Publications by authors named "Bas van Breukelen"

39Publications

Schistosoma mansoni infection affects the proteome and lipidome of circulating extracellular vesicles in the host.

Mol Biochem Parasitol 2020 07 27;238:111296. Epub 2020 Jun 27.

Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.molbiopara.2020.111296DOI Listing
July 2020

An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas.

Cell Rep 2015 Jun 11;11(11):1834-43. Epub 2015 Jun 11.

Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.05.029DOI Listing
June 2015

Spatial Organization in Protein Kinase A Signaling Emerged at the Base of Animal Evolution.

J Proteome Res 2015 Jul 24;14(7):2976-87. Epub 2015 Jun 24.

†Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

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http://dx.doi.org/10.1021/acs.jproteome.5b00370DOI Listing
July 2015

Proteome adaptation of Saccharomyces cerevisiae to severe calorie restriction in Retentostat cultures.

J Proteome Res 2014 Aug 18;13(8):3542-53. Epub 2014 Jul 18.

Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH, Utrecht, The Netherlands.

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http://dx.doi.org/10.1021/pr5003388DOI Listing
August 2014

Facilitating protein disulfide mapping by a combination of pepsin digestion, electron transfer higher energy dissociation (EThcD), and a dedicated search algorithm SlinkS.

Mol Cell Proteomics 2014 Oct 30;13(10):2776-86. Epub 2014 Jun 30.

From the ‡Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands; §Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands

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http://dx.doi.org/10.1074/mcp.O114.039057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4189002PMC
October 2014

Daily rhythms in the cyanobacterium synechococcus elongatus probed by high-resolution mass spectrometry-based proteomics reveals a small defined set of cyclic proteins.

Mol Cell Proteomics 2014 Aug 27;13(8):2042-55. Epub 2014 Mar 27.

From the ‡Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands;

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http://dx.doi.org/10.1074/mcp.M113.035840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4125736PMC
August 2014

Identification of enriched PTM crosstalk motifs from large-scale experimental data sets.

J Proteome Res 2014 Jan 23;13(1):249-59. Epub 2013 Oct 23.

Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.

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http://dx.doi.org/10.1021/pr4005579DOI Listing
January 2014

Deep proteome profiling of circulating granulocytes reveals bactericidal/permeability-increasing protein as a biomarker for severe atherosclerotic coronary stenosis.

J Proteome Res 2012 Nov 11;11(11):5235-44. Epub 2012 Oct 11.

Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Utrecht, The Netherlands.

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http://pubs.acs.org/doi/10.1021/pr3004375
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http://dx.doi.org/10.1021/pr3004375DOI Listing
November 2012

Current challenges in software solutions for mass spectrometry-based quantitative proteomics.

Amino Acids 2012 Sep 22;43(3):1087-108. Epub 2012 Jul 22.

Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht, The Netherlands.

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http://dx.doi.org/10.1007/s00726-012-1289-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418498PMC
September 2012

High confidence and sensitivity four-dimensional fractionation for human plasma proteome analysis.

Amino Acids 2012 Nov 21;43(5):2199-202. Epub 2012 Mar 21.

Department of Medicine, University of Padua, Padua, Italy.

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http://dx.doi.org/10.1007/s00726-012-1267-1DOI Listing
November 2012

Database independent proteomics analysis of the ostrich and human proteome.

Proc Natl Acad Sci U S A 2012 Jan 22;109(2):407-12. Epub 2011 Dec 22.

Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

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http://dx.doi.org/10.1073/pnas.1108399108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3258627PMC
January 2012

Evaluating experimental bias and completeness in comparative phosphoproteomics analysis.

PLoS One 2011 10;6(8):e23276. Epub 2011 Aug 10.

Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0023276PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154393PMC
December 2011

Improving SRM assay development: a global comparison between triple quadrupole, ion trap, and higher energy CID peptide fragmentation spectra.

J Proteome Res 2011 Sep 21;10(9):4334-41. Epub 2011 Jul 21.

Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

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http://dx.doi.org/10.1021/pr200156bDOI Listing
September 2011

Deconvolution of overlapping isotopic clusters improves quantification of stable isotope-labeled peptides.

J Proteomics 2011 Sep 15;74(10):2204-9. Epub 2011 May 15.

BiomolecularMass Spectrometry and Proteomics Group, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences,Utrecht University, CH Utrecht, The Netherlands.

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http://dx.doi.org/10.1016/j.jprot.2011.04.022DOI Listing
September 2011

A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data.

