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Items: 1 to 50 of 72

1.

Virtual experiments to assess opportunities and pitfalls of CSIA in physical-chemical heterogeneous aquifers.

Thouement HAA, Van Breukelen BM.

J Contam Hydrol. 2020 Mar 20;231:103638. doi: 10.1016/j.jconhyd.2020.103638. [Epub ahead of print]

PMID:
32240881
2.

Do CSIA data from aquifers inform on natural degradation of chlorinated ethenes in aquitards?

Thouement HAA, Kuder T, Heimovaara TJ, van Breukelen BM.

J Contam Hydrol. 2019 Oct;226:103520. doi: 10.1016/j.jconhyd.2019.103520. Epub 2019 Jul 8.

3.

Urban hydrogeology: Transport routes and mixing of water and solutes in a groundwater influenced urban lowland catchment.

Yu L, Rozemeijer JC, van der Velde Y, van Breukelen BM, Ouboter M, Broers HP.

Sci Total Environ. 2019 Aug 15;678:288-300. doi: 10.1016/j.scitotenv.2019.04.428. Epub 2019 Apr 29.

PMID:
31075595
4.

Subsurface landfill leachate contamination affects microbial metabolic potential and gene expression in the Banisveld aquifer.

Tas N, Brandt BW, Braster M, van Breukelen BM, Röling WFM.

FEMS Microbiol Ecol. 2018 Oct 1;94(10). doi: 10.1093/femsec/fiy156.

5.

Modeling 3D-CSIA data: Carbon, chlorine, and hydrogen isotope fractionation during reductive dechlorination of TCE to ethene.

Van Breukelen BM, Thouement HAA, Stack PE, Vanderford M, Philp P, Kuder T.

J Contam Hydrol. 2017 Sep;204:79-89. doi: 10.1016/j.jconhyd.2017.07.003. Epub 2017 Jul 17.

6.

Comment on "Thermally Released Arsenic in Porewater from Sediments in the Cold Lake Area of Alberta, Canada".

Van Breukelen BM, Bonte M.

Environ Sci Technol. 2016 Jul 5;50(13):7263-4. doi: 10.1021/acs.est.6b02106. Epub 2016 Jun 15. No abstract available.

PMID:
27301586
7.

Reactive transport modeling of subsurface arsenic removal systems in rural Bangladesh.

Rahman MM, Bakker M, Patty CH, Hassan Z, Röling WF, Ahmed KM, van Breukelen BM.

Sci Total Environ. 2015 Dec 15;537:277-93. doi: 10.1016/j.scitotenv.2015.07.140. Epub 2015 Aug 15.

PMID:
26282762
8.

An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas.

Giansanti P, Aye TT, van den Toorn H, Peng M, van Breukelen B, Heck AJ.

Cell Rep. 2015 Jun 23;11(11):1834-43. doi: 10.1016/j.celrep.2015.05.029. Epub 2015 Jun 11.

9.

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

Peng M, Aye TT, Snel B, van Breukelen B, Scholten A, Heck AJ.

J Proteome Res. 2015 Jul 2;14(7):2976-87. doi: 10.1021/acs.jproteome.5b00370. Epub 2015 Jun 24.

PMID:
26066639
10.

Biodegradation: Updating the concepts of control for microbial cleanup in contaminated aquifers.

Meckenstock RU, Elsner M, Griebler C, Lueders T, Stumpp C, Aamand J, Agathos SN, Albrechtsen HJ, Bastiaens L, Bjerg PL, Boon N, Dejonghe W, Huang WE, Schmidt SI, Smolders E, Sørensen SR, Springael D, van Breukelen BM.

Environ Sci Technol. 2015 Jun 16;49(12):7073-81. doi: 10.1021/acs.est.5b00715. Epub 2015 Jun 5. Review.

PMID:
26000605
11.

Diverse arsenic- and iron-cycling microbial communities in arsenic-contaminated aquifers used for drinking water in Bangladesh.

Hassan Z, Sultana M, van Breukelen BM, Khan SI, Röling WF.

FEMS Microbiol Ecol. 2015 Apr;91(4). pii: fiv026. doi: 10.1093/femsec/fiv026. Epub 2015 Mar 15.

