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    Ole Nørregaard Jensen
2020

Middle-Down Proteomic Analyses with Ion Mobility Separations of Endogenous Isomeric Proteoforms

Shliaha, P. V., Gorshkov, V., Kovalchuk, S. I., Schwämmle, V., Baird, M. A., Shvartsburg, A. A. & Jensen, O. N., 17. jan. 2020, I : Analytical chemistry.

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Histones
Isomers
Ions
Spectrometry
Chromatography

Visualization of the dynamics of histone modifications and their crosstalk using PTM-CrossTalkMapper

Kirsch, R., Jensen, O. N. & Schwämmle, V., 1. jan. 2020, (Accepteret/In press) I : Methods.

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Histones
Research Design
Proteins
Nucleosomes
Acetylation
2019
23 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, I : Analytical Chemistry. 91, 2, s. 1479-1485 7 s.

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Pulse time modulation
Ultrahigh vacuum
Mass spectrometers
Isomers
Histones
85 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, I : Molecular and Cellular Proteomics. 18, 2, s. 383-390

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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. maj 2019, I : Analytical Chemistry. 91, 10, s. 6918-6925

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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, I : Nature Structural and Molecular Biology. 26, 11, s. 999-1012 32 s.

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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, I : Analytical Chemistry. 91, 15, s. 10188-10196

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Serine
Polymers
Peptides
Amino Acids, Peptides, and Proteins
Signal transduction
2018
106 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, I : Nature Structural and Molecular Biology. 25, 3, s. 225-232

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Epigenomics
Maintenance
Histones
Lysine
Mouse Embryonic Stem Cells
68 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, I : Genetics. 210, 3, s. 969-982

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Caenorhabditis elegans
Epigenomics
Embryonic Structures
Oocytes
Mothers

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

Jensen, O. N., 2018.

Publikation: Konferencebidrag uden forlag/tidsskriftPosterForskning

115 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, I : Plant Methods. 14, 1, s. 1-13 72.

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proteomics
barley
mass spectrometry
digestion
deoxycholic acid
68 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, I : Analytical Chemistry. 90, 17, s. 10425–10433

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Photodissociation
Histones
Mass spectrometry
Bioinformatics
Peptides
82 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 flere, 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, I : Nature Chemical Biology. 14, 3, s. 206-214

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Proteins
Proteome
Databases
RNA
DNA
113 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, I : Analytical Chemistry. 90, 4, s. 2918-2925

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Ions
Electrospray ionization
Ion sources
Proteome
Binary mixtures
58 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, I : Analytical Chemistry. 90, 21, s. 12519-12526

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Gases
Proteins
Proteomics
Mass spectrometry
Amino Acids
79 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, I : Proceedings of the National Academy of Sciences of the United States of America. 115, 3, s. E400-E408

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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. (red.). Humana Press, Bind 1841. s. 249-260 (Methods in Molecular Biology).

Publikation: Bidrag til bog/antologi/rapport/konference-proceedingBidrag til bog/antologiForskningpeer review

Streptomyces coelicolor
Microbiology
84 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, I : Molecular and Cellular Proteomics. 17, 8, s. 1591-1611

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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, I : Cancer Research. 78, 15, s. 4114-4125

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Histones
Oligodendroglioma
Neoplasms
Histone Deacetylases
Amino Acid Substitution
33 Downloads (Pure)

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

Schwämmle, V. & Jensen, O. N., sep. 2018, I : Bioinformatics. 34, 17, s. 2965–2972

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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, I : Journal of Proteomics. 156, s. 40-51

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Plasma (human)
Biotin
Amino Acids
Protein Carbonylation
Carbonylation
163 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, I : Scientific Reports. 7, 14 s., 45103.

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Minocycline
Histones
Retina
Rodentia
Diabetic Retinopathy
180 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, I : Nucleic Acids Research. 45, 16, s. 9272-9289

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Histones
Mammals
Hepatocytes
Cell Cycle
Protein Isoforms
131 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, I : Analytical Chemistry. 89, 10, s. 5461-5466

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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, I : Nature Medicine. 23, 4, s. 483-492

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Pediatrics
Polycomb Repressive Complex 2
Glioma
Genes
Tumors
118 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, I : RSC Advances. 7, 28, s. 17154-17163 10 s.

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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, I : Analytical Chemistry. 89, 17, s. 9491-9501

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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, I : Proteomics. 17, 6, 5 s., 1600248.

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Phosphorylation
Adipogenesis
Adipocytes
Gene expression
Nuclear Proteins
100 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, I : Analytical Chemistry. 89, 21, s. 11332–11340

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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, I : Proteomics. 16, 3, s. 459–464

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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, I : Proteomics. 16, 6, s. 907-914

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Heat-Shock Response
Mass spectrometers
Proteome
Ions
Isotope Labeling
192 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, I : Nature Communications. 7, 12467, 11 s.

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Peptidoglycan
compartments
membranes
Membranes
Growth
290 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, I : Molecular and Cellular Proteomics. 15, 8, s. 2715-2729

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Crosstalk
Histones
Chromatin
Methylation
Stem cells