-
1
-
-
84871983086
-
Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry
-
Gillette, M. A., and Carr, S. A. (2013) Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry. Nat Methods 10, 28-34
-
(2013)
Nat Methods
, vol.10
, pp. 28-34
-
-
Gillette, M.A.1
Carr, S.A.2
-
2
-
-
84861990380
-
Selected reaction monitoring-based proteomics: Workflows, potential, pitfalls and future directions
-
Picotti, P., and Aebersold, R. (2012) Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat. Methods 9, 555-566
-
(2012)
Nat. Methods
, vol.9
, pp. 555-566
-
-
Picotti, P.1
Aebersold, R.2
-
3
-
-
80052539443
-
LC-MS/MS in the clinical laboratory - Where to from here?
-
Grebe, S. K. G., and Singh, R. J. J. (2011) LC-MS/MS in the clinical laboratory - where to from here? Clin. Biochem. Rev. 32, 5-31
-
(2011)
Clin. Biochem. Rev.
, vol.32
, pp. 5-31
-
-
Grebe, S.K.G.1
Singh, R.J.J.2
-
4
-
-
0016584941
-
The scope of mass spectrometry in clinical chemistry
-
Lawson, A. M. (1975) The scope of mass spectrometry in clinical chemistry. Clin. Chem. 21, 803-824
-
(1975)
Clin. Chem.
, vol.21
, pp. 803-824
-
-
Lawson, A.M.1
-
5
-
-
0025346679
-
Stable isotopes in the management and diagnosis of inborn errors of metabolism
-
Parsons, H. G. (1990) Stable isotopes in the management and diagnosis of inborn errors of metabolism. Can. J. Physiol. Pharmacol. 68, 950-954
-
(1990)
Can. J. Physiol. Pharmacol.
, vol.68
, pp. 950-954
-
-
Parsons, H.G.1
-
7
-
-
0018008685
-
Use of mass spectrometry for confirmation of animal drug residues
-
Sphon, J. A. (1978) Use of mass spectrometry for confirmation of animal drug residues. J. Assoc. Off. Anal. Chem. 61, 1247-1252
-
(1978)
J. Assoc. Off. Anal. Chem.
, vol.61
, pp. 1247-1252
-
-
Sphon, J.A.1
-
8
-
-
0032128052
-
Determination of sulfonic acid degradates of chloroacetanilide and chloroacetamide herbicides in groundwater by LC/MS/MS
-
Vargo, J. D. (1998) Determination of sulfonic acid degradates of chloroacetanilide and chloroacetamide herbicides in groundwater by LC/MS/MS. Anal. Chem. 70, 2699-2703
-
(1998)
Anal. Chem.
, vol.70
, pp. 2699-2703
-
-
Vargo, J.D.1
-
9
-
-
34447562825
-
Noninvasive human metabolome analysis for differential diagnosis of inborn errors of metabolism
-
Kuhara, T. (2007) Noninvasive human metabolome analysis for differential diagnosis of inborn errors of metabolism. J. Chromatog. 855, 42-50
-
(2007)
J. Chromatog.
, vol.855
, pp. 42-50
-
-
Kuhara, T.1
-
10
-
-
0036841898
-
Comprehensive screening of urine samples from inborn errors of metabolism by electrospray tandem mass spectrometry
-
Pitt, J. J., Eggington, M., and Kahler, S. G. (2002) Comprehensive screening of urine samples from inborn errors of metabolism by electrospray tandem mass spectrometry. Clin. Chem. 48, 1970-1980
-
(2002)
Clin. Chem.
, vol.48
, pp. 1970-1980
-
-
Pitt, J.J.1
Eggington, M.2
Kahler, S.G.3
-
11
-
-
79951896481
-
Best practices in a tiered approach to metabolite quantification: Views and recommendations of the european bioanalysis forum
-
Timmerman, P., Anders, Kall, M., Gordon, B., Laakso, S., Freisleben, A., and Hucker, R. (2010) Best practices in a tiered approach to metabolite quantification: Views and recommendations of the European Bioanalysis Forum. Bioanalysis 2, 1185-1194
-
(2010)
Bioanalysis
, vol.2
, pp. 1185-1194
-
-
Timmerman, P.1
Anders Kall, M.2
Gordon, B.3
Laakso, S.4
Freisleben, A.5
Hucker, R.6
-
12
-
-
84865723412
-
European Bioanalysis Forum recommendation on method establishment and bioanalysis of biomarkers in support of drug development
-
Timmerman, P., Herling, C., Stoellner, D., Jaitner, B., Pihl, S., Elsby, K., Henderson, N., Barroso, B., Fischmann, S., Companjen, A., Versteilen, A., Bates, S., Kingsley, C., and Kunz, U. (2012) European Bioanalysis Forum recommendation on method establishment and bioanalysis of biomarkers in support of drug development. Bioanalysis 4, 1883-1894
-
(2012)
Bioanalysis
, vol.4
, pp. 1883-1894
-
-
Timmerman, P.1
Herling, C.2
Stoellner, D.3
Jaitner, B.4
Pihl, S.5
Elsby, K.6
Henderson, N.7
Barroso, B.8
Fischmann, S.9
Companjen, A.10
Versteilen, A.11
Bates, S.12
Kingsley, C.13
Kunz, U.14
-
13
-
-
84859135065
-
Large meets small': Connecting the bioanalytical community around peptide and protein bioanalysis with LCMS(/MS)
-
Timmerman, P., Lausecker, B., Barosso, B., van Amsterdam, P., Luedtke, S., and Dijksman, J. (2012) 'Large Meets Small': connecting the bioanalytical community around peptide and protein bioanalysis with LCMS(/ MS). Bioanalysis 4, 627-631
-
(2012)
Bioanalysis
, vol.4
, pp. 627-631
-
-
Timmerman, P.1
Lausecker, B.2
Barosso, B.3
Van Amsterdam, P.4
Luedtke, S.5
Dijksman, J.6
-
14
-
-
37049085797
-
Quality concepts and practices applies to sampling - An exploratory study
-
Thompson, M., and Ramsey, M. H. (1995) Quality concepts and practices applies to sampling - an exploratory study. Analyst 120, 261-270
-
(1995)
Analyst
, vol.120
, pp. 261-270
-
-
Thompson, M.1
Ramsey, M.H.2
-
16
-
-
0037487096
-
Establishing the fitness for purpose of mass spectrometric methods
-
Bethem, R., Boison, J., Gale, J., Heller, D., Lehotay, S., Loo, J., Musser, S., Price, P., and Stein, S. (2003) Establishing the fitness for purpose of mass spectrometric methods. J. Amer. Soc. Mass Spectrom. 14, 528-541
-
(2003)
J. Amer. Soc. Mass Spectrom.
, vol.14
, pp. 528-541
-
-
Bethem, R.1
Boison, J.2
Gale, J.3
Heller, D.4
Lehotay, S.5
Loo, J.6
Musser, S.7
Price, P.8
Stein, S.9
-
17
-
-
32544451155
-
Fit-for-purpose method development and validation for successful biomarker measurement
-
Lee, J. W., Devanarayan, V., Barrett, Y. C., Weiner, R., Allinson, J., Fountain, S., Keller, S., Weinryb, I., Green, M., Duan, L., Rogers, J. A., Millham, R., O'Brien, P. J., Sailstad, J., Khan, M., Ray, C., and Wagner, J. A. (2006) Fit-for-purpose method development and validation for successful biomarker measurement. Pharm. Res. 23, 312-328
-
(2006)
Pharm. Res.
