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Items: 40

1.

Vegetative Cell and Spore Proteomes of Clostridioides difficile Show Finite Differences and Reveal Potential Protein Markers.

Abhyankar WR, Zheng L, Brul S, de Koster CG, de Koning LJ.

J Proteome Res. 2019 Oct 14. doi: 10.1021/acs.jproteome.9b00413. [Epub ahead of print]

PMID:
31557040
2.

Proteomics and microscopy tools for the study of antimicrobial resistance and germination mechanisms of bacterial spores.

Abhyankar WR, Wen J, Swarge BN, Tu Z, de Boer R, Smelt JPPM, de Koning LJ, Manders E, de Koster CG, Brul S.

Food Microbiol. 2019 Aug;81:89-96. doi: 10.1016/j.fm.2018.03.006. Epub 2018 Mar 14. Review.

3.

Mapping the Contact Sites of the Escherichia coli Division-Initiating Proteins FtsZ and ZapA by BAMG Cross-Linking and Site-Directed Mutagenesis.

Roseboom W, Nazir MG, Meiresonne NY, Mohammadi T, Verheul J, Buncherd H, Bonvin AMJJ, de Koning LJ, de Koster CG, de Jong L, den Blaauwen T.

Int J Mol Sci. 2018 Sep 26;19(10). pii: E2928. doi: 10.3390/ijms19102928.

4.

Correction to "Stoichiometry, Absolute Abundance, and Localization of Proteins in the Bacillus cereus Spore Coat Insoluble Fraction Determined Using a QconCAT Approach".

Stelder SK, Benito de Moya C, Hoefsloot HCJ, de Koning LJ, Brul S, de Koster CG.

J Proteome Res. 2018 Jul 6;17(7):2562. doi: 10.1021/acs.jproteome.8b00313. Epub 2018 Jun 1. No abstract available.

5.

"One-Pot" Sample Processing Method for Proteome-Wide Analysis of Microbial Cells and Spores.

Swarge BN, Roseboom W, Zheng L, Abhyankar WR, Brul S, de Koster CG, de Koning LJ.

Proteomics Clin Appl. 2018 Sep;12(5):e1700169. doi: 10.1002/prca.201700169. Epub 2018 Apr 16.

6.

Stoichiometry, Absolute Abundance, and Localization of Proteins in the Bacillus cereus Spore Coat Insoluble Fraction Determined Using a QconCAT Approach.

Stelder SK, Benito de Moya C, Hoefsloot HCJ, de Koning LJ, Brul S, de Koster CG.

J Proteome Res. 2018 Feb 2;17(2):903-917. doi: 10.1021/acs.jproteome.7b00732. Epub 2018 Jan 4. Erratum in: J Proteome Res. 2018 Jul 6;17(7):2562.

7.

The Influence of Sporulation Conditions on the Spore Coat Protein Composition of Bacillus subtilis Spores.

Abhyankar WR, Kamphorst K, Swarge BN, van Veen H, van der Wel NN, Brul S, de Koster CG, de Koning LJ.

Front Microbiol. 2016 Oct 13;7:1636. eCollection 2016.

8.

Bacillus subtilis Spore Inner Membrane Proteome.

Zheng L, Abhyankar W, Ouwerling N, Dekker HL, van Veen H, van der Wel NN, Roseboom W, de Koning LJ, Brul S, de Koster CG.

J Proteome Res. 2016 Feb 5;15(2):585-94. doi: 10.1021/acs.jproteome.5b00976. Epub 2016 Jan 13.

PMID:
26731423
9.

Quantitative proteomics analysis of an ethanol- and a lactate-producing mutant strain of Synechocystis sp. PCC6803.

Borirak O, de Koning LJ, van der Woude AD, Hoefsloot HC, Dekker HL, Roseboom W, de Koster CG, Hellingwerf KJ.

Biotechnol Biofuels. 2015 Aug 5;8:111. doi: 10.1186/s13068-015-0294-z. eCollection 2015.

10.

Time-series analysis of the transcriptome and proteome of Escherichia coli upon glucose repression.

Borirak O, Rolfe MD, de Koning LJ, Hoefsloot HC, Bekker M, Dekker HL, Roseboom W, Green J, de Koster CG, Hellingwerf KJ.

