resonance technique. J. Immunol. Methods 341, 86-96
-
(2009)
J. Immunol. Methods
, vol.341
, pp. 86-96
-
-
Pope, M.E.1
Soste, M.V.2
Eyford, B.A.3
Anderson, N.L.4
Pearson, T.W.5
-
35
-
-
78650838718
-
MALDI immunoscreening (MiSCREEN): A method for selection of anti-peptide monoclonal antibodies for use in immunoproteomics
-
Razavi, M., Pope, M. E., Soste, M. V., Eyford, B. A., Jackson, A. M., Anderson, N. L., and Pearson, T. W. (2011) MALDI immunoscreening (MiSCREEN): A method for selection of anti-peptide monoclonal antibodies for use in immunoproteomics. J. Immunol. Methods 364, 50-64
-
(2011)
J. Immunol. Methods
, vol.364
, pp. 50-64
-
-
Razavi, M.1
Pope, M.E.2
Soste, M.V.3
Eyford, B.A.4
Jackson, A.M.5
Anderson, N.L.6
Pearson, T.W.7
|