, vol.23
, pp. 312-328
-
-
Lee, J.W.1
Devanarayan, V.2
Barrett, Y.C.3
Weiner, R.4
Allinson, J.5
Fountain, S.6
Keller, S.7
Weinryb, I.8
Green, M.9
Duan, L.10
Rogers, J.A.11
Millham, R.12
O'Brien, P.J.13
Sailstad, J.14
Khan, M.15
Ray, C.16
Wagner, J.A.17
-
18
-
-
33845205234
-
Biomarker assay translation from discovery to clinical studies in cancer drug development: Quantification of emerging protein biomarkers
-
Lee, J. W., Figeys, D., and Vasilescu, J. (2007) Biomarker assay translation from discovery to clinical studies in cancer drug development: quantification of emerging protein biomarkers. Adv. Cancer Res. 96, 269-298
-
(2007)
Adv. Cancer Res.
, vol.96
, pp. 269-298
-
-
Lee, J.W.1
Figeys, D.2
Vasilescu, J.3
-
19
-
-
78049260524
-
Fit-for-purpose biomarker method validation for application in clinical trials of anticancer drugs
-
On Behalf Of The Bioanalysis and Quality Assurance (BAQA) Group of the ECMC
-
Cummings, J., Raynaud, F., Jones, L., Sugar, R., and Dive, C., on behalf of the Bioanalysis and Quality Assurance (BAQA) Group of the ECMC (2010) Fit-for-purpose biomarker method validation for application in clinical trials of anticancer drugs. Br. J. Cancer 103, 1313-1317
-
(2010)
Br. J. Cancer
, vol.103
, pp. 1313-1317
-
-
Cummings, J.1
Raynaud, F.2
Jones, L.3
Sugar, R.4
Dive, C.5
-
20
-
-
3042735127
-
The need for guidelines in publication of peptide and protein identification data
-
Carr, S. A., Aebersold, R., Baldwin, M., Burlingame, A., Clauser, K., and Nesvizhski, A. (2004) The need for guidelines in publication of peptide and protein identification data. Mol. Cell. Proteomics 3, 531-533
-
(2004)
Mol. Cell. Proteomics
, vol.3
, pp. 531-533
-
-
Carr, S.A.1
Aebersold, R.2
Baldwin, M.3
Burlingame, A.4
Clauser, K.5
Nesvizhski, A.6
-
21
-
-
33646907086
-
Reporting protein identification data: The next generation of guidelines
-
Bradshaw, R. A., Burlingame, A. L., Carr, S., and Aebersold R. (2006) Reporting protein identification data: the next generation of guidelines. Mol. Cell. Proteomics. 5, 787-788
-
(2006)
Mol. Cell. Proteomics.
, vol.5
, pp. 787-788
-
-
Bradshaw, R.A.1
Burlingame, A.L.2
Carr, S.3
Aebersold, R.4
-
22
-
-
78751599905
-
Updating the MCP Proteomic publication guidelines
-
Chalkley, R. J., Clauser, K. R., and Carr, S. A. (2009) Updating the MCP Proteomic publication guidelines. ASBMB Today, 16-17
-
(2009)
ASBMB Today
, pp. 16-17
-
-
Chalkley, R.J.1
Clauser, K.R.2
Carr, S.A.3
-
23
-
-
84895516816
-
-
http://www.mcponline.org.libproxy.mit.edu/site/misc/PhialdelphiaGuide linesFINALDRAFT.pdf
-
-
-
-
24
-
-
0003484310
-
-
Department of Health and Human Services, US FDA, Center for Drug Evaluation and Research, Rockville, MD, U.S.A. (Rev. 1, September, 2013)
-
Guidance for Industry: Bioanalytical Method Validation. (2001) US Department of Health and Human Services, US FDA, Center for Drug Evaluation and Research, Rockville, MD, U.S.A. (Rev. 1, September, 2013)
-
(2001)
Guidance for Industry: Bioanalytical Method Validation
-
-
-
25
-
-
81055146012
-
-
EMA, Committee for Medicinal Products for Human Use, London, UK
-
(2011) Guideline on Bioanalytical Method Validation. EMA, Committee for Medicinal Products for Human Use, London, UK
-
(2011)
Guideline on Bioanalytical Method Validation
-
-
-
26
-
-
84867355005
-
White paper on recent issues in bioanalysis and alignment of multiple guidelines
-
DeSilva et al. (2012) White paper on recent issues in bioanalysis and alignment of multiple guidelines. Bioanalysis 4, 2213-2226
-
(2012)
Bioanalysis
, vol.4
, pp. 2213-2226
-
-
De, S.1
-
27
-
-
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., et al. (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
-
28
-
-
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. Nat. Acad. Sci. 100, 6940-6945
-
(2003)
Proc. Nat. Acad. Sci.
, vol.100
, pp. 6940-6945
-
-
Gerber, S.A.1
Rush, J.2
Stemman, O.3
Kirschner, M.W.4
Gygi, S.P.5
-
29
-
-
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 2, 2212
-
(2007)
Mol. Cell. Proteomics
, vol.2
, pp. 2212
-
-
Keshishian, H.1
Addona, T.2
Burgess, M.3
Kuhn, E.4
Carr, S.A.5
-
30
-
-
38849105619
-
Quantification of NTproBNP in rat serum using immunoprecipitation and LC/MS/MS: A Biomarker of drug-induced cardiac hypertrophy
-
Berna, M. J., Ott, L., Engle, S., Watson, D., Solter, P., and Ackermann, B. (2008) Quantification of NTproBNP in rat serum using immunoprecipitation and LC/MS/MS: a Biomarker of drug-induced cardiac hypertrophy. Anal. Chem. 80, 561-566
-
(2008)
Anal. Chem.
, vol.80
, pp. 561-566
-
-
Berna, M.J.1
Ott, L.2
Engle, S.3
Watson, D.4
Solter, P.5
Ackermann, B.6
-
31
-
-
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. L., 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, 633-685
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 633-685
-
-
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.L.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..