PMID:
25778510
12.

ROCK1 is a potential combinatorial drug target for BRAF mutant melanoma.

Smit MA, Maddalo G, Greig K, Raaijmakers LM, Possik PA, van Breukelen B, Cappadona S, Heck AJ, Altelaar AF, Peeper DS.

Mol Syst Biol. 2014 Dec 23;10:772. doi: 10.15252/msb.20145450.

13.

Completeness of patient records in community pharmacies post-discharge after in-patient medication reconciliation: a before-after study.

Karapinar-Çarkıt F, van Breukelen BR, Borgsteede SD, Janssen MJ, Egberts AC, van den Bemt PM.

Int J Clin Pharm. 2014 Aug;36(4):807-14. doi: 10.1007/s11096-014-9965-2. Epub 2014 Jun 11.

PMID:
25027255
14.

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

Binai NA, Bisschops MM, van Breukelen B, Mohammed S, Loeff L, Pronk JT, Heck AJ, Daran-Lapujade P, Slijper M.

J Proteome Res. 2014 Aug 1;13(8):3542-53. doi: 10.1021/pr5003388. Epub 2014 Jul 18.

PMID:
25000127
15.

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

Liu F, van Breukelen B, Heck AJ.

Mol Cell Proteomics. 2014 Oct;13(10):2776-86. doi: 10.1074/mcp.O114.039057. Epub 2014 Jun 30.

16.

Combined source apportionment and degradation quantification of organic pollutants with CSIA: 1. Model derivation.

Lutz SR, Van Breukelen BM.

Environ Sci Technol. 2014 Jun 3;48(11):6220-8. doi: 10.1021/es405400w. Epub 2014 May 22.

PMID:
24852716
17.

Combined source apportionment and degradation quantification of organic pollutants with CSIA: 2. Model validation and application.

Lutz SR, Van Breukelen BM.

Environ Sci Technol. 2014 Jun 3;48(11):6229-36. doi: 10.1021/es4054016. Epub 2014 May 22.

PMID:
24805367
18.

qcML: an exchange format for quality control metrics from mass spectrometry experiments.

Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJ, Mechtler K, Aebersold R, Gevaert K, Vizcaíno JA, Hermjakob H, Kohlbacher O, Martens L.

Mol Cell Proteomics. 2014 Aug;13(8):1905-13. doi: 10.1074/mcp.M113.035907. Epub 2014 Apr 23.

19.

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

Guerreiro AC, Benevento M, Lehmann R, van Breukelen B, Post H, Giansanti P, Maarten Altelaar AF, Axmann IM, Heck AJ.

Mol Cell Proteomics. 2014 Aug;13(8):2042-55. doi: 10.1074/mcp.M113.035840. Epub 2014 Mar 27.

20.

Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis.

Low TY, van Heesch S, van den Toorn H, Giansanti P, Cristobal A, Toonen P, Schafer S, Hübner N, van Breukelen B, Mohammed S, Cuppen E, Heck AJ, Guryev V.

Cell Rep. 2013 Dec 12;5(5):1469-78. doi: 10.1016/j.celrep.2013.10.041. Epub 2013 Nov 27.

21.

Impacts of shallow geothermal energy production on redox processes and microbial communities.

Bonte M, Röling WF, Zaura E, van der Wielen PW, Stuyfzand PJ, van Breukelen BM.

Environ Sci Technol. 2013 Dec 17;47(24):14476-84. doi: 10.1021/es4030244. Epub 2013 Dec 4.

PMID:
24266518
22.

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

Peng M, Scholten A, Heck AJ, van Breukelen B.

J Proteome Res. 2014 Jan 3;13(1):249-59. doi: 10.1021/pr4005579. Epub 2013 Oct 23.

PMID:
24087892
23.

3D-CSIA: carbon, chlorine, and hydrogen isotope fractionation in transformation of TCE to ethene by a Dehalococcoides culture.

Kuder T, van Breukelen BM, Vanderford M, Philp P.

Environ Sci Technol. 2013 Sep 3;47(17):9668-77. doi: 10.1021/es400463p. Epub 2013 Aug 23.

PMID:
23895211
24.

Temperature-induced impacts on groundwater quality and arsenic mobility in anoxic aquifer sediments used for both drinking water and shallow geothermal energy production.

