Publications of J. Cox

Journal Article (127)

101.
Journal Article
Mortensen, P.; Gouw, J. W.; Olsen, J. V.; Ong, S. E.; Rigbolt, K. T. G.; Bunkenborg, J.; Cox, J.; Foster, L. J.; Heck, A. J. R.; Blagoev, B. et al.; Andersen, J. S.; Mann, M.: MSQuant, an Open Source Platform for Mass Spectrometry-Based Quantitative Proteomics. Journal of Proteome Research 9 (1), pp. 393 - 403 (2010)
102.
Journal Article
Choudhary, C.; Olsen, J. V.; Brandts, C.; Cox, J.; Reddy, P. N. G.; Boehmer, F. D.; Gerke, V.; Schmidt-Arras, D. E.; Berdel, W. E.; Mueller-Tidow, C. et al.; Mann, M.; Serve, H.: Mislocalized Activation of Oncogenic RTKs Switches Downstream Signaling Outcomes. Molecular Cell 36 (2), pp. 326 - 339 (2009)
103.
Journal Article
Gnad, F.; de Godoy, L. M. F.; Cox, J.; Neuhauser, N.; Ren, S.; Olsen, J. V.; Mann, M.: High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast. Proteomics 9 (20), pp. 4642 - 4652 (2009)
104.
Journal Article
Sharma, K.; Weber, C.; Bairlein, M.; Greff, Z.; Keri, G.; Cox, J.; Olsen, J. V.; Daub, H.: Proteomics strategy for quantitative protein interaction profiling in cell extracts. Nature Methods 6 (10), pp. 741 - 744 (2009)
105.
Journal Article
Cox, J.; Mann, M.: Computational Principles of Determining and Improving Mass Precision and Accuracy for Proteome Measurements in an Orbitrap. Journal of the American Society for Mass Spectrometry 20 (8), pp. 1477 - 1485 (2009)
106.
Journal Article
Bonaldi, T.; Vitale, E.; Nielsen, M. L.; Cox, J.; Mann, M.: Analysis of in vivo histone methylation kinetics by Heavy Methyl SILAC. Amino Acids 37 (Suppl. Suppl. 1), p. 66 - 66 (2009)
107.
Journal Article
Golebiowski, F.; Matic, I.; Tatham, M. H.; Cole, C.; Yin, Y.; Nakamura, A.; Cox, J.; Barton, G. J.; Mann, M.; Hay, R. T.: System-Wide Changes to SUMO Modifications in Response to Heat Shock. Science Signaling 72 (2), ra24, pp. [1] - [12] (2009)
108.
Journal Article
Golebiowski, F.; Matic, I.; Tatham, M. H.; Cole, C.; Yin, Y. L.; Nakamura, A.; Cox, J.; Barton, G. J.; Mann, M.; Hay, R. T.: System-Wide Changes to SUMO Modifications in Response to Heat Shock. Science Signaling 2 (72), ra24, pp. [1] - [12] (2009)
109.
Journal Article
Cox, J.; Hubner, N. C.; Mann, M.: How Much Peptide Sequence Information Is Contained in Ion Trap Tandem Mass Spectra? Journal of the American Society for Mass Spectrometry 19 (12), pp. 1813 - 1820 (2008)
110.
Journal Article
Cox, J.; Mann, M.: MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nature Biotechnology 26 (12), pp. 1367 - 1372 (2008)
111.
Journal Article
Zanivan, S.; Gnad, F.; Wickström, S. A.; Geiger, T.; Macek, B.; Cox, J.; Fässler, R.; Mann, M.: Solid Tumor Proteome and Phosphoproteome Analysis by High Resolution Mass Spectrometry. Journal of Proteome Research 7 (12), pp. 5314 - 5326 (2008)
112.
Journal Article
Schimmel, J.; Larsen, K. M.; Matic, I.; van Hagen, M.; Cox, J.; Mann, M.; Andersen, J. S.; Vertegaal, A. C. O.: The Ubiquitin-Proteasome System Is a Key Component of the SUMO-2/3 Cycle. Molecular & Cellular Proteomics 7 (11), pp. 2107 - 2122 (2008)
113.
Journal Article
de Godoy, L. M. F.; Olsen, J. V.; Cox, J.; Nielsen, M. L.; Hubner, N. C.; Fröhlich, F.; Walther, T. C.; Mann, M.: Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455 (7217), pp. 1251 - 1254 (2008)
114.
Journal Article
Bonaldi, T.; Straub, T.; Cox, J.; Kumar, C.; Becker, P. B.; Mann, M.: Combined use of RNAi and quantitative proteomics to study gene function in Drosophila. Molecular Cell 31 (5), pp. 762 - 772 (2008)
115.
Journal Article
Waanders, L. F.; Almeida, R.; Prosser, S.; Cox, J.; Eikel, D.; Allen, M. H.; Schultz, G. A.; Mann, M.: A novel chromatographic method allows on-line reanalysis of the proteome. Molecular & Cellular Proteomics 7 (8), pp. 1452 - 1459 (2008)
116.
Journal Article
Nielsen, M. L.; Vermeulen, M.; Bonaldi, T.; Cox, J.; Moroder, L.; Mann, M.: Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry. Nature Methods 5 (6), pp. 459 - 460 (2008)
117.
Journal Article
Olsen, J. V.; Butter, F.; Hubner, N.; Cox, J.; Hyman, A.; Mann, M.: SILAC based quantitative proteomics to determine specific protein-protein and protein-DNA interactions. FEBS Journal 275 (Suppl. Suppl. 1), p. 29 - 29 (2008)
118.
Journal Article
Graumann, J.; Hubner, N. C.; Kim, J.B.; Ko, K.; Moser, M.; Kumar, C.; Cox, J.; Schöler, H.; Mann, M.: SILAC-labeling and proteome quantitation of mouse embryonic stem cells to a depth of 5111 proteins. Special Issue: 8th International Symposium On Mass Spectrometry In The Life Sciences, pp. 672 - 683 (2008)
119.
Journal Article
Graumann, J.; Hubner, N. C.; Kim, J. B.; Ko, K.; Moser, M.; Kumar, C.; Cox, J.; Schöler, H.; Mann, M.: Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins. Molecular & Cellular Proteomics 7 (4), pp. 672 - 683 (2008)
120.
Journal Article
Lu, A.; Waanders, L. F.; Almeida, R.; Li, G. Q.; Allen, M.; Cox, J.; Olsen, J. V.; Bonaldi, T.; Mann, M.: Nanoelectrospray peptide mapping revisited: Composite survey spectra allow high dynamic range protein characterization without LCMS on an orbitrap mass spectrometer. International Journal of Mass Spectrometry 268 (2-3), pp. 158 - 167 (2007)
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