Biochim Biophys Acta. 2015 Oct;1854(10 Pt A):1269-79. doi: 10.1016/j.bbapap.2015.05.017. Epub 2015 Jun 4.

11.

Comprehensive Two-Dimensional Liquid Chromatography with Stationary-Phase-Assisted Modulation Coupled to High-Resolution Mass Spectrometry Applied to Proteome Analysis of Saccharomyces cerevisiae.

Vonk RJ, Gargano AF, Davydova E, Dekker HL, Eeltink S, de Koning LJ, Schoenmakers PJ.

Anal Chem. 2015;87(10):5387-94. doi: 10.1021/acs.analchem.5b00708. Epub 2015 May 5.

PMID:
25894977
12.

Temperature Dependence of the Proteome Profile of the Psychrotolerant Pathogenic Food Spoiler Bacillus weihenstephanensis Type Strain WSBC 10204.

Stelder SK, Mahmud SA, Dekker HL, de Koning LJ, Brul S, de Koster CG.

J Proteome Res. 2015 May 1;14(5):2169-76. doi: 10.1021/pr501307t. Epub 2015 Apr 22.

PMID:
25853650
13.

Post-polymerization photografting on methacrylate-based monoliths for separation of intact proteins and protein digests with comprehensive two-dimensional liquid chromatography hyphenated with high-resolution mass spectrometry.

Vonk RJ, Wouters S, Barcaru A, Vivó-Truyols G, Eeltink S, de Koning LJ, Schoenmakers PJ.

Anal Bioanal Chem. 2015 May;407(13):3817-29. doi: 10.1007/s00216-015-8615-4. Epub 2015 Mar 24.

14.

Reinforcement of Bacillus subtilis spores by cross-linking of outer coat proteins during maturation.

Abhyankar W, Pandey R, Ter Beek A, Brul S, de Koning LJ, de Koster CG.

Food Microbiol. 2015 Feb;45(Pt A):54-62. doi: 10.1016/j.fm.2014.03.007. Epub 2014 Mar 18.

PMID:
25481062
15.

Spore proteomics: the past, present and the future.

Abhyankar W, de Koning LJ, Brul S, de Koster CG.

FEMS Microbiol Lett. 2014 Sep;358(2):137-44. doi: 10.1111/1574-6968.12568. Epub 2014 Aug 28. Review.

16.

A gas phase cleavage reaction of cross-linked peptides for protein complex topology studies by peptide fragment fingerprinting from large sequence database.

Buncherd H, Roseboom W, de Koning LJ, de Koster CG, de Jong L.

J Proteomics. 2014 Aug 28;108:65-77. doi: 10.1016/j.jprot.2014.05.003. Epub 2014 May 17.

PMID:
24840472
17.

Isolation of cross-linked peptides by diagonal strong cation exchange chromatography for protein complex topology studies by peptide fragment fingerprinting from large sequence databases.

Buncherd H, Roseboom W, Ghavim B, Du W, de Koning LJ, de Koster CG, de Jong L.

J Chromatogr A. 2014 Jun 27;1348:34-46. doi: 10.1016/j.chroma.2014.04.083. Epub 2014 May 2.

PMID:
24819016
18.

In pursuit of protein targets: proteomic characterization of bacterial spore outer layers.

Abhyankar W, Hossain AH, Djajasaputra A, Permpoonpattana P, Ter Beek A, Dekker HL, Cutting SM, Brul S, de Koning LJ, de Koster CG.

J Proteome Res. 2013 Oct 4;12(10):4507-21. doi: 10.1021/pr4005629. Epub 2013 Sep 23.

PMID:
23998435
19.

Iron restriction-induced adaptations in the wall proteome of Candida albicans.

Sorgo AG, Brul S, de Koster CG, de Koning LJ, Klis FM.

Microbiology. 2013 Aug;159(Pt 8):1673-82. doi: 10.1099/mic.0.065599-0. Epub 2013 May 31.

PMID:
23728625
20.

Surface stress induces a conserved cell wall stress response in the pathogenic fungus Candida albicans.

Heilmann CJ, Sorgo AG, Mohammadi S, Sosinska GJ, de Koster CG, Brul S, de Koning LJ, Klis FM.

