Publications of J. Cox

Cox, J.; Michalski, A.; Mann, M.: Software Lock Mass by Two-Dimensional Minimization of Peptide Mass Errors. Journal of the American Society for Mass Spectrometry 22 (8), pp. 1373 - 1380 (2011)

Thakur, S. S.; Geiger, T.; Chatterjee, B.; Bandilla, P.; Fröhlich, F.; Cox, J.; Mann, M.: Deep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation. Molecular & Cellular Proteomics 10 (8), M110.003699, pp. [1] - [9] (2011)

Cox, J.; Neuhauser, N.; Michalski, A.; Scheltema, R. A.; Olsen, J. V.; Mann, M.: Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment. Journal of Proteome Research 10 (4), pp. 1794 - 1805 (2011)

Michalski, A.; Cox, J.; Mann, M.: More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC-MS/MS. Journal of Proteome Research 10 (4), pp. 1785 - 1793 (2011)

Geiger, T.; Wisniewski, J. R.; Cox, J.; Zanivan, S.; Kruger, M.; Ishihama, Y.; Mann, M.: Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics. Nature Protocols 6 (2), pp. 147 - 157 (2011)

Lundberg, E.; Fagerberg, L.; Klevebring, D.; Matic, I.; Geiger, T.; Cox, J.; Älgenäs, C.; Lundeberg, J.; Mann, M.; Uhlen, M.: Defining the transcriptome and proteome in three functionally different human cell lines. Molecular Systems Biology 6, 450, pp. [1] - [9] (2010)

Nagaraj, N.; D'Souza, R. C. J.; Cox, J.; Olsen, J. V.; Mann, M.: Feasibility of Large-Scale Phosphoproteomics with Higher Energy Collisional Dissociation Fragmentation. Journal of Proteome Research 9 (12), pp. 6786 - 6794 (2010)

Geiger, T.; Cox, J.; Mann, M.: Proteomics on an Orbitrap Benchtop Mass Spectrometer Using All-ion Fragmentation. Molecular & Cellular Proteomics 9 (10), pp. 2252 - 2261 (2010)

Geiger, T.; Cox, J.; Mann, M.: Proteomic Changes Resulting from Gene Copy Number Variations in Cancer Cells. PLoS Genetics 6 (9), e1001090, pp. [1] - [11] (2010)

Gnad, F.; Ren, S. B.; Choudhary, C.; Cox, J.; Mann, M.: Predicting post-translational lysine acetylation using support vector machines. Bioinformatics 26 (13), pp. 1666 - 1668 (2010)

Schreiber, T. B.; Mäusbacher, N.; Keri, G.; Cox, J.; Daub, H.: An Integrated Phosphoproteomics Work Flow Reveals Extensive Network Regulation in Early Lysophosphatidic Acid Signaling. Molecular & Cellular Proteomics 9 (6), pp. 1047 - 1062 (2010)

Hubner, N. C.; Bird, A. W.; Cox, J.; Splettstoesser, B.; Bandilla, P.; Poser, I.; Hyman, A.; Mann, M.: Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. Journal of Cell Biology 189 (4), pp. 739 - 754 (2010)

Geiger, T.; Cox, J.; Ostasiewicz, P.; Wisniewski, J. R.; Mann, M.: Super-SILAC mix for quantitative proteomics of human tumor tissue. Nature Methods 7 (5), pp. 383 - 385 (2010)

Luber, C. A.; Cox, J.; Lauterbach, H.; Fancke, B.; Selbach, M.; Tschopp, J.; Akira, S.; Wiegand, M.; Hochrein, H.; O'Keeffe, M. et al.; Mann, M.: Quantitative Proteomics Reveals Subset-Specific Viral Recognition in Dendritic Cells. Immunity 32 (2), pp. 279 - 289 (2010)

Olsen, J. V.; Vermeulen, M.; Santamaria, A.; Kumar, C.; Miller, M. L.; Jensen, L. J.; Gnad, F.; Cox, J.; Jensen, T. S.; Nigg, E. A. et al.; Brunak, S.; Mann, M.: Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis. Science Signaling 3 (104), ra3, pp. [1] - [15] (2010)

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)

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)

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)

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)

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)