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Items: 1 to 50 of 55

1.

Interpretation of Tandem Mass Spectra of Posttranslationally Modified Peptides.

Bunkenborg J, Matthiesen R.

Methods Mol Biol. 2020;2051:199-230. doi: 10.1007/978-1-4939-9744-2_8.

PMID:
31552630
2.

Introduction to Mass Spectrometry-Based Proteomics.

Matthiesen R, Bunkenborg J.

Methods Mol Biol. 2020;2051:1-58. doi: 10.1007/978-1-4939-9744-2_1.

PMID:
31552623
3.

Enhanced trypsin on a budget: Stabilization, purification and high-temperature application of inexpensive commercial trypsin for proteomics applications.

Heissel S, Frederiksen SJ, Bunkenborg J, Højrup P.

PLoS One. 2019 Jun 27;14(6):e0218374. doi: 10.1371/journal.pone.0218374. eCollection 2019.

4.

DNA damage-induced dynamic changes in abundance and cytosol-nuclear translocation of proteins involved in translational processes, metabolism, and autophagy.

Bennetzen MV, Kosar M, Bunkenborg J, Payne MR, Bartkova J, Lindström MS, Lukas J, Andersen JS, Bartek J, Larsen DH.

Cell Cycle. 2018;17(17):2146-2163. doi: 10.1080/15384101.2018.1515552. Epub 2018 Sep 22.

5.

Discrimination of Isoleucine and Leucine by Dimethylation-Assisted MS3.

Maibom-Thomsen S, Heissel S, Mørtz E, Højrup P, Bunkenborg J.

Anal Chem. 2018 Aug 7;90(15):9055-9059. doi: 10.1021/acs.analchem.8b01375. Epub 2018 Jul 27.

PMID:
30015478
6.

Evaluation of spectral libraries and sample preparation for DIA-LC-MS analysis of host cell proteins: A case study of a bacterially expressed recombinant biopharmaceutical protein.

Heissel S, Bunkenborg J, Kristiansen MP, Holmbjerg AF, Grimstrup M, Mørtz E, Kofoed T, Højrup P.

Protein Expr Purif. 2018 Jul;147:69-77. doi: 10.1016/j.pep.2018.03.002. Epub 2018 Mar 9.

PMID:
29526817
7.

Draft Nuclear Genome Sequence of the Halophilic and Beta-Carotene-Accumulating Green Alga Dunaliella salina Strain CCAP19/18.

Polle JEW, Barry K, Cushman J, Schmutz J, Tran D, Hathwaik LT, Yim WC, Jenkins J, McKie-Krisberg Z, Prochnik S, Lindquist E, Dockter RB, Adam C, Molina H, Bunkenborg J, Jin E, Buchheim M, Magnuson J.

Genome Announc. 2017 Oct 26;5(43). pii: e01105-17. doi: 10.1128/genomeA.01105-17.

8.

Covalent perturbation as a tool for validation of identifications and PTM mapping applied to bovine alpha-crystallin.

Bunkenborg J, Falkenby LG, Harder LM, Molina H.

Proteomics. 2016 Feb;16(4):545-53. doi: 10.1002/pmic.201500068. Epub 2016 Feb 2.

PMID:
26644245
9.

Centrosomes. Regulated assembly of a supramolecular centrosome scaffold in vitro.

Woodruff JB, Wueseke O, Viscardi V, Mahamid J, Ochoa SD, Bunkenborg J, Widlund PO, Pozniakovsky A, Zanin E, Bahmanyar S, Zinke A, Hong SH, Decker M, Baumeister W, Andersen JS, Oegema K, Hyman AA.

Science. 2015 May 15;348(6236):808-12. doi: 10.1126/science.aaa3923.

10.

A redox-dependent dimerization switch regulates activity and tolerance for reactive oxygen species of barley seed glutathione peroxidase.

Navrot N, Skjoldager N, Bunkenborg J, Svensson B, Hägglund P.

Plant Physiol Biochem. 2015 May;90:58-63. doi: 10.1016/j.plaphy.2015.03.003. Epub 2015 Mar 10.

PMID:
25796076
11.

The Caenorhabditis elegans pericentriolar material components SPD-2 and SPD-5 are monomeric in the cytoplasm before incorporation into the PCM matrix.

Wueseke O, Bunkenborg J, Hein MY, Zinke A, Viscardi V, Woodruff JB, Oegema K, Mann M, Andersen JS, Hyman AA.

