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2019
16 Downloads (Pure)

Differential Ion Mobility Separations/Mass Spectrometry with High Resolution in Both Dimensions

Baird, M. A., Anderson, G. A., Shliaha, P. V., Jensen, O. N. & Shvartsburg, A. A., 15. Jan 2019, In : Analytical Chemistry. 91, 2, p. 1479-1485 7 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Pulse time modulation
Ultrahigh vacuum
Mass spectrometers
Isomers
Histones
68 Downloads (Pure)

FlashPack: Fast and simple preparation of ultra-high performance capillary columns for LC-MS

Kovalchuk, S. I., Jensen, O. N. & Rogowska-Wrzesinska, A., 1. Feb 2019, In : Molecular and Cellular Proteomics. 18, 2, p. 383-390

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Liquid chromatography
Liquid Chromatography
Sorbents
Biomolecules
Complex Mixtures

High-Resolution Differential Ion Mobility Separations/Orbitrap Mass Spectrometry without Buffer Gas Limitations

Baird, M. A., Shliaha, P. V., Anderson, G. A., Moskovets, E., Laiko, V., Makarov, A. A., Jensen, O. N. & Shvartsburg, A. A., 21. May 2019, In : Analytical Chemistry. 91, 10, p. 6918-6925

Research output: Contribution to journalJournal articleResearchpeer-review

Mass spectrometry
Buffers
Gases
Ions
Vacuum

PRMT5 methylome profiling uncovers a direct link to splicing regulation in acute myeloid leukemia

Radzisheuskaya, A., Shliaha, P. V., Grinev, V., Lorenzini, E., Kovalchuk, S., Shlyueva, D., Gorshkov, V., Hendrickson, R. C., Jensen, O. N. & Helin, K., Nov 2019, In : Nature Structural and Molecular Biology. 26, 11, p. 999-1012 32 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Protein-Arginine N-Methyltransferases
Acute Myeloid Leukemia
Myeloid Cells
Essential Genes
Alternative Splicing

Selective enrichment of phosphorylated peptides by monolithic polymers surface imprinted with bis-imidazolium moieties by UV-initiated cryopolymerization

Liu, M., Torsetnes, S. B., Wierzbicka, C., Jensen, O. N., Sellergren, B. & Irgum, K., 2019, In : Analytical Chemistry. 91, 15, p. 10188-10196

Research output: Contribution to journalJournal articleResearchpeer-review

Serine
Polymers
Peptides
Amino Acids, Peptides, and Proteins
Signal transduction
2018
95 Downloads (Pure)

Accurate H3K27 methylation can be established de novo by SUZ12-directed PRC2

Højfeldt, J. W., Laugesen, A., Willumsen, B. M., Damhofer, H., Hedehus, L., Tvardovskiy, A., Mohammad, F., Jensen, O. N. & Helin, K., 1. Mar 2018, In : Nature Structural and Molecular Biology. 25, 3, p. 225-232

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Epigenomics
Maintenance
Histones
Lysine
Mouse Embryonic Stem Cells
60 Downloads (Pure)

Distinct Roles of Two Histone Methyltransferases in Transmitting H3K36me3-Based Epigenetic Memory Across Generations in Caenorhabditis elegans

Kreher, J., Takasaki, T., Cockrum, C., Sidoli, S., Garcia, B. A., Jensen, O. N. & Strome, S., 1. Nov 2018, In : Genetics. 210, 3, p. 969-982

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Caenorhabditis elegans
Epigenomics
Embryonic Structures
Oocytes
Mothers

Elucidation of histone proteoform dynamics during aging by using middle-down mass spectrometry

Jensen, O. N., 2018.

Research output: Contribution to conference without publisher/journalPosterResearch

103 Downloads (Pure)

Evaluation of sample preparation methods for mass spectrometry-based proteomic analysis of barley leaves

Wang, W. Q., Jensen, O. N., Møller, I. M., Hebelstrup, K. H. & Rogowska-Wrzesinska, A., 25. Aug 2018, In : Plant Methods. 14, 1, p. 1-13 72.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
proteomics
barley
mass spectrometry
digestion
deoxycholic acid
60 Downloads (Pure)

Extensive Characterization of Heavily Modified Histone Tails by 193 nm Ultraviolet Photodissociation Mass Spectrometry via a Middle-Down Strategy

Greer, S. M., Sidoli, S., Coradin, M., Schack Jespersen, M., Schwämmle, V., Jensen, O. N., Garcia, B. A. & Brodbelt, J. S., Sep 2018, In : Analytical Chemistry. 90, 17, p. 10425–10433

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Photodissociation
Histones
Mass spectrometry
Bioinformatics
Peptides
75 Downloads (Pure)

How many human proteoforms are there?

