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Department of Molecular Biology and Genetics

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Peer-reviewed articles

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Wagner, S. A., Beli, P., Weinert, B. T., Schölz, C. F., Kelstrup, C. D., Young, C., Nielsen, M. L., Olsen, J. V., Brakebusch, C. & Choudhary, C. R. (2012). Proteomic analyses reveal divergent ubiquitylation site patterns in murinetissues. Molecular and Cellular Proteomics. https://doi.org/10.1074/mcp.M112.017905

Mantri, M., Webby, C. J., Loik, N. D., Hamed, R. B., Nielsen, M. L., McDonough, M. A., McCullagh, J. S. O., Böttger, A., Schofield, C. J. & Wolf, A. (2012). Self-hydroxylation of the splicing factor lysyl hydroxylase, JMJD6. MedChemComm, 3(1), 80-85. https://doi.org/10.1039/c1md00225b

Povlsen, L. K., Beli, P., Wagner, S. A., Poulsen, S. L., Sylvestersen, K. B., Poulsen, J. W., Nielsen, M. L., Bekker-Jensen, S., Mailand, N. & Choudhary, C. (2012). Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. Nature Cell Biology, 14(10), 1089-1098. https://doi.org/10.1038/ncb2579

Jungmichel, S., Clapperton, J. A., Janette, L., Hari, F. J., Spycher, C., Pavic, L., Li, J., Haire, L. F., Bonalli, M., Larsen, D. H., Lukas, C., Lukas, J., MacMillan, D., Nielsen, M. L., Stucki, M. & Smerdon, S. J. (2012). The molecular basis of ATM-dependent dimerization of the Mdc1 DNA damage checkpoint mediator. Nucleic Acids Research, 40(9), 4913-4928. https://doi.org/10.1093/nar/gkr1300

Wagner, S. A., Beli, P., Weinert, B. T., Nielsen, M. L., Cox, J., Mann, M. & Choudhary, C. (2011). A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Molecular and Cellular Proteomics, 10(10). https://doi.org/10.1074/mcp.m111.013284

Marín-Vicente, C., Guerrero-Valero, M., Nielsen, M. L., Savitski, M. M., Gómez-Fernández, J. C., Zubarev, R. A. & Corbalán-García, S. (2011). ATP enhances neuronal differentiation of PC12 cells by activating PKCα interactions with cytoskeletal proteins. Journal of proteome Research, 10(2), 529-540. https://doi.org/10.1021/pr100742r

Danielsen, J. M. R., Sylvestersen, K. B., Bekker-Jensen, S., Szklarczyk, D., Poulsen, J. W., Horn, H., Jensen, L. J., Mailand, N. & Nielsen, M. L. (2011). Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. Molecular and Cellular Proteomics, 10(3). https://doi.org/10.1074/mcp.M110.003590

Vesterlund, M., Zadjali, F., Persson, T., Nielsen, M. L., Kessler, B. M., Norstedt, G. & Flores-Morales, A. (2011). The SOCS2 ubiquitin ligase complex regulates growth hormone receptor levels. PLoS One, 6(9), Article e25358. https://doi.org/10.1371/journal.pone.0025358

Choudhary, C., Kumar, C., Gnad, F., Nielsen, M. L., Rehman, M., Walther, T. C., Olsen, J. V. & Mann, M. (2009). Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science, 325(5942), 834-840. https://doi.org/10.1126/science.1175371

Fäith, M., Savitski, M. M., Nielsen, M. L., Kjeldsen, F., Andren, P. E. & Zubarev, R. A. (2008). Analytical utility of small neutral losses from reduced species in electron capture dissociation studied using SwedECD database. Analytical Chemistry, 80(21), 8089-8094. https://doi.org/10.1021/ac800944u

De Godoy, L. M. F., Olsen, J. V., Cox, J., Nielsen, M. L., Hubner, N. C., Fröhlich, F., Walther, T. C. & Mann, M. (2008). Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature, 455(7217), 1251-1254. https://doi.org/10.1038/nature07341

Zubarev, R. A., Nielsen, M. L., Fung, E. M., Savitski, M. M., Kel-Margoulis, O., Wingender, E. & Kel, A. (2008). Identification of dominant signaling pathways from proteomics expression data. Journal of Proteomics, 71(1), 89-96. https://doi.org/10.1016/j.jprot.2008.01.004

Frank, A. M., Savitski, M. M., Nielsen, M. L., Zubarev, R. A. & Pevzner, P. A. (2007). De novo peptide sequencing and identification with precision mass spectrometry. Journal of proteome Research, 6(1), 114-123. https://doi.org/10.1021/pr060271u

Samgina, T. Y., Artemenko, K. A., Gorshkov, V. A., Lebedev, A. T., Nielsen, M. L., Savitski, M. M. & Zubarevand, R. A. (2007). Electrospray ionization tandem mass spectrometry sequencing of novel skin peptides from Ranid frogs containing disulfide bridges. European Journal of Mass Spectrometry, 13(2), 155-163. https://doi.org/10.1255/ejms.867