Mol Biol Cell. 2014 Oct 1;25(19):2984-92. doi: 10.1091/mbc.E13-09-0514. Epub 2014 Aug 7.

12.

S100A11 is required for efficient plasma membrane repair and survival of invasive cancer cells.

Jaiswal JK, Lauritzen SP, Scheffer L, Sakaguchi M, Bunkenborg J, Simon SM, Kallunki T, Jäättelä M, Nylandsted J.

Nat Commun. 2014 May 8;5:3795. doi: 10.1038/ncomms4795.

13.

Glycopeptide enrichment using a combination of ZIC-HILIC and cotton wool for exploring the glycoproteome of wheat flour albumins.

Dedvisitsakul P, Jacobsen S, Svensson B, Bunkenborg J, Finnie C, Hägglund P.

J Proteome Res. 2014 May 2;13(5):2696-703. doi: 10.1021/pr401282r. Epub 2014 Apr 1.

PMID:
24654981
14.

Inducing autophagy: a comparative phosphoproteomic study of the cellular response to ammonia and rapamycin.

Harder LM, Bunkenborg J, Andersen JS.

Autophagy. 2014 Feb;10(2):339-55. doi: 10.4161/auto.26863. Epub 2013 Nov 26.

15.

The human cap-binding complex is functionally connected to the nuclear RNA exosome.

Andersen PR, Domanski M, Kristiansen MS, Storvall H, Ntini E, Verheggen C, Schein A, Bunkenborg J, Poser I, Hallais M, Sandberg R, Hyman A, LaCava J, Rout MP, Andersen JS, Bertrand E, Jensen TH.

Nat Struct Mol Biol. 2013 Dec;20(12):1367-76. doi: 10.1038/nsmb.2703. Epub 2013 Nov 24.

16.

Identification of thioredoxin target disulfides using isotope-coded affinity tags.

Hägglund P, Bunkenborg J, Maeda K, Finnie C, Svensson B.

Methods Mol Biol. 2014;1072:677-85. doi: 10.1007/978-1-62703-631-3_47.

PMID:
24136556
17.

Cutting edge proteomics: benchmarking of six commercial trypsins.

Bunkenborg J, Espadas G, Molina H.

J Proteome Res. 2013 Aug 2;12(8):3631-41. doi: 10.1021/pr4001465. Epub 2013 Jul 2.

PMID:
23819575
18.

The barley grain thioredoxin system - an update.

Hägglund P, Björnberg O, Navrot N, Mørch Jensen J, Maeda K, Kirkensgaard K, Shahpiri A, Sultan A, Bunkenborg J, Gubler F, Barrero JM, Henriksen A, Finnie C, Svensson B.

Front Plant Sci. 2013 May 21;4:151. doi: 10.3389/fpls.2013.00151. eCollection 2013.

19.

Interpretation of tandem mass spectra of posttranslationally modified peptides.

Bunkenborg J, Matthiesen R.

Methods Mol Biol. 2013;1007:139-71. doi: 10.1007/978-1-62703-392-3_6.

PMID:
23666725
20.

Introduction to mass spectrometry-based proteomics.

Matthiesen R, Bunkenborg J.

Methods Mol Biol. 2013;1007:1-45. doi: 10.1007/978-1-62703-392-3_1.

PMID:
23666720
21.

Data extraction from proteomics raw data: an evaluation of nine tandem MS tools using a large Orbitrap data set.

Mancuso F, Bunkenborg J, Wierer M, Molina H.

J Proteomics. 2012 Sep 18;75(17):5293-303. doi: 10.1016/j.jprot.2012.06.012. Epub 2012 Jun 20.

PMID:
22728601
22.

Friend or food: different cues to the autophagosomal proteome.

Becker AC, Bunkenborg J, Eisenberg T, Harder LM, Schroeder S, Madeo F, Andersen JS, Dengjel J.

Autophagy. 2012 Jun;8(6):995-6. doi: 10.4161/auto.20286. Epub 2012 May 10.

23.

Identification of autophagosome-associated proteins and regulators by quantitative proteomic analysis and genetic screens.

Dengjel J, Høyer-Hansen M, Nielsen MO, Eisenberg T, Harder LM, Schandorff S, Farkas T, Kirkegaard T, Becker AC, Schroeder S, Vanselow K, Lundberg E, Nielsen MM, Kristensen AR, Akimov V, Bunkenborg J, Madeo F, Jäättelä M, Andersen JS.