Aebersold, R., Agar, J. N., Amster, I. J., Baker, M. S., Bertozzi, C. R., Boja, E. S., Costello, C. E., Cravatt, B. F., Fenselau, C., Garcia, B. A., Ge, Y., Gunawardena, J., Hendrickson, R. C., Hergenrother, P. J., Huber, C. G., Ivanov, A. R., Jensen, O. N., Jewett, M. C., Kelleher, N. L., Kiessling, L. L. & 33 others, Krogan, N. J., Larsen, M. R., Loo, J. A., Ogorzalek Loo, R. R., Lundberg, E., MacCoss, M. J., Mallick, P., Mootha, V. K., Mrksich, M., Muir, T. W., Patrie, S. M., Pesavento, J. J., Pitteri, S. J., Rodriguez, H., Saghatelian, A., Sandoval, W., Schlüter, H., Sechi, S., Slavoff, S. A., Smith, L. M., Snyder, M. P., Thomas, P. M., Uhlén, M., Van Eyk, J. E., Vidal, M., Walt, D. R., White, F. M., Williams, E. R., Wohlschlager, T., Wysocki, V. H., Yates, N. A., Young, N. L. & Zhang, B., 14. Feb 2018, In : Nature Chemical Biology. 14, 3, p. 206-214

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Proteins
Proteome
Databases
RNA
DNA
104 Downloads (Pure)

Linear and Differential Ion Mobility Separations of Middle-Down Proteoforms

Garabedian, A., Baird, M. A., Porter, J., Jeanne Dit Fouque, K., Shliaha, P. V., Jensen, O. N., Williams, T. D., Fernandez-Lima, F. & Shvartsburg, A. A., 2018, In : Analytical Chemistry. 90, 4, p. 2918-2925

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Ions
Electrospray ionization
Ion sources
Proteome
Binary mixtures
52 Downloads (Pure)

Maximizing Sequence Coverage in Top-Down Proteomics By Automated Multi-modal Gas-phase Protein Fragmentation

Shliaha, P. V., Gibb, S., Gorshkov, V., Jespersen, M. S., Andersen, G. R., Bailey, D., Schwartz, J., Eliuk, S., Schwämmle, V. & Jensen, O. N., 25. Sep 2018, In : Analytical Chemistry. 90, 21, p. 12519-12526

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Gases
Proteins
Proteomics
Mass spectrometry
Amino Acids
69 Downloads (Pure)

Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics

Bergauer, K., Fernandez-Guerra, A., Garcia, J. A. L., Sprenger, R. R., Stepanauskas, R., Pachiadaki, M. G., Jensen, O. N. & Herndl, G. J., 16. Jan 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 3, p. E400-E408

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Archaeal Proteins
Heterotrophic Processes
Metagenomics
Particulate Matter
Proteins

Phosphoproteomics in Microbiology: Protocols for Studying Streptomyces coelicolor Differentiation

Manteca, A., Rioseras, B., Rogowska-Wrzesinska, A. & Jensen, O. N., 2018, Microbial Proteomics: Methods and Protocols. Becher, D. (ed.). Humana Press, Vol. 1841. p. 249-260 (Methods in Molecular Biology).

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

Streptomyces coelicolor
Microbiology
74 Downloads (Pure)

Quantitative proteome and phosphoproteome analyses of Streptomyces coelicolor reveal proteins and phosphoproteins modulating differentiation and secondary metabolism

Rioseras, B., Sliaha, P. V., Gorshkov, V., Yagüe, P., López-García, M. T., González-Quiñónez, N., Kovalchuk, S., Rogowska-Wrzesinska, A., Jensen, O. N. & Manteca, A., 1. Aug 2018, In : Molecular and Cellular Proteomics. 17, 8, p. 1591-1611

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Streptomyces coelicolor
Secondary Metabolism
Phosphoproteins
Proteome
Phosphorylation