-
32
-
-
68749094119
-
Full dynamic range proteome analysis of S. Cerevisiae by targeted proteomics
-
doi: 10.1016/j.cell.2009.05.051. Epub 2009 Aug 6
-
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. doi: 10.1016/j.cell.2009.05.051. Epub 2009 Aug 6
-
(2009)
Cell
, vol.138
, pp. 795-806
-
-
Picotti, P.1
Bodenmiller, B.2
Mueller, L.N.3
Domon, B.4
Aebersold, R.5
-
33
-
-
79953305842
-
Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry
-
Whiteaker, J. R., Zhao, L., Abbatiello, S. E., Burgess, M., Kuhn, E., Lin, C. W., Pope, M. E., Razavi, M., Anderson, N. L., Pearson, T. W., Carr, S. A., and Paulovich, A. G. (2011) Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry. Mol. Cell. Proteomics 10, M110.005645
-
(2011)
Mol. Cell. Proteomics
, vol.10
-
-
Whiteaker, J.R.1
Zhao, L.2
Abbatiello, S.E.3
Burgess, M.4
Kuhn, E.5
Lin, C.W.6
Pope, M.E.7
Razavi, M.8
Anderson, N.L.9
Pearson, T.W.10
Carr, S.A.11
Paulovich, A.G.12
-
34
-
-
84866538934
-
Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum
-
Shi, T., Fillmore, T. L., Sun, X., Zhao, R., Schepmoes, A. A., Hossain, M., Xie, F., Wu, S., Kim, J. S., Jones, N., Moore, R. J., Pasa-Tolic, L., Kagan, J., Rodland, K. D., Liu, T., Tang, K., Camp, D. G., Smith, R. D., and Qian, W. J. (2012) Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum. Proc. Natl. Acad. Sci. U.S.A. 109, 15395-15400
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 15395-15400
-
-
Shi, T.1
Fillmore, T.L.2
Sun, X.3
Zhao, R.4
Schepmoes, A.A.5
Hossain, M.6
Xie, F.7
Wu, S.8
Kim, J.S.9
Jones, N.10
Moore, R.J.11
Pasa-Tolic, L.12
Kagan, J.13
Rodland, K.D.14
Liu, T.15
Tang, K.16
Camp, D.G.17
Smith, R.D.18
Qian, W.J.19
-
35
-
-
79952284442
-
Mutant proteins as cancerspecific biomarkers
-
Wang, Q., Chaerkady, R., Wu, J., Hwang, H. J., Papadopoulos, N., Kopelovich, L., Maitra. A., Matthaei, H., Eshleman, J. R., Hruban, R. H., Kinzler, K. W., Pandey, A., and Vogelstein, B. (2011) Mutant proteins as cancerspecific biomarkers. Proc. Natl. Acad. Sci. U.S.A. 108, 2444-2449
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 2444-2449
-
-
Wang, Q.1
Chaerkady, R.2
Wu, J.3
Hwang, H.J.4
Papadopoulos, N.5
Kopelovich, L.6
Maitra, A.7
Matthaei, H.8
Eshleman, J.R.9
Hruban, R.H.10
Kinzler, K.W.11
Pandey, A.12
Vogelstein, B.13
-
36
-
-
79960269601
-
A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease
-
Addona, T. A., Shi, X., Keshishian, H., Mani, D. R., Burgess, M., Gillette, M. A., Clauser, K. R., Shen, D., Lewis, G. D., Farrell, L. A., Fifer, M. A., Sabatine, M. S., Gerszten, R. E., and Carr, S. A. (2011) A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease. Nat. Biotechnol. 29, 635-643
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 635-643
-
-
Addona, T.A.1
Shi, X.2
Keshishian, H.3
Mani, D.R.4
Burgess, M.5
Gillette, M.A.6
Clauser, K.R.7
Shen, D.8
Lewis, G.D.9
Farrell, L.A.10
Fifer, M.A.11
Sabatine, M.S.12
Gerszten, R.E.13
Carr, S.A.14
-
37
-
-
79960214321
-
A targeted proteomics-based pipeline for verification of biomarkers in plasma
-
Whiteaker, J. R., Lin, C., Kennedy, J., Hou, L., Trute, M., Sokal, I., Yan, P., Schoenherr, R. M., Zhao, L., Voytovich, U. J., Kelly-Spratt, K. S., Krasnoselsky, A., Gafken, P. R., Hogan, J. M., Jones, L. A., Wang, P., Amon, L., Chodosh, L. A., Nelson, P. S., McIntosh, M. W., Kemp, C. J., and Paulovich, A. G. (2011) A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat. Biotech. 29, 625-634
-
(2011)
Nat. Biotech.
, vol.29
, pp. 625-634
-
-
Whiteaker, J.R.1
Lin, C.2
Kennedy, J.3
Hou, L.4
Trute, M.5
Sokal, I.6
Yan, P.7
Schoenherr, R.M.8
Zhao, L.9
Voytovich, U.J.10
Kelly-Spratt, K.S.11
Krasnoselsky, A.12
Gafken, P.R.13
Hogan, J.M.14
Jones, L.A.15
Wang, P.16
Amon, L.17
Chodosh, L.A.18
Nelson, P.S.19
McIntosh, M.W.20
Kemp, C.J.21
Paulovich, A.G.22
more..
-
38
-
-
84860869256
-
MRM-based multiplexed quantitation of 67 putative cardiovascular disease biomarkers in human plasma
-
Domanski, D., Percy, A. J., Yang, J., Chambers, A. G., Hill, J. S., Freue, G. V., and Borchers, C. H. (2012) MRM-based multiplexed quantitation of 67 putative cardiovascular disease biomarkers in human plasma. Proteomics 12, 1222-1243
-
(2012)
Proteomics
, vol.12
, pp. 1222-1243
-
-
Domanski, D.1
Percy, A.J.2
Yang, J.3
Chambers, A.G.4
Hill, J.S.5
Freue, G.V.6
Borchers, C.H.7
-
39
-
-
84857847927
-
Multiplex targeted proteomic assay for biomarker detection in plasma: A pancreatic cancer biomarker case study
-
Pan, S., Chen, R., Brand, R. E., Hawley, S., Tamura, Y., Gafken, P. R., Milless, B. P., Goodlett, D. R., Rush, J., and Brentnall, T. A. (2012) Multiplex targeted proteomic assay for biomarker detection in plasma: A pancreatic cancer biomarker case study. J. Proteome Res. 11, 1937-1948
-
(2012)
J. Proteome Res.
, vol.11
, pp. 1937-1948
-
-
Pan, S.1
Chen, R.2
Brand, R.E.3
Hawley, S.4
Tamura, Y.5
Gafken, P.R.6
Milless, B.P.7
Goodlett, D.R.8
Rush, J.9
Brentnall, T.A.10
-
40
-
-
84863923380
-
Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics
-
Huttenhain, R., Soste, M., Selevsek, N., Rost, H., Sethi, A., Carapito, C., Farrah, T., Deutsch, E. W., Kusebauch, U., Moritz R. L., Nimeus-Malmstrom, E., Rinner, O., and Aebersold, R. (2012) Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Sci. Transl. Med. 4, 1-13
-
(2012)
Sci. Transl. Med.
, vol.4
, pp. 1-13
-
-
Huttenhain, R.1
Soste, M.2
Selevsek, N.3
Rost, H.4
Sethi, A.5
Carapito, C.6
Farrah, T.7
Deutsch, E.W.8
Kusebauch, U.9
Moritz, R.L.10
Nimeus-Malmstrom, E.11
Rinner, O.12
Aebersold, R.13
-
41
-
-
84878449123
-
Measurement of thyroglobulin by liquid chromatography-tandem mass spectrometry in serum and plasma in the presence of antithyroglobulin autoantibodies
-
Kushnir, M. M., Rockwood, A. L., Roberts, W. L., Abraham, D., Hoofnagle, A. N., and Meikle, A. W. (2013) Measurement of thyroglobulin by liquid chromatography-tandem mass spectrometry in serum and plasma in the presence of antithyroglobulin autoantibodies. Clinical Chemistry 59, 982-990
-
(2013)
Clinical Chemistry
, vol.59
, pp. 982-990
-
-
Kushnir, M.M.1
Rockwood, A.L.2
Roberts, W.L.3
Abraham, D.4
Hoofnagle, A.N.5
Meikle, A.W.6
-
42
-
-
84873385425
-
Sequential protein and peptide immunoaffinity capture for mass spectrometry-based quantification of total human beta-nerve growth factor
-
Neubert, H., Muirhead, D., Kabir, M., Grace, C., Cleton, A., and Arends, R. (2013) Sequential protein and peptide immunoaffinity capture for mass spectrometry-based quantification of total human beta-nerve growth factor. Anal. Chem. 85, 1719-1726
-
(2013)
Anal. Chem.