Mol Cell Proteomics. 2012 Mar;11(3):M111.014035. doi: 10.1074/mcp.M111.014035. Epub 2012 Feb 6.

24.

ErbB2-associated changes in the lysosomal proteome.

Nylandsted J, Becker AC, Bunkenborg J, Andersen JS, Dengjel J, Jäättelä M.

Proteomics. 2011 Jul;11(14):2830-8. doi: 10.1002/pmic.201000734. Epub 2011 Jun 14.

PMID:
21674799
25.

SIRT3 deacetylates mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase 2 and regulates ketone body production.

Shimazu T, Hirschey MD, Hua L, Dittenhafer-Reed KE, Schwer B, Lombard DB, Li Y, Bunkenborg J, Alt FW, Denu JM, Jacobson MP, Verdin E.

Cell Metab. 2010 Dec 1;12(6):654-61. doi: 10.1016/j.cmet.2010.11.003.

26.

The minotaur proteome: avoiding cross-species identifications deriving from bovine serum in cell culture models.

Bunkenborg J, García GE, Paz MI, Andersen JS, Molina H.

Proteomics. 2010 Aug;10(16):3040-4. doi: 10.1002/pmic.201000103.

PMID:
20641139
27.

Site-specific phosphorylation dynamics of the nuclear proteome during the DNA damage response.

Bennetzen MV, Larsen DH, Bunkenborg J, Bartek J, Lukas J, Andersen JS.

Mol Cell Proteomics. 2010 Jun;9(6):1314-23. doi: 10.1074/mcp.M900616-MCP200. Epub 2010 Feb 16.

28.

Identification of thioredoxin target disulfides in proteins released from barley aleurone layers.

Hägglund P, Bunkenborg J, Yang F, Harder LM, Finnie C, Svensson B.

J Proteomics. 2010 Apr 18;73(6):1133-6. doi: 10.1016/j.jprot.2010.01.007. Epub 2010 Jan 28.

PMID:
20114090
29.

Up-regulated proteins in the fluid bathing the tumour cell microenvironment as potential serological markers for early detection of cancer of the breast.

Gromov P, Gromova I, Bunkenborg J, Cabezon T, Moreira JM, Timmermans-Wielenga V, Roepstorff P, Rank F, Celis JE.

Mol Oncol. 2010 Feb;4(1):65-89. doi: 10.1016/j.molonc.2009.11.003. Epub 2009 Nov 23.

30.

MSQuant, an open source platform for mass spectrometry-based quantitative proteomics.

Mortensen P, Gouw JW, Olsen JV, Ong SE, Rigbolt KT, Bunkenborg J, Cox J, Foster LJ, Heck AJ, Blagoev B, Andersen JS, Mann M.

J Proteome Res. 2010 Jan;9(1):393-403. doi: 10.1021/pr900721e.

PMID:
19888749
31.

Identification of thioredoxin disulfide targets using a quantitative proteomics approach based on isotope-coded affinity tags.

Hägglund P, Bunkenborg J, Maeda K, Svensson B.

J Proteome Res. 2008 Dec;7(12):5270-6.

PMID:
19367707
32.

Mammalian Sir2 homolog SIRT3 regulates global mitochondrial lysine acetylation.

Lombard DB, Alt FW, Cheng HL, Bunkenborg J, Streeper RS, Mostoslavsky R, Kim J, Yancopoulos G, Valenzuela D, Murphy A, Yang Y, Chen Y, Hirschey MD, Bronson RT, Haigis M, Guarente LP, Farese RV Jr, Weissman S, Verdin E, Schwer B.

Mol Cell Biol. 2007 Dec;27(24):8807-14. Epub 2007 Oct 8.

33.

An enzymatic deglycosylation scheme enabling identification of core fucosylated N-glycans and O-glycosylation site mapping of human plasma proteins.

Hägglund P, Matthiesen R, Elortza F, Højrup P, Roepstorff P, Jensen ON, Bunkenborg J.

J Proteome Res. 2007 Aug;6(8):3021-31. Epub 2007 Jul 18.

PMID:
17636988
34.

A mass spectrometry-friendly database for cSNP identification.

Schandorff S, Olsen JV, Bunkenborg J, Blagoev B, Zhang Y, Andersen JS, Mann M.

Nat Methods. 2007 Jun;4(6):465-6. No abstract available.

PMID:
17538625
35.

Quantitation of multisite EGF receptor phosphorylation using mass spectrometry and a novel normalization approach.