Savitski, M. M., Kjeldsen, F., Nielsen, M. L. & Zubarev, R. A. (2007). Hydrogen Rearrangement to and from Radical z Fragments in Electron Capture Dissociation of Peptides. Journal of The American Society for Mass Spectrometry, 18(1), 113-120. https://doi.org/10.1016/j.jasms.2006.09.008

Savitski, M. M., Kjeldsen, F., Nielsen, M. L. & Zubarev, R. A. (2007). Relative specificities of water and ammonia losses from backbone fragments in collision-activated dissociation. Journal of proteome Research, 6(7), 2669-2673. https://doi.org/10.1021/pr070121z

Savitski, M. M., Nielsen, M. L. & Zubarev, R. A. (2007). Side-chain losses in electron capture dissociation to improve peptide identification. Analytical Chemistry, 79(6), 2296-2302. https://doi.org/10.1021/ac0619332

Fälth, M., Savitski, M. M., Nielsen, M. L., Kjeldsen, F., Andren, P. E. & Zubarev, R. A. (2007). SwedCAD, a database of annotated high-mass accuracy MS/MS spectra of tryptic peptides. Journal of proteome Research, 6(10), 4063-4067. https://doi.org/10.1021/pr070345h

Lerner, M., Corcoran, M., Cepeda, D., Nielsen, M. L., Zubarev, R., Pontén, F., Uhlén, M., Hober, S., Grandér, D. & Sangfelt, O. (2007). The RBCC gene RFP2 (Leu5) encodes a novel transmembrane E3 ubiquitin ligase involved in ERAD. Molecular Biology of the Cell, 18(5), 1670-1682. https://doi.org/10.1091/mbc.E06-03-0248

Nielsen, M. L., Savitski, M. M. & Zubarev, R. A. (2005). Improving protein identification using complementary fragmentation techniques in fourier transform mass spectrometry. Molecular and Cellular Proteomics, 4(6), 835-845. https://doi.org/10.1074/mcp.T400022-MCP200

Nielsen, M. L., Savitski, M. M., Kjeldsen, F. & Zubarev, R. A. (2004). Physicochemical properties determining the detection probability of tryptic peptides in fourier transform mass spectrometry. A correlation study. Analytical Chemistry, 76(19), 5872-5877. https://doi.org/10.1021/ac049571q

Rappsilber, J., Moniatte, M., Nielsen, M. L., Podtelejnikov, A. V. & Mann, M. (2003). Experiences and perspectives of MALDI MS and MS/MS in proteomic research. International Journal of Mass Spectrometry, 226(1), 223-237. https://doi.org/10.1016/S1387-3806(02)00976-4

Haselmann, K. F., Budnik, B. A., Kjeldsen, F., Nielsen, M. L., Olsen, J. V. & Zubarev, R. A. (2002). Electronic excitation gives informative fragmentation of polypeptide cations and anions. European Journal of Mass Spectrometry, 8(2), 117-121. https://doi.org/10.1255/ejms.479

Olsen, J. V., Kristensen, D. B., Nielsen, M. L., Wisniewski, J. R., Jespersen, G., Ong, S. E. & Mann, M. (2002). Mass difference scanning of isotopically labeled peptides for protein quantification by LC-MS/MS. 273-274. Paper presented at Proceedings - 50th ASMS Conference on Mass Spectrometry and Allied Topics, Orlando, FL, United States.

Nielsen, M. L., Bennett, K. L., Larsen, B., Moniatte, M. & Mann, M. (2002). Peptide end sequencing by orthogonal MALDI tandem mass spectrometry. Journal of proteome Research, 1(1), 63-71. https://doi.org/10.1021/pr0155174

Nielsen, M. L., Bennett, K. L., Larsen, B., Wisniewski, J. R., Podtelejnikov, A. & Mann, M. (2002). Quantitation and end sequencing of ¹⁸O labelled peptides by orthogonal MALDI tandem mass spectrometry. 327-328. Paper presented at Proceedings - 50th ASMS Conference on Mass Spectrometry and Allied Topics, Orlando, FL, United States.

Olsen, J. V., Haselmann, K. F., Nielsen, M. L., Budnik, B. A., Nielsen, P. E. & Zubarev, R. A. (2001). Comparison of electron capture dissociation and collisionally activated dissociation of polycations of peptide nucleic acids. Rapid Communications in Mass Spectrometry, 15(12), 969-974. https://doi.org/10.1002/rcm.317

Zubarev, R. A., Nielsen, M. L. & Budnik, B. A. (2000). Tandem ionization mass spectrometry of biomolecules. European Journal of Mass Spectrometry, 6(3), 235-240. https://doi.org/10.1255/ejms.351

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Revised 11.05.2026