, vol.85
, pp. 1719-1726
-
-
Neubert, H.1
Muirhead, D.2
Kabir, M.3
Grace, C.4
Cleton, A.5
Arends, R.6
-
43
-
-
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
-
44
-
-
67649511917
-
Isotope dilution strategies for absolute quantitative proteomics
-
Brun, V., Masselon, C., Garin, J., and Dupuis, A. (2009) Isotope dilution strategies for absolute quantitative proteomics. J. Proteomics 72, 740-749
-
(2009)
J. Proteomics
, vol.72
, pp. 740-749
-
-
Brun, V.1
Masselon, C.2
Garin, J.3
Dupuis, A.4
-
45
-
-
71049137289
-
Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma
-
Kuzyk, M. A., Smith, D., Yang, J. C., Cross, T. J., Jackson, A. M., Hardie, D. B., Anderson, N. L., and Borchers, C. H. (2009) Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma. Mol. Cell. Proteomics 8, 1860-1877
-
(2009)
Mol. Cell. Proteomics
, vol.8
, pp. 1860-1877
-
-
Kuzyk, M.A.1
Smith, D.2
Yang, J.C.3
Cross, T.J.4
Jackson, A.M.5
Hardie, D.B.6
Anderson, N.L.7
Borchers, C.H.8
-
46
-
-
84865791474
-
Peptide production and decay rates affect the quantitative accuracy of protein cleavage isotope dilution mass spectrometry (PC-IDMS)
-
Shuford, C. M., Sederoff, R. R., Chiang, V. L., and Muddiman, D. C. (2012) Peptide production and decay rates affect the quantitative accuracy of protein cleavage isotope dilution mass spectrometry (PC-IDMS). Mol. Cell. Proteomics 11, 814-823
-
(2012)
Mol. Cell. Proteomics
, vol.11
, pp. 814-823
-
-
Shuford, C.M.1
Sederoff, R.R.2
Chiang, V.L.3
Muddiman, D.C.4
-
47
-
-
0032011562
-
Matrix effect in quantitative LC/MS/MS analyses of biological fluids: A method for determination of finasteride in human plasma at picogram per milliliter concentrations
-
Matuszewski, B. K., Constanzer, M. L., and Chavez-Eng, C. M. (1998) Matrix effect in quantitative LC/MS/MS analyses of biological fluids: a method for determination of finasteride in human plasma at picogram per milliliter concentrations. Anal. Chem. 70, 882-889
-
(1998)
Anal. Chem.
, vol.70
, pp. 882-889
-
-
Matuszewski, B.K.1
Constanzer, M.L.2
Chavez-Eng, C.M.3
-
48
-
-
0034487744
-
Mechanistic investigation of ionization suppression in electrospray ionization
-
King, R., Bonfiglio, R., Fernandez-Metzler, C., Miller-Stein, C., and Olah, T. (2000) Mechanistic investigation of ionization suppression in electrospray ionization. J. Am. Soc. Mass Spectrom. 11, 942-950
-
(2000)
J. Am. Soc. Mass Spectrom.
, vol.11
, pp. 942-950
-
-
King, R.1
Bonfiglio, R.2
Fernandez-Metzler, C.3
Miller-Stein, C.4
Olah, T.5
-
49
-
-
75749126208
-
Automated Detection of inaccurate and imprecise transitions in quantitative assays of peptides by multiple monitoring mass spectrometry
-
Abbatiello, S. E., Mani, D. R., Keshishian, H., and Carr, S. A. (2010) Automated Detection of inaccurate and imprecise transitions in quantitative assays of peptides by multiple monitoring mass spectrometry. Clin. Chem. 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
-
50
-
-
79955595074
-
MProphet: Automated data processing and statistical validation for large-scale SRM experiments
-
Reiter, L., Rinner, O., Picotti, P., Hüttenhain, R., Beck, M., Brusniak, M. Y., Hengartner, M. O., and Aebersold, R. (2011) mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat. Methods 8, 430-435
-
(2011)
Nat. Methods
, vol.8
, pp. 430-435
-
-
Reiter, L.1
Rinner, O.2
Picotti, P.3
Hüttenhain, R.4
Beck, M.5
Brusniak, M.Y.6
Hengartner, M.O.7
Aebersold, R.8
-
51
-
-
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
-
52
-
-
38349037650
-
Isotope-labeled protein standards
-
Brun, V., Dupuis, A., Adrait, A., Marcellin, M., Thomas, D., Court, M., Vandenesch, F., and Garin, J. (2007) Isotope-labeled protein standards. Mol. Cell. Proteomics 6, 2139-2149
-
(2007)
Mol. Cell. Proteomics
, vol.6
, pp. 2139-2149
-
-
Brun, V.1
Dupuis, A.2
Adrait, A.3
Marcellin, M.4
Thomas, D.5
Court, M.6
Vandenesch, F.7
Garin, J.8
-
53
-
-
33947427090
-
A liquid chromatography-mass spectrometry method for the quantification of urinary albumin using a novel N-15- isotopically labeled albumin internal standard
-
Singh, R., Crow, F. W., Babic, N., Lutz, W. H., Lieske, J. C., Larson, T. S., and Kumar, R. (2007) A liquid chromatography-mass spectrometry method for the quantification of urinary albumin using a novel N-15- isotopically labeled albumin internal standard. Clin. Chem. 53, 540-542
-
(2007)
Clin. Chem.
, vol.53
, pp. 540-542
-
-
Singh, R.1
Crow, F.W.2
Babic, N.3
Lutz, W.H.4
Lieske, J.C.5
Larson, T.S.6
Kumar, R.7
-
54
-
-
45749100868
-
Mass spectrometry-based approaches toward absolute quantitative proteomics
-
Kito, K., and Ito, T. (2008) Mass spectrometry-based approaches toward absolute quantitative proteomics. Current Genomics 9, 263-274
-
(2008)
Current Genomics
, vol.9
, pp. 263-274
-
-
Kito, K.1
Ito, T.2
-
55
-
-
84867026555
-
PSAQ standards for accurate MS-based quantification of proteins: From the concept to biomedical applications
-
Picard, G., Lebert, D., Louwagie, M., Adrait, A., Huillet, C., Vandenesch, F., Bruley, C., Garin, J., Jaquinod, M., and Brun, V. (2012) PSAQ standards for accurate MS-based quantification of proteins: from the concept to biomedical applications. J. Mass Spectrom. 47, 1353-1363
-
(2012)
J. Mass Spectrom.
, vol.47
, pp. 1353-1363
-
-
Picard, G.1
Lebert, D.2
Louwagie, M.3
Adrait, A.4
Huillet, C.5
Vandenesch, F.6
Bruley, C.7
Garin, J.8
Jaquinod, M.9
Brun, V.10
-
56
-
-
84860880032
-
Inter-laboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma
-
Kuhn, E., Whiteaker, J. R., Mani, D. R., Jackson, A. M., Zhao, L., Pope, M. E., Smith, D., Rivera, K. D., Anderson, N. L., Skates, S. J., Pearson, T. W., Paulovich, A. G., and Carr, S. A. (2012) Inter-laboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma. Mol. Cell. Proteomics 11, M111.013854
-
(2012)
Mol. Cell. Proteomics
, vol.11
-
-
Kuhn, E.1
Whiteaker, J.R.2
Mani, D.R.3
Jackson, A.M.4
Zhao, L.5
Pope, M.E.6
Smith, D.7
Rivera, K.D.8
Anderson, N.L.9
Skates, S.J.10
Pearson, T.W.11
Paulovich, A.G.12
Carr, S.A.13
-
57
-
-
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
-
58
-
-
79960859298
-
A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer
-
Remily-Wood, E. R., Liu, R. Z., Xiang, Y., Chen, Y., Thomas, C. E., Rajyaguru, N., Kaufman, L. M., Ochoa, J. E., Hazlehurst, L., Pinilla-Ibarz, J., Lancet, J., Zhang, G. L., Haura, E., Shibata, D., Yeatman, T., Smalley, K. S. M., Dalton, W. S., Huang, E. N., Scott, E., Bloom, G. C., Eschrich, S. A., and Koomen, J. M. (2011) A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer. Proteomics Clin. Appl. 5, 383-396
-
(2011)
Proteomics Clin. Appl.