Bonte M, van Breukelen BM, Stuyfzand PJ.

Water Res. 2013 Sep 15;47(14):5088-100. doi: 10.1016/j.watres.2013.05.049. Epub 2013 Jun 4.

PMID:
23870436
25.

The impact of low-temperature seasonal aquifer thermal energy storage (SATES) systems on chlorinated solvent contaminated groundwater: modeling of spreading and degradation.

Zuurbier KG, Hartog N, Valstar J, Post VE, van Breukelen BM.

J Contam Hydrol. 2013 Apr;147:1-13. doi: 10.1016/j.jconhyd.2013.01.002. Epub 2013 Jan 30.

PMID:
23435174
26.

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

Bleijerveld OB, Wijten P, Cappadona S, McClellan EA, Polat AN, Raijmakers R, Sels JW, Colle L, Grasso S, van den Toorn HW, van Breukelen B, Stubbs A, Pasterkamp G, Heck AJ, Hoefer IE, Scholten A.

J Proteome Res. 2012 Nov 2;11(11):5235-44. doi: 10.1021/pr3004375. Epub 2012 Oct 11.

PMID:
23020738
27.

The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.

Côté RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HW, van Breukelen B, Heck AJ, Hulstaert N, Martens L, Reisinger F, Csordas A, Ovelleiro D, Perez-Rivevol Y, Barsnes H, Hermjakob H, Vizcaíno JA.

Mol Cell Proteomics. 2012 Dec;11(12):1682-9. doi: 10.1074/mcp.O112.021543. Epub 2012 Sep 4.

28.

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

Cappadona S, Baker PR, Cutillas PR, Heck AJ, van Breukelen B.

Amino Acids. 2012 Sep;43(3):1087-108. doi: 10.1007/s00726-012-1289-8. Epub 2012 Jul 22. Review.

29.

Transverse hydrodynamic dispersion effects on isotope signals in groundwater chlorinated solvents' plumes.

Van Breukelen BM, Rolle M.

Environ Sci Technol. 2012 Jul 17;46(14):7700-8. doi: 10.1021/es301058z. Epub 2012 Jun 28.

PMID:
22681629
30.

Protease bias in absolute protein quantitation.

Peng M, Taouatas N, Cappadona S, van Breukelen B, Mohammed S, Scholten A, Heck AJ.

Nat Methods. 2012 May 30;9(6):524-5. doi: 10.1038/nmeth.2031. No abstract available.

PMID:
22669647
31.

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

Millioni R, Tolin S, Fadini GP, Falda M, van Breukelen B, Tessari P, Arrigoni G.

Amino Acids. 2012 Nov;43(5):2199-202. doi: 10.1007/s00726-012-1267-1. Epub 2012 Mar 21.

PMID:
22434181
32.

Database independent proteomics analysis of the ostrich and human proteome.

Altelaar AF, Navarro D, Boekhorst J, van Breukelen B, Snel B, Mohammed S, Heck AJ.

Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):407-12. doi: 10.1073/pnas.1108399108. Epub 2011 Dec 22.

33.

Evaluating experimental bias and completeness in comparative phosphoproteomics analysis.

Boekhorst J, Boersema PJ, Tops BB, van Breukelen B, Heck AJ, Snel B.

PLoS One. 2011;6(8):e23276. doi: 10.1371/journal.pone.0023276. Epub 2011 Aug 10.

34.

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

de Graaf EL, Altelaar AF, van Breukelen B, Mohammed S, Heck AJ.

J Proteome Res. 2011 Sep 2;10(9):4334-41. doi: 10.1021/pr200156b. Epub 2011 Jul 21.

PMID:
21726076
35.

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

Cappadona S, Muñoz J, Spee WP, Low TY, Mohammed S, van Breukelen B, Heck AJ.

J Proteomics. 2011 Sep 6;74(10):2204-9. doi: 10.1016/j.jprot.2011.04.022. Epub 2011 May 15.

PMID:
21616183
36.

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

Ahmad I, Suits F, Hoekman B, Swertz MA, Byelas H, Dijkstra M, Hooft R, Katsubo D, van Breukelen B, Bischoff R, Horvatovich P.