The tumor suppressor CIC directly regulates MAPK pathway genes via histone deacetylation

Weissmann, S., Cloos, P. A., Sidoli, S., Jensen, O. N., Pollard, S. & Helin, K., 2018, In : Cancer Research. 78, 15, p. 4114-4125

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
Histones
Oligodendroglioma
Neoplasms
Histone Deacetylases
Amino Acid Substitution
29 Downloads (Pure)

VSClust: Feature-based variance-sensitive clustering of omics data

Schwämmle, V. & Jensen, O. N., Sep 2018, In : Bioinformatics. 34, 17, p. 2965–2972

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Cluster Analysis
Workflow
Proteins
2017

A biotin enrichment strategy identifies novel carbonylated amino acids in proteins from human plasma

Havelund, J. F., Wojdyla, K., Davies, M. J., Jensen, O. N., Møller, I. M. & Rogowska-Wrzesinska, A., 3. Jan 2017, In : Journal of Proteomics. 156, p. 40-51

Research output: Contribution to journalJournal articleResearchpeer-review

Plasma (human)
Biotin
Amino Acids
Protein Carbonylation
Carbonylation
152 Downloads (Pure)

Abnormal levels of histone methylation in the retinas of diabetic rats are reversed by minocycline treatment

Wang, W., Sidoli, S., Zhang, W., Wang, Q., Wang, L., Jensen, O. N., Guo, L., Zhao, X. & Zheng, L., 2017, In : Scientific Reports. 7, 14 p., 45103.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Minocycline
Histones
Retina
Rodentia
Diabetic Retinopathy
173 Downloads (Pure)

Accumulation of histone variant H3.3 with age is associated with profound changes in the histone methylation landscape

Tvardovskiy, A., Schwämmle, V., Kempf, S. J., Rogowska-Wrzesinska, A. & Jensen, O. N., 2017, In : Nucleic Acids Research. 45, 16, p. 9272-9289

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Histones
Mammals
Hepatocytes
Cell Cycle
Protein Isoforms
121 Downloads (Pure)

Characterization of Complete Histone Tail Proteoforms Using Differential Ion Mobility Spectrometry

Shliaha, P. V., Baird, M. A., Nielsen, M. M., Gorshkov, V., Bowman, A. P., Kaszycki, J. L., Jensen, O. N. & Shvartsburg, A. A., 2017, In : Analytical Chemistry. 89, 10, p. 5461-5466

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Histones
Spectrometry
Ions
Acetylation
Phosphorylation

EZH2 is a potential therapeutic target for H3K27M-mutant pediatric gliomas

Mohammad, F., Weissmann, S., Leblanc, B., Pandey, D. P., Højfeldt, J. W., Comet, I., Zheng, C., Johansen, J. V., Rapin, N., Porse, B. T., Tvardovskiy, A., Jensen, O. N., Olaciregui, N. G., Lavarino, C., Suñol, M., De Torres, C., Mora, J., Carcaboso, A. M. & Helin, K., 2017, In : Nature Medicine. 23, 4, p. 483-492

Research output: Contribution to journalJournal articleResearchpeer-review

Pediatrics
Polycomb Repressive Complex 2
Glioma
Genes
Tumors
113 Downloads (Pure)

Hierarchically templated beads with tailored pore structure for phosphopeptide capture and phosphoproteomics

Wierzbicka, C., Torsetnes, S. B., Jensen, O. N., Shinde, S. & Sellergren, B., 2017, In : RSC Advances. 7, 28, p. 17154-17163 10 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Phosphopeptides
Pore structure
Peptides
Phosphotyrosine
Silicon Dioxide

Molecularly Imprinted Porous Monolithic Materials from Melamine-Formaldehyde for Selective Trapping of Phosphopeptides

Liu, M., Tran, T. M., Abbas Elhaj, A. A., Bøen Torsetnes, S., Jensen, O. N., Sellergren, B. & Irgum, K., 2017, In : Analytical Chemistry. 89, 17, p. 9491-9501

Research output: Contribution to journalJournal articleResearchpeer-review

Phosphopeptides
Polyethers
Surface-Active Agents
Phosphoserine
Phosphotyrosine

Nuclear phosphoproteome analysis of 3T3-L1 preadipocyte differentiation reveals system-wide phosphorylation of transcriptional regulators

Rabiee, A., Schwämmle, V., Sidoli, S., Dai, J., Rogowska-Wrzesinska, A., Mandrup, S. & Jensen, O. N., 2017, In : Proteomics. 17, 6, 5 p., 1600248.