, vol.5
, pp. 383-396
-
-
Remily-Wood, E.R.1
Liu, R.Z.2
Xiang, Y.3
Chen, Y.4
Thomas, C.E.5
Rajyaguru, N.6
Kaufman, L.M.7
Ochoa, J.E.8
Hazlehurst, L.9
Pinilla-Ibarz, J.10
Lancet, J.11
Zhang, G.L.12
Haura, E.13
Shibata, D.14
Yeatman, T.15
Smalley, K.S.M.16
Dalton, W.S.17
Huang, E.N.18
Scott, E.19
Bloom, G.C.20
Eschrich, S.A.21
Koomen, J.M.22
more..
-
59
-
-
84870656540
-
Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer
-
Gallien, S., Duriez, E., Crone, C., Kellmann, M., Moehring, T., and Domon, B. (2012) Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer. Mol. Cell. Proteomics 11, 1709-1723
-
(2012)
Mol. Cell. Proteomics
, vol.11
, pp. 1709-1723
-
-
Gallien, S.1
Duriez, E.2
Crone, C.3
Kellmann, M.4
Moehring, T.5
Domon, B.6
-
60
-
-
66749171697
-
Statistical design of quantitative mass spectrometry-based proteomic experiments
-
Oberg, A. L., and Vitek, O. (2009) Statistical design of quantitative mass spectrometry-based proteomic experiments. J. Proteome Res. 8, 2144-2156
-
(2009)
J. Proteome Res.
, vol.8
, pp. 2144-2156
-
-
Oberg, A.L.1
Vitek, O.2
-
61
-
-
23144442824
-
Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides
-
Beynon, R. J., Doherty, M. K., Pratt, J. M., and Gaskell, S. J. (2005) Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat. Methods 2, 587
-
(2005)
Nat. Methods
, vol.2
, pp. 587
-
-
Beynon, R.J.1
Doherty, M.K.2
Pratt, J.M.3
Gaskell, S.J.4
-
62
-
-
0027414009
-
Evaluation of regression procedures for methods comparison studies
-
Linnet, K. (1993) Evaluation of regression procedures for methods comparison studies. Clin. Chem. 39, 424-432
-
(1993)
Clin. Chem.
, vol.39
, pp. 424-432
-
-
Linnet, K.1
-
63
-
-
23544462582
-
Limits for qualitative detection and quantitative determination
-
Currie, L. A. (1968) Limits for qualitative detection and quantitative determination. Anal. Chem. 40, 586-593
-
(1968)
Anal. Chem.
, vol.40
, pp. 586-593
-
-
Currie, L.A.1
-
64
-
-
1842503865
-
Partly nonparametric approach for determining the limit of detection
-
Linnet, K., and Kondratovichm M. (2004) Partly nonparametric approach for determining the limit of detection. Clin. Chem. 50, 732-740
-
(2004)
Clin. Chem.
, vol.50
, pp. 732-740
-
-
Linnet, K.1
Kondratovichm, M.2
-
65
-
-
84875604405
-
Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics
-
Mani, D. R., Abbatiello, S. E., and Carr, S. A. (2012) Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics. Bioinformatics 13, S9
-
(2012)
Bioinformatics
, vol.13
-
-
Mani, D.R.1
Abbatiello, S.E.2
Carr, S.A.3
-
66
-
-
0242354101
-
Quantitation of endogenous analytes in biofluid without a true blank matrix
-
Li, W., and Cohen, L.H. (2003) Quantitation of endogenous analytes in biofluid without a true blank matrix Anal. Chem. 75, 5854-5859
-
(2003)
Anal. Chem.
, vol.75
, pp. 5854-5859
-
-
Li, W.1
Cohen, L.H.2
-
67
-
-
84862317182
-
Sequential multiplexed analyte quantification using peptide immunoaffinity enrichment coupled to mass spectrometry Mol
-
10.1074/mcp.M111.015347
-
Whiteaker, J. R., Zhao, L., Lin, C., Yan, P., and Paulovich, A. G. (2011) Sequential multiplexed analyte quantification using peptide immunoaffinity enrichment coupled to mass spectrometry Mol. Cell. Proteomics 10.1074/mcp.M111.015347
-
(2011)
Cell. Proteomics
-
-
Whiteaker, J.R.1
Zhao, L.2
Lin, C.3
Yan, P.4
Paulovich, A.G.5
-
68
-
-
84895541599
-
Reversing the Curve: Determining LOD in the Presence of Endogenous Signal using SID-MRM-MS
-
Monday poster MP01, poster number 004
-
Kuhn, E., Ross, J., Abbatiello, S. E., Mani, D. R., and Carr, S. A. (2012) Reversing the Curve: Determining LOD in the Presence of Endogenous Signal using SID-MRM-MS. Presented at the 60th Annual Conference on Mass Spectrometry, Monday poster MP01, poster number 004
-
(2012)
Presented at the 60th Annual Conference on Mass Spectrometry
-
-
Kuhn, E.1
Ross, J.2
Abbatiello, S.E.3
Mani, D.R.4
Carr, S.A.5
-
69
-
-
84884373799
-
Design, implementation, and multi-site evaluation of a system suitability protocol for the quantitative assessment of instrument performance in LC-MRM-MS
-
doi: 10.1074/mcp.M112.027078
-
Abbatiello, S. E., Mani, D. R., Schilling, B., Maclean, B., Zimmerman, L. J., Feng, X., Cusack, M. P., Sedransk, N., Hall, S. C., Addona, T., Allen, S., Dodder, N. G., Ghosh, M., Held, J. M., Hedrick, V., Inerowicz, H. D., Jackson, A., Keshishian, H., Kim, J. W., Lyssand, J. S., Riley, C. P., Rudnick, P., Sadowski, P., Shaddox, K., Smith, D., Tomazela, D., Wahlander, A., Waldemarson, S., Whitwell, C. A., You, J., Zhang, S., Kins-inger, C. R., Mesri, M., Rodriguez, H., Borchers, C. H., Buck, C., Fisher, S. J., Gibson, B. W., Liebler, D., Maccoss, M., Neubert, T. A., Paulovich, A., Regnier, F., Skates, S. J., Tempst, P., Wang, M., and Carr, S. A. (2013) Design, implementation, and multi-site evaluation of a system suitability protocol for the quantitative assessment of instrument performance in LC-MRM-MS. Mol. Cell. Proteomics 12, 2623-2639. doi: 10.1074/mcp.M112.027078
-
(2013)
Mol. Cell. Proteomics
, vol.12
, pp. 2623-2639
-
-
Abbatiello, S.E.1
Mani, D.R.2
Schilling, B.3
Maclean, B.4
Zimmerman, L.J.5
Feng, X.6
Cusack, M.P.7
Sedransk, N.8
Hall, S.C.9
Addona, T.10
Allen, S.11
Dodder, N.G.12
Ghosh, M.13
Held, J.M.14
Hedrick, V.15
Inerowicz, H.D.16
Jackson, A.17
Keshishian, H.18
Kim, J.W.19
Lyssand, J.S.20
Riley, C.P.21
Rudnick, P.22
Sadowski, P.23
Shaddox, K.24
Smith, D.25
Tomazela, D.26
Wahlander, A.27
Waldemarson, S.28
Whitwell, C.A.29
You, J.30
Zhang, S.31
Kins-Inger, C.R.32
Mesri, M.33
Rodriguez, H.34
Borchers, C.H.35
Buck, C.36
Fisher, S.J.37
Gibson, B.W.38
Liebler, D.39
Maccoss, M.40
Neubert, T.A.41
Paulovich, A.42
Regnier, F.43
Skates, S.J.44
Tempst, P.45
Wang, M.46
Carr, S.A.47
more..