Bioinformatics 2011 Apr 23;27(8):1176-8. Epub 2011 Feb 23.

Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btr094DOI Listing
April 2011

RockerBox: analysis and filtering of massive proteomics search results.

J Proteome Res 2011 Mar 7;10(3):1420-4. Epub 2011 Feb 7.

Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

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http://dx.doi.org/10.1021/pr1010185DOI Listing
March 2011

Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.

BMC Genomics 2010 Dec 2;11:685. Epub 2010 Dec 2.

Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.

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http://dx.doi.org/10.1186/1471-2164-11-685DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091791PMC
December 2010

LysNDeNovo: an algorithm enabling de novo sequencing of Lys-N generated peptides fragmented by electron transfer dissociation.

Proteomics 2010 Mar;10(6):1196-201

Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.

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http://doi.wiley.com/10.1002/pmic.200900405
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http://dx.doi.org/10.1002/pmic.200900405DOI Listing
March 2010

Profiling of N-acetylated protein termini provides in-depth insights into the N-terminal nature of the proteome.

Mol Cell Proteomics 2010 May 7;9(5):928-39. Epub 2010 Jan 7.

Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

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http://dx.doi.org/10.1074/mcp.M900463-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2871424PMC
May 2010

In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling.

Mol Cell Proteomics 2010 Jan 21;9(1):84-99. Epub 2009 Sep 21.

Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.

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http://dx.doi.org/10.1074/mcp.M900291-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808269PMC
January 2010

StatQuant: a post-quantification analysis toolbox for improving quantitative mass spectrometry.

Bioinformatics 2009 Jun 31;25(11):1472-3. Epub 2009 Mar 31.

Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrech, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btp181DOI Listing
June 2009

A versatile peptide pI calculator for phosphorylated and N-terminal acetylated peptides experimentally tested using peptide isoelectric focusing.

Proteomics 2008 Dec;8(23-24):4898-906

Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.

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http://doi.wiley.com/10.1002/pmic.200800295
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http://dx.doi.org/10.1002/pmic.200800295DOI Listing
December 2008

Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes.

Genome Biol 2008 Oct 1;9(10):R144. Epub 2008 Oct 1.

Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan, The Netherlands.

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http://dx.doi.org/10.1186/gb-2008-9-10-r144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760871PMC
October 2008

Multiplexed proteomics mapping of yeast RNA polymerase II and III allows near-complete sequence coverage and reveals several novel phosphorylation sites.

Anal Chem 2008 May 17;80(10):3584-92. Epub 2008 Apr 17.

Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands.

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http://dx.doi.org/10.1021/ac7024283DOI Listing
May 2008

Online automated in vivo zebrafish phosphoproteomics: from large-scale analysis down to a single embryo.

J Proteome Res 2008 Apr 29;7(4):1555-64. Epub 2008 Feb 29.

Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands.

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http://dx.doi.org/10.1021/pr700667wDOI Listing
April 2008

Highly robust, automated, and sensitive online TiO2-based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster.

J Proteome Res 2008 Feb 23;7(2):687-97. Epub 2007 Nov 23.

Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands.

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http://dx.doi.org/10.1021/pr700605zDOI Listing
February 2008

Targeted analysis of protein termini.

J Proteome Res 2007 Dec 10;6(12):4634-45. Epub 2007 Oct 10.

Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, the Netherlands.

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http://dx.doi.org/10.1021/pr070375kDOI Listing
December 2007

Resolving stoichiometries and oligomeric states of glutamate synthase protein complexes with curve fitting and simulation of electrospray mass spectra.

Rapid Commun Mass Spectrom 2006 ;20(16):2490-6

Utrecht University, Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands.

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http://dx.doi.org/10.1002/rcm.2620DOI Listing
November 2007

Analysis of the cGMP/cAMP interactome using a chemical proteomics approach in mammalian heart tissue validates sphingosine kinase type 1-interacting protein as a genuine and highly abundant AKAP.

J Proteome Res 2006 Jun;5(6):1435-47

Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands.

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http://dx.doi.org/10.1021/pr0600529DOI Listing
June 2006

Adenovirus type 5 DNA binding protein stimulates binding of DNA polymerase to the replication origin.

J Virol 2003 Jan;77(2):915-22

Department of Physiological Chemistry and Centre for Biomedical Genetics, University Medical Center Utrecht, The Netherlands.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC140850PMC
http://dx.doi.org/10.1128/jvi.77.2.915-922.2003DOI Listing
January 2003