Research output: Contribution to journalJournal articleResearchpeer-review

Phosphorylation
Adipogenesis
Adipocytes
Gene expression
Nuclear Proteins
89 Downloads (Pure)

Phosphotyrosine biased enrichment of tryptic peptides from cancer cells by combining pY-MIP and TiO2 affinity resins

Bllaci, L., Torsetnes, S. B., Wierzbicka, C. K., Shinde, S., Sellergren, B., Rogowska-Wrzesinska, A. & Jensen, O. N., 2017, In : Analytical Chemistry. 89, 21, p. 11332–11340

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Phosphopeptides
Phosphotyrosine
Polymers
Resins
Cells
2016

Dynamic changes of histone H3 marks during Caenorhabditis elegans lifecycle revealed by middle-down proteomics

Sidoli, S., Vandamme, J., Salcini, A. E. & Jensen, O. N., 2016, In : Proteomics. 16, 3, p. 459–464

Research output: Contribution to journalJournal articleResearchpeer-review

Caenorhabditis elegans
Histones
Mammals
Protein Sequence Analysis
Tandem Mass Spectrometry

High-performance hybrid Orbitrap mass spectrometers for quantitative proteome analysis: Observations and implications

Williamson, J. C., Edwards, A. V. G., Verano-Braga, T., Schwämmle, V., Kjeldsen, F., Jensen, O. N. & Larsen, M. R., Mar 2016, In : Proteomics. 16, 6, p. 907-914

Research output: Contribution to journalJournal articleResearchpeer-review

Heat-Shock Response
Mass spectrometers
Proteome
Ions
Isotope Labeling
172 Downloads (Pure)

Subcompartmentalization by cross-membranes during early growth of Streptomyces hyphae

Yagüe, P., Willemse, J., Koning, R. I., Rioseras, B., López-García, M. T., Gonzalez-Quiñonez, N., Lopez-Iglesias, C., Shliaha, P. V., Rogowska-Wrzesinska, A., Koster, A. J., Jensen, O. N., van Wezel, G. P. & Manteca, Á., 2016, In : Nature Communications. 7, 12467, 11 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Peptidoglycan
compartments
membranes
Membranes
Growth
276 Downloads (Pure)

Systems Level Analysis of Histone H3 Post-translational Modifications (PTMs) Reveals Features of PTM Crosstalk in Chromatin Regulation

Schwämmle, V., Sidoli, S., Ruminowicz, C., Wu, X., Lee, C-F., Helin, K. & Jensen, O. N., 2016, In : Molecular and Cellular Proteomics. 15, 8, p. 2715-2729

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Crosstalk
Histones
Chromatin
Methylation
Stem cells
2015

A laser ablation ICP-MS based method for multiplexed immunoblot analysis: applications to manganese-dependent protein dynamics of photosystem II in barley (Hordeum vulgare L.)

de Bang, T. C., Petersen, J., Pedas, P. R., Rogowska-Wrzesinska, A., Jensen, O. N., Schjoerring, J. K., Jensen, P. E., Thelen, J. J. & Husted, S., Aug 2015, In : Plant Journal. 83, 3, p. 555-65

Research output: Contribution to journalJournal articleResearchpeer-review

Photosystem II Protein Complex
Manganese
photosystem II
Hordeum vulgare
lasers

Detection and differentiation of 22kDa and 20kDa Growth Hormone proteoforms in human plasma by LC-MS/MS

Sanmartín, G. S., Bache, N., Bosch, J., Gutierrez-Gallego, R., Segura, J. & Jensen, O. N., 2015, In : B B A - Proteins and Proteomics. 1854, 4, p. 284-290

Research output: Contribution to journalJournal articleResearchpeer-review

124 Downloads (Pure)

H3K23me2 is a new heterochromatic mark in Caenorhabditis elegans

Vandamme, J., Sidoli, S., Mariani, L., Friis, C., Christensen, J., Helin, K., Jensen, O. N. & Salcini, A. E., 2015, In : Nucleic Acids Research. 43, 20, p. 9694-9710

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Caenorhabditis elegans
Histones
Histone Demethylases
Chromatin Immunoprecipitation
Germ Cells

Modulation of cell metabolic pathways and oxidative stress signaling contribute to acquired melphalan resistance in multiple myeloma cells

Zub, K. A., Sousa, M. M. L. D., Sarno, A., Sharma, A., Demirovic, A., Rao, S., Young, C., Aas, P. A., Ericsson, I., Sundan, A., Jensen, O. N. & Slupphaug, G., 2015, In : PLOS ONE. 10, 3, 20 p., e0119857.