-
70
-
-
77956391635
-
Online high-flow peptide immunoaffinity enrichment and nanoflow LC-MS/MS: Assay development for total salivary pepsin/pepsinogen
-
Neubert, H., Gale, J., and Muirhead, D. (2010) Online high-flow peptide immunoaffinity enrichment and nanoflow LC-MS/MS: 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
-
71
-
-
34548169013
-
Clinical validation of an immunoaffinity LC-MS/MS assay for the quantification of a collagen type II neoepitope peptide: A biomarker of matrix metalloproteinase activity and osteoarthritis in human urine
-
Li, W., Nemirovskiy, O., Fountain, S., Mathews, W. R., and Szekely-Klepser, G. (2007) Clinical validation of an immunoaffinity LC-MS/MS assay for the quantification of a collagen type II neoepitope peptide: A biomarker of matrix metalloproteinase activity and osteoarthritis in human urine. Anal. Biochem. 369, 41-53
-
(2007)
Anal. Biochem.
, vol.369
, pp. 41-53
-
-
Li, W.1
Nemirovskiy, O.2
Fountain, S.3
Mathews, W.R.4
Szekely-Klepser, G.5
-
72
-
-
84865576726
-
Quantitative mass spectrometry in proteomics: Critical review update from 2007 to the present
-
Bantscheff, M., Lemeer, S., Savitski, M. M., and Kuster, B. (2012) Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present. Anal. Bioanal. Chem. 404, 939-965
-
(2012)
Anal. Bioanal. Chem.
, vol.404
, pp. 939-965
-
-
Bantscheff, M.1
Lemeer, S.2
Savitski, M.M.3
Kuster, B.4
-
73
-
-
84886507551
-
Validation of hepcidin quantification in plasma using LC-HRMS and discovery of a new hepcidin isoform
-
Rochat, B., Peduzzi, D., McMullen, J., Favre, A., Kottelat, E., Favrat, B., Tissot, J. D., Angelillo-Scherrer, A., Bromirski, M., and Waldvogel, S. (2013) Validation of hepcidin quantification in plasma using LC-HRMS and discovery of a new hepcidin isoform. Bioanalysis 5, 2509-2520
-
(2013)
Bioanalysis
, vol.5
, pp. 2509-2520
-
-
Rochat, B.1
Peduzzi, D.2
McMullen, J.3
Favre, A.4
Kottelat, E.5
Favrat, B.6
Tissot, J.D.7
Angelillo-Scherrer, A.8
Bromirski, M.9
Waldvogel, S.10
-
74
-
-
84887108791
-
Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia
-
Epub 2013 Sep 29
-
Jaffe, J. D., Wang, Y., Chan, H. M., Zhang, J., Huether, R., Kryukov, G. V., Bhang, H. E., Taylor, J. E., Hu, M., Englund, N. P, Yan, F., Wang, Z., McDonald, R. E., 3rd, Wei, L., Ma, J., Easton, J., Yu, Z., Debeaumount, R., Gibaja, V., Venkatesan, K., Schlegel, R., Sellers, W. R., Keen, N., Liu, J., Caponigro, G., Barretina, J., Cooke, V. G., Mullighan, C., Carr, S. A., Downing, J. R., Garraway, L. A., and Stegmeier, F. (2013) Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia. Nat. Genet. 45, 1386-1391, Epub 2013 Sep 29
-
(2013)
Nat. Genet.
, vol.45
, pp. 1386-1391
-
-
Jaffe, J.D.1
Wang, Y.2
Chan, H.M.3
Zhang, J.4
Huether, R.5
Kryukov, G.V.6
Bhang, H.E.7
Taylor, J.E.8
Hu, M.9
Englund, N.P.10
Yan, F.11
Wang, Z.12
McDonald III, R.E.13
Wei, L.14
Ma, J.15
Easton, J.16
Yu, Z.17
Debeaumount, R.18
Gibaja, V.19
Venkatesan, K.20
Schlegel, R.21
Sellers, W.R.22
Keen, N.23
Liu, J.24
Caponigro, G.25
Barretina, J.26
Cooke, V.G.27
Mullighan, C.28
Carr, S.A.29
Downing, J.R.30
Garraway, L.A.31
Stegmeier, F.32
more..
-
75
-
-
79952112715
-
Mass spectrometric protein identification using the global proteome machine
-
Fenyö, D., Eriksson, J., and Beavis, R. (2010) Mass spectrometric protein identification using the global proteome machine. Methods Mol Biol. 673, 189-202
-
(2010)
Methods Mol Biol
, vol.673
, pp. 189-202
-
-
Fenyö, D.1
Eriksson, J.2
Beavis, R.3
-
76
-
-
77449108855
-
The peptideatlas project
-
Deutsch, E. W. (2010) The peptideatlas project. Methods Mol. Biol. 604, 285-296
-
(2010)
Methods Mol. Biol.