Boeri Erba E, Matthiesen R, Bunkenborg J, Schulze WX, Di Stefano P, Cabodi S, Tarone G, Defilippi P, Jensen ON.

J Proteome Res. 2007 Jul;6(7):2768-85. Epub 2007 May 25.

PMID:
17523611
36.

Quantitative proteomic assessment of very early cellular signaling events.

Dengjel J, Akimov V, Olsen JV, Bunkenborg J, Mann M, Blagoev B, Andersen JS.

Nat Biotechnol. 2007 May;25(5):566-8. Epub 2007 Apr 22.

PMID:
17450129
37.
38.

Reversible lysine acetylation controls the activity of the mitochondrial enzyme acetyl-CoA synthetase 2.

Schwer B, Bunkenborg J, Verdin RO, Andersen JS, Verdin E.

Proc Natl Acad Sci U S A. 2006 Jul 5;103(27):10224-10229. doi: 10.1073/pnas.0603968103. Epub 2006 Jun 20.

39.

Modification-specific proteomics of plasma membrane proteins: identification and characterization of glycosylphosphatidylinositol-anchored proteins released upon phospholipase D treatment.

Elortza F, Mohammed S, Bunkenborg J, Foster LJ, Nühse TS, Brodbeck U, Peck SC, Jensen ON.

J Proteome Res. 2006 Apr;5(4):935-43.

PMID:
16602701
40.

On-bead chemical synthesis and display of phosphopeptides for affinity pull-down proteomics.

Brandt M, Madsen JC, Bunkenborg J, Jensen ON, Gammeltoft S, Jensen KJ.

Chembiochem. 2006 Apr;7(4):623-30.

PMID:
16502475
41.

VEMS 3.0: algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins.

Matthiesen R, Trelle MB, Højrup P, Bunkenborg J, Jensen ON.

J Proteome Res. 2005 Nov-Dec;4(6):2338-47.

PMID:
16335983
42.

Serum protein profiling by miniaturized solid-phase extraction and matrix-assisted laser desorption/ionization mass spectrometry.

Callesen AK, Mohammed S, Bunkenborg J, Kruse TA, Cold S, Mogensen O, Christensen Rd, Vach W, Jørgensen PE, Jensen ON.

Rapid Commun Mass Spectrom. 2005;19(12):1578-86.

PMID:
15915448
43.

A proteomic analysis of human hemodialysis fluid.

Molina H, Bunkenborg J, Reddy GH, Muthusamy B, Scheel PJ, Pandey A.

Mol Cell Proteomics. 2005 May;4(5):637-50. Epub 2005 Feb 20.

44.

Comprehensive proteomic analysis of human pancreatic juice.

Grønborg M, Bunkenborg J, Kristiansen TZ, Jensen ON, Yeo CJ, Hruban RH, Maitra A, Goggins MG, Pandey A.

J Proteome Res. 2004 Sep-Oct;3(5):1042-55.

PMID:
15473694
45.

Database-independent, database-dependent, and extended interpretation of peptide mass spectra in VEMS V2.0.

Matthiesen R, Bunkenborg J, Stensballe A, Jensen ON, Welinder KG, Bauw G.

Proteomics. 2004 Sep;4(9):2583-93.

PMID:
15352233
46.
47.

A proteomic analysis of human bile.

Kristiansen TZ, Bunkenborg J, Gronborg M, Molina H, Thuluvath PJ, Argani P, Goggins MG, Maitra A, Pandey A.

Mol Cell Proteomics. 2004 Jul;3(7):715-28. Epub 2004 Apr 14.

48.

Screening for N-glycosylated proteins by liquid chromatography mass spectrometry.

Bunkenborg J, Pilch BJ, Podtelejnikov AV, Wiśniewski JR.

Proteomics. 2004 Feb;4(2):454-65.

PMID:
14760718
49.

Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria.

Mootha VK, Bunkenborg J, Olsen JV, Hjerrild M, Wisniewski JR, Stahl E, Bolouri MS, Ray HN, Sihag S, Kamal M, Patterson N, Lander ES, Mann M.

Cell. 2003 Nov 26;115(5):629-40.

50.

Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics.

Mootha VK, Lepage P, Miller K, Bunkenborg J, Reich M, Hjerrild M, Delmonte T, Villeneuve A, Sladek R, Xu F, Mitchell GA, Morin C, Mann M, Hudson TJ, Robinson B, Rioux JD, Lander ES.

Proc Natl Acad Sci U S A. 2003 Jan 21;100(2):605-10. Epub 2003 Jan 14.

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