Research output: Contribution to journalJournal articleResearchpeer-review

myeloma
Melphalan
Oxidative stress
Metabolic Networks and Pathways
biochemical pathways
671 Downloads (Pure)

NADH-Cytochrome b5 Reductase 3 Promotes Colonization and Metastasis Formation and Is a Prognostic Marker of Disease-Free and Overall Survival in Estrogen Receptor-Negative Breast Cancer

Lund, R. R., Leth-Larsen, R., Caterino, T. D., Terp, M. G., Nissen, J., Lænkholm, A-V., Jensen, O. N. & Ditzel, H. J., Nov 2015, In : Molecular and Cellular Proteomics. 14, 11, p. 2988-99

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Cytochrome-B(5) Reductase
Cytochromes b5
Cytochrome Reductases
Estrogen Receptors
Disease-Free Survival

Quantitative analysis of proteome and lipidome dynamics reveals functional regulation of global lipid metabolism

Casanovas, A., Sprenger, R. R., Tarasov, K., Ruckerbauer, D. E., Hannibal-Bach, H. K., Zanghellini, J., Jensen, O. N. & Ejsing, C. S., 19. Mar 2015, In : Chemistry & Biology. 22, 3, p. 412-25 14 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Proteome
Lipid Metabolism
Sterols
Metabolism
Chemical analysis

Targeted mass spectrometry analysis of the proteins IGF1, IGF2, IBP2, IBP3 and A2GL by blood protein precipitation

Such-Sanmartín, G., Bache, N., Callesen, A. K., Rogowska-Wrzesinska, A. & Jensen, O. N., 15. Jan 2015, In : Journal of Proteomics. 113, p. 29-37 9 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Mass spectrometry
Blood Proteins
Biomarkers
Liquid chromatography
Liquid Chromatography

The human oral metaproteome reveals potential biomarkers for caries disease

Belda-Ferre, P., Williamson, J., Simón-Soro, Á., Artacho, A., Jensen, O. N. & Mira, A., Oct 2015, In : Proteomics. 15, 20, p. 3497-3507

Research output: Contribution to journalJournal articleResearchpeer-review

Biomarkers
Dental Plaque
Proteins
Bearings (structural)
Biofilms
158 Downloads (Pure)

Top-down and Middle-down Protein Analysis Reveals that Intact and Clipped Human Histones Differ in Post-translational Modification Patterns

Tvardovskiy, A., Wrzesinski, K., Sidoli, S., Fey, S. J., Rogowska-Wrzesinska, A. & Jensen, O. N., 30. Sep 2015, In : Molecular and Cellular Proteomics. 14, 12, p. 3142-3153

Research output: Contribution to journalJournal articleResearchpeer-review

Histones
Proteins
Hepatocytes
Mass spectrometry
Acetylation

Tumor suppressor ASXL1 is essential for the activation of INK4B expression in response to oncogene activity and anti-proliferative signals

Wu, X., Bekker-Jensen, I. H., Christensen, J., Rasmussen, K. D., Sidoli, S., Qi, Y., Kong, Y., Wang, X., Cui, Y., Xiao, Z., Xu, G., Williams, K., Rappsilber, J., Sønderby, C. K., Winther, O., Jensen, O. N. & Helin, K., 2015, In : Cell Research. 25, 11, p. 1205–1218

Research output: Contribution to journalJournal articleResearchpeer-review

Mutation
Histones
Transcriptional Activation
Lysine
Neoplasms

Two distinct modes for propagation of histone PTMs across the cell cycle

Alabert, C., Barth, T. K., Reverón-Gómez, N., Sidoli, S., Schmidt, A., Jensen, O. N., Imhof, A. & Groth, A., 15. Mar 2015, In : Genes & Development. 29, 6, p. 585-90 6 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Histones
Cell Cycle
Isotope Labeling
Epigenomics
Amino Acids