, vol.604
, pp. 285-296
-
-
Deutsch, E.W.1
-
77
-
-
84874762979
-
The proteomics identifications (PRIDE) database and associated tools: Status in 2013
-
(Database issue), Epub 2012 Nov 29
-
Vizcaíno, J. A., Cô té, R. G., Csordas, A., Dianes, J. A., Fabregat, A., Foster, J. M., Griss, J., Alpi, E., Birim, M., Contell, J., O'Kelly, G., Schoenegger, A., Ovelleiro, D., Perez-Riverol, Y., Reisinger, F., Ríos, D., Wang, R., and Hermjakob, H. (2013) The proteomics identifications (PRIDE) database and associated tools: Status in 2013. Nucleic Acids Res. 41 (Database issue), D1063-D1069, Epub 2012 Nov 29
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Vizcaíno, J.A.1
Côté, R.G.2
Csordas, A.3
Dianes, J.A.4
Fabregat, A.5
Foster, J.M.6
Griss, J.7
Alpi, E.8
Birim, M.9
Contell, J.10
O'Kelly, G.11
Schoenegger, A.12
Ovelleiro, D.13
Perez-Riverol, Y.14
Reisinger, F.15
Ríos, D.16
Wang, R.17
Hermjakob, H.18
-
78
-
-
84895536541
-
A database of mass spectrometric assays for the yeast proteome
-
Picotti, P., Lam, H., Campbell, D., Deutsch, E. W., Mirzaei, H., Ranish, J., Domon, B., and Aebersold, R. (2013) A database of mass spectrometric assays for the yeast proteome. Mol. Cell. Proteomics 12, 1005-1016
-
(2013)
Mol. Cell. Proteomics
, vol.12
, pp. 1005-1016
-
-
Picotti, P.1
Lam, H.2
Campbell, D.3
Deutsch, E.W.4
Mirzaei, H.5
Ranish, J.6
Domon, B.7
Aebersold, R.8
-
79
-
-
84875969679
-
N-glycoprotein SRMAtlas: A resource of mass spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications
-
Hü ttenhain, R., Surinova, S., Ossola, R., Sun, Z., Campbell, D., Cerciello, F., Schiess, R., Bausch-Fluck, D., Rosenberger, G., Chen, J., Rinner, O., Kusebauch, U., Hajdú ch, M., Moritz, R. L, Wollscheid, B., and Aebersold, R. (2013) 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, 1005-1016
-
(2013)
Mol. Cell. Proteomics
, vol.12
, pp. 1005-1016
-
-
Hüttenhain, R.1
Surinova, S.2
Ossola, R.3
Sun, Z.4
Campbell, D.5
Cerciello, F.6
Schiess, R.7
Bausch-Fluck, D.8
Rosenberger, G.9
Chen, J.10
Rinner, O.11
Kusebauch, U.12
Hajdúch, M.13
Moritz, R.L.14
Wollscheid, B.15
Aebersold, R.16
-
80
-
-
14744293536
-
Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra
-
Venable, J. D., Dong, M. Q., Wohlschlegel, J., Dillin, A., and Yates, J. R. (2004) Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat. Methods 1, 39-45
-
(2004)
Nat. Methods
, vol.1
, pp. 39-45
-
-
Venable, J.D.1
Dong, M.Q.2
Wohlschlegel, J.3
Dillin, A.4
Yates, J.R.5
-
81
-
-
80052796321
-
Software for quantitative proteomic analysis using stable isotope labeling and data independent acquisition
-
doi: 10.1021/ac201555m. Epub 2011 Aug 23
-
Huang, X., Liu, M., Nold, M. J., Tian, C., Fu, K., Zheng, J., Geromanos, S. J., and Ding, S. J. (2011) Software for quantitative proteomic analysis using stable isotope labeling and data independent acquisition. Anal. Chem. 15, 6971-6979. doi: 10.1021/ac201555m. Epub 2011 Aug 23
-
(2011)
Anal. Chem.
, vol.15
, pp. 6971-6979
-
-
Huang, X.1
Liu, M.2
Nold, M.J.3
Tian, C.4
Fu, K.5
Zheng, J.6
Geromanos, S.J.7
Ding, S.J.8
-
82
-
-
84861860481
-
Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: A new concept for consistent and accurate proteome analysis
-
10.1074/mcp.O111.016717. Epub 2012 Jan 18
-
Gillet, L. C., Navarro, P., Tate, S., Rö st, H., Selevsek, N., Reiter, L., Bonner, R., and Aebersold, R. (2012) 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, 10.1074/mcp.O111.016717. Epub 2012 Jan 18
-
Mol. Cell. Proteomics
, vol.11
, pp. 2012
-
-
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
-
83
-
-
84881477986
-
Multiplexed MS/MS for improved data-independent acquisition
-
10.1038/nmeth 2528, Epub 2013 Jun 23
-
Egertson, J. D., Kuehn, A., Merrihew, G. E., Bateman, N. W., Maclean, B. X., Ting, Y. S., Canterbury, J. D., Marsh, D. M., Kellmann, M., Zabrouskov, V., Wu, C. C., and Maccoss, M. J. (2013) Multiplexed MS/MS for improved data-independent acquisition. Nat. Methods 10, 744-746. 10.1038/nmeth. 2528. Epub 2013 Jun 23
-
(2013)
Nat. Methods
, vol.10
, pp. 744-746
-
-
Egertson, J.D.1
Kuehn, A.2
Merrihew, G.E.3
Bateman, N.W.4
Maclean, B.X.5
Ting, Y.S.6
Canterbury, J.D.7
Marsh, D.M.8
Kellmann, M.9
Zabrouskov, V.10
Wu, C.C.11
Maccoss, M.J.12
-
84
-
-
68049114653
-
Precursor acquisition independent from ion count: How to dive deeper into the proteomics ocean
-
10.1021/ac900888s
-
Panchaud, A., Scherl, A., Shaffer, S. A., von Haller, P. D., Kulasekara, H. D., Miller, S. I., and Goodlett, D. R. (2009) Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Anal. Chem. 81, 6481-6488. 10.1021/ac900888s
-
(2009)
Anal. Chem.
, vol.81
, pp. 6481-6488
-
-
Panchaud, A.1
Scherl, A.2
Shaffer, S.A.3
Von Haller, P.D.4
Kulasekara, H.D.5
Miller, S.I.6
Goodlett, D.R.7
-
85
-
-
84860869167
-
Using iRT, a normalized retention time for more targeted measurement of peptides
-
10.1002/pmic201100463
-
Escher, C., Reiter, L., MacLean, B., Ossola, R., Herzog, F., Chilton, J., MacCoss, M. J., and Rinner, O. (2012) Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics 12, 1111-1121. 10.1002/pmic. 201100463
-
(2012)
Proteomics
, vol.12
, pp. 1111-1121
-
-
Escher, C.1
Reiter, L.2
Maclean, B.3
Ossola, R.4
Herzog, F.5
Chilton, J.6
Maccoss, M.J.7
Rinner, O.8
-
86
-
-
74049131716
-
High-throughput generation of selected reaction-monitoring assays for proteins and proteomes
-
10.1038/nmeth1408 Epub 2009 Dec 6
-
Picotti, P., Rinner, O., Stallmach, R., Dautel, F., Farrah, T., Domon, B., Wenschuh, H., and Aebersold, R. (2010) High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat. Methods 7, 43-46. 10.1038/nmeth. 1408. Epub 2009 Dec 6
-
(2010)
Nat. Methods
, vol.7
, pp. 43-46
-
-
Picotti, P.1
Rinner, O.2
Stallmach, R.3
Dautel, F.4
Farrah, T.5
Domon, B.6
Wenschuh, H.7
Aebersold, R.8
-
87
-
-
79955809067
-
Methods for peptide and protein quantitation by liquid chromatography- multiple reaction monitoring mass spectrometry
-
10.1074/mcp.M110.006593. Epub 2011 Feb 27
-
Zhang, H., Liu, Q., Zimmerman, L. J., Ham, A. J., Slebos, R. J., Rahman, J., Kikuchi, T., Massion, P. P., Carbone, D. P., Billheimer, D., and Liebler, D. C. (2011) Methods for peptide and protein quantitation by liquid chromatography- multiple reaction monitoring mass spectrometry. Mol. Cell. Proteomics 10, 10.1074/mcp.M110.006593. Epub 2011 Feb 27
-
Mol. Cell. Proteomics
, vol.10
, pp. 2011
-
-
Zhang, H.1
Liu, Q.2
Zimmerman, L.J.3
Ham, A.J.4
Slebos, R.J.5
Rahman, J.6
Kikuchi, T.7
Massion, P.P.8
Carbone, D.P.9
Billheimer, D.10
Liebler, D.C.11
-
88
-
-
80052431797
-
Rapid verification of candidate serological biomarkers using gel-based, labelfree multiple reaction monitoring
-
10.1021/pr2002098. Epub 2011 Jul 26
-
Tang, H. Y., Beer, L. A., Barnhart, K. T., and Speicher, D. W. (2011) Rapid verification of candidate serological biomarkers using gel-based, labelfree multiple reaction monitoring. J. Proteome Res. 10, 4005-4017 10.1021/pr2002098. Epub 2011 Jul 26
-
(2011)