Bioinformatics. 2011 Apr 15;27(8):1176-8. doi: 10.1093/bioinformatics/btr094. Epub 2011 Feb 23.

PMID:
21349866
37.

RockerBox: analysis and filtering of massive proteomics search results.

van den Toorn HW, Muñoz J, Mohammed S, Raijmakers R, Heck AJ, van Breukelen B.

J Proteome Res. 2011 Mar 4;10(3):1420-4. doi: 10.1021/pr1010185. Epub 2011 Feb 7.

PMID:
21184612
38.

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

Helbig AO, Rosati S, Pijnappel PW, van Breukelen B, Timmers MH, Mohammed S, Slijper M, Heck AJ.

BMC Genomics. 2010 Dec 2;11:685. doi: 10.1186/1471-2164-11-685.

39.

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

van Breukelen B, Georgiou A, Drugan MM, Taouatas N, Mohammed S, Heck AJ.

Proteomics. 2010 Mar;10(6):1196-201. doi: 10.1002/pmic.200900405.

PMID:
20077410
40.

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

Helbig AO, Gauci S, Raijmakers R, van Breukelen B, Slijper M, Mohammed S, Heck AJ.

Mol Cell Proteomics. 2010 May;9(5):928-39. doi: 10.1074/mcp.M900463-MCP200. Epub 2010 Jan 7.

41.

On-the-fly targeted selection of labeled peptides in liquid chromatography/mass spectrometry based quantitative proteomics.

Barbu IM, Smith DF, van Breukelen B, van der Burgt YE, Duursma MC, Heck AJ, Heeren RM, Krijgsveld J.

Rapid Commun Mass Spectrom. 2010 Jan;24(2):239-41. doi: 10.1002/rcm.4385. No abstract available.

PMID:
20013948
42.

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

Boersema PJ, Foong LY, Ding VM, Lemeer S, van Breukelen B, Philp R, Boekhorst J, Snel B, den Hertog J, Choo AB, Heck AJ.

Mol Cell Proteomics. 2010 Jan;9(1):84-99. doi: 10.1074/mcp.M900291-MCP200. Epub 2009 Sep 21.

43.

Modeling chlorine isotope trends during sequential transformation of chlorinated ethenes.

Hunkeler D, Van Breukelen BM, Elsner M.

Environ Sci Technol. 2009 Sep 1;43(17):6750-6.

PMID:
19764245
44.

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

van Breukelen B, van den Toorn HW, Drugan MM, Heck AJ.

Bioinformatics. 2009 Jun 1;25(11):1472-3. doi: 10.1093/bioinformatics/btp181. Epub 2009 Mar 31.

PMID:
19336442
45.

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

Gauci S, van Breukelen B, Lemeer SM, Krijgsveld J, Heck AJ.

Proteomics. 2008 Dec;8(23-24):4898-906. doi: 10.1002/pmic.200800295.

PMID:
19003858
46.

Seasonal dynamics in leachate hydrochemistry and natural attenuation in surface run-off water from a tropical landfill.

Mangimbulude JC, van Breukelen BM, Krave AS, van Straalen NM, Röling WF.

Waste Manag. 2009 Feb;29(2):829-38. doi: 10.1016/j.wasman.2008.06.020. Epub 2008 Oct 10.

PMID:
18848774
47.

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

Boekhorst J, van Breukelen B, Heck A Jr, Snel B.

Genome Biol. 2008 Oct 1;9(10):R144. doi: 10.1186/gb-2008-9-10-r144.

48.

Spatial heterogeneity in sediment-associated bacterial and eukaryotic communities in a landfill leachate-contaminated aquifer.

Brad T, van Breukelen BM, Braster M, van Straalen NM, Röling WF.

FEMS Microbiol Ecol. 2008 Sep;65(3):534-43. doi: 10.1111/j.1574-6941.2008.00533.x. Epub 2008 Jul 8.

49.
50.

Eukaryotic diversity in an anaerobic aquifer polluted with landfill leachate.

Brad T, Braster M, van Breukelen BM, van Straalen NM, Röling WF.

Appl Environ Microbiol. 2008 Jul;74(13):3959-68. doi: 10.1128/AEM.02820-07. Epub 2008 May 9.

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