J. Proteome Res.
, vol.10
, pp. 4005-4017
-
-
Tang, H.Y.1
Beer, L.A.2
Barnhart, K.T.3
Speicher, D.W.4
-
89
-
-
84861833387
-
Label-free quantitation of protein modifications by pseudo selected reaction monitoring with internal reference peptides
-
Epub ahead of print
-
Sherrod, S. D., Myers, M. V., Li, M., Myers, J. S., Carpenter, K. L., Maclean, B., Maccoss, M. J., Liebler, D. C., and Ham, A. J. (2012) Label-free quantitation of protein modifications by pseudo selected reaction monitoring with internal reference peptides. J. Proteome Res. [Epub ahead of print]
-
(2012)
J. Proteome Res.
-
-
Sherrod, S.D.1
Myers, M.V.2
Li, M.3
Myers, J.S.4
Carpenter, K.L.5
Maclean, B.6
Maccoss, M.J.7
Liebler, D.C.8
Ham, A.J.9
-
90
-
-
84879593559
-
Review of software tools for design and analysis of large scale MRM proteomic datasets
-
10.1016/j.ymeth. 2013.05.004. Epub 2013 May 21
-
Colangelo, C. M., Chung, L., Bruce, C., and Cheung, K. H. (20130 Review of software tools for design and analysis of large scale MRM proteomic datasets. Methods 61, 287-298. 10.1016/j.ymeth. 2013.05.004. Epub 2013 May 21
-
(2013)
Methods
, vol.61
, pp. 287-298
-
-
Colangelo, C.M.1
Chung, L.2
Bruce, C.3
Cheung, K.H.4
-
91
-
-
84860862170
-
An assessment of current bioinformatic solutions for analyzing LC-MS data acquired by selected reaction monitoring technology
-
10.1002/pmic.201100571
-
Brusniak, M. Y., Chu, C. S., Kusebauch, U., Sartain, M. J., Watts, J. D., and Moritz, R. L. (2012) An assessment of current bioinformatic solutions for analyzing LC-MS data acquired by selected reaction monitoring technology. Proteomics 12, 1176-1184. 10.1002/pmic. 201100571
-
(2012)
Proteomics
, vol.12
, pp. 1176-1184
-
-
Brusniak, M.Y.1
Chu, C.S.2
Kusebauch, U.3
Sartain, M.J.4
Watts, J.D.5
Moritz, R.L.6
-
92
-
-
0038703389
-
-
General Principles Of Software Validation; Final Guidance For Industry And FDA Staff. Document Issued On:January 11, This document supersedes the draft document, Version 1.1, dated June 9, 1997
-
General Principles of Software Validation; Final Guidance for Industry and FDA Staff. Document issued on: January 11, 2002. This document supersedes the draft document, "General Principles of Software Validation, Version 1.1, dated June 9, 1997. http://www.fda.gov/downloads/ RegulatoryInformation/ Guidances/ucm126955.pdf
-
(2002)
General Principles of Software Validation
-
-
-
93
-
-
77951965920
-
Skyline: An open source document editor for creating and analyzing targeted proteomics experiments
-
10.1093/bioinformatics/btq054. Epub 2010 Feb 9
-
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. 10.1093/bioinformatics/ btq054. Epub 2010 Feb 9
-
(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
-
94
-
-
84895529575
-
-
Note that you must register on the Genepattern website in order to access, Registration is free
-
http://genepattern.broadinstitute.org/gp/pages/index.jsf?lsid-QuaSAR. Note that you must register on the Genepattern website in order to access. Registration is free
-
-
-
-
95
-
-
84894412736
-
Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies
-
Surinova, S., Hü ttenhain, R., Chang, C. Y., Espona, L., Vitek O., and Aebersold, R. (2013) Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies. Nature Protocols 8, 1602-1619
-
(2013)
Nature Protocols
, vol.8
, pp. 1602-1619
-
-
Surinova, S.1
Hüttenhain, R.2
Chang, C.Y.3
Espona, L.4
Vitek, O.5
Aebersold, R.6
-
96
-
-
84860856503
-
PASSEL: The PeptideAtlas SRM experiment library
-
Farrah, T., Deutsch, E. W., Kreisberg, R., Sun, Z., Campbell, D. S., Mendoza, L., Kusebauch, U., Brusniak, M. Y., Huttenhain, R., Schiess, R., Selevsek, N., Aebersold, R., and Moritz, R. L. (2012) PASSEL: The PeptideAtlas SRM experiment library. Proteomics 12, 1170-1175
-
(2012)
Proteomics
, vol.12
, pp. 1170-1175
-
-
Farrah, T.1
Deutsch, E.W.2
Kreisberg, R.3
Sun, Z.4
Campbell, D.S.5
Mendoza, L.6
Kusebauch, U.7
Brusniak, M.Y.8
Huttenhain, R.9
Schiess, R.10
Selevsek, N.11
Aebersold, R.12
Moritz, R.L.13
-
97
-
-
84888290429
-
Guidelines for reporting quantitative mass spectrometry based experiments in proteomics
-
in press
-
Martínez-Bartolomé, S., Deutsch, E. W., Binz, P. A., Jones, A. R., Eisenacher, M., Mayer, G., Campos, A., Canals, F., Bech-Serra, J. J., Carrascal, M., Gay, M., Paradela, A., Navajas, R., Marcilla, M., Herná ez, M. L., Gutié rrez-Blá zquez, M. D., Velarde, L. F., Aloria, K., Beaskoetxea, J., Medina-Aunon, J. A., and Albar, J. P. (2013) Guidelines for reporting quantitative mass spectrometry based experiments in proteomics. J. Proteomics in press
-
J. Proteomics
, pp. 2013
-
-
Martínez-Bartolomé, S.1
Deutsch, E.W.2
Binz, P.A.3
Jones, A.R.4
Eisenacher, M.5
Mayer, G.6
Campos, A.7
Canals, F.8
Bech-Serra, J.J.9
Carrascal, M.10
Gay, M.11
Paradela, A.12
Navajas, R.13
Marcilla, M.14
Hernáez, M.L.15
Gutiérrez- Blázquez, M.D.16
Velarde, L.F.17
Aloria, K.18
Beaskoetxea, J.19
Medina-Aunon, J.A.20
Albar, J.P.21
more..
-
98
-
-
84875880985
-
If a job is worth doing, it is worth doing twice. Nature (2013) 496: 7 and Editorial Staff. Reducing our irreproducibility
-
Russell, J. F. (2013) If a job is worth doing, it is worth doing twice. Nature (2013) 496: 7 and Editorial Staff. Reducing our irreproducibility. Nature 496, 398
-
(2013)
Nature
, vol.496
, pp. 398
-
-
Russell, J.F.1
-
99
-
-
84869233177
-
Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics
-
10.1074/mcp.O112.020131:
-
Peterson, A. C., Russell, J. D., Bailey, D. J., Westphall, M. S., and Coon, J. J. (2012) Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol. Cell. Proteomics 11, 10.1074/mcp.O112.020131:1475-1488
-
(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
|