Eukaryot Cell. 2013 Feb;12(2):254-64. doi: 10.1128/EC.00278-12. Epub 2012 Dec 14.

21.

Isoenzyme expression changes in response to high temperature determine the metabolic regulation of increased glycolytic flux in yeast.

Postmus J, Aardema R, de Koning LJ, de Koster CG, Brul S, Smits GJ.

FEMS Yeast Res. 2012 Aug;12(5):571-81. doi: 10.1111/j.1567-1364.2012.00807.x. Epub 2012 Apr 30.

22.

Selective enrichment and identification of cross-linked peptides to study 3-D structures of protein complexes by mass spectrometry.

Buncherd H, Nessen MA, Nouse N, Stelder SK, Roseboom W, Dekker HL, Arents JC, Smeenk LE, Wanner MJ, van Maarseveen JH, Yang X, Lewis PJ, de Koning LJ, de Koster CG, de Jong L.

J Proteomics. 2012 Apr 3;75(7):2205-15. doi: 10.1016/j.jprot.2012.01.025. Epub 2012 Feb 4.

PMID:
22326961
23.

Effects of fluconazole on the secretome, the wall proteome, and wall integrity of the clinical fungus Candida albicans.

Sorgo AG, Heilmann CJ, Dekker HL, Bekker M, Brul S, de Koster CG, de Koning LJ, Klis FM.

Eukaryot Cell. 2011 Aug;10(8):1071-81. doi: 10.1128/EC.05011-11. Epub 2011 May 27.

24.

Hyphal induction in the human fungal pathogen Candida albicans reveals a characteristic wall protein profile.

Heilmann CJ, Sorgo AG, Siliakus AR, Dekker HL, Brul S, de Koster CG, de Koning LJ, Klis FM.

Microbiology. 2011 Aug;157(Pt 8):2297-2307. doi: 10.1099/mic.0.049395-0. Epub 2011 May 20.

PMID:
21602216
25.

Identification of the peroxidase-generated intermolecular dityrosine cross-link in bovine α-lactalbumin.

Heijnis WH, Dekker HL, de Koning LJ, Wierenga PA, Westphal AH, de Koster CG, Gruppen H, van Berkel WJ.

J Agric Food Chem. 2011 Jan 12;59(1):444-9. doi: 10.1021/jf104298y. Epub 2010 Dec 16.

PMID:
21162537
26.

Mass spectrometric quantification of the adaptations in the wall proteome of Candida albicans in response to ambient pH.

Sosinska GJ, de Koning LJ, de Groot PW, Manders EM, Dekker HL, Hellingwerf KJ, de Koster CG, Klis FM.

Microbiology. 2011 Jan;157(Pt 1):136-46. doi: 10.1099/mic.0.044206-0. Epub 2010 Sep 23.

PMID:
20864472
27.

Selective enrichment of azide-containing peptides from complex mixtures.

Nessen MA, Kramer G, Back J, Baskin JM, Smeenk LE, de Koning LJ, van Maarseveen JH, de Jong L, Bertozzi CR, Hiemstra H, de Koster CG.

J Proteome Res. 2009 Jul;8(7):3702-11. doi: 10.1021/pr900257z.

28.

An innovative method to study target protein-drug interactions by mass spectrometry.

Müller MQ, de Koning LJ, Schmidt A, Ihling C, Syha Y, Rau O, Mechtler K, Schubert-Zsilavecz M, Sinz A.

J Med Chem. 2009 May 14;52(9):2875-9. doi: 10.1021/jm9000665.

PMID:
19379014
29.

Identification and quantitation of newly synthesized proteins in Escherichia coli by enrichment of azidohomoalanine-labeled peptides with diagonal chromatography.

Kramer G, Sprenger RR, Back J, Dekker HL, Nessen MA, van Maarseveen JH, de Koning LJ, Hellingwerf KJ, de Jong L, de Koster CG.

Mol Cell Proteomics. 2009 Jul;8(7):1599-611. doi: 10.1074/mcp.M800392-MCP200. Epub 2009 Mar 25.

30.

Disulfide bond structure and domain organization of yeast beta(1,3)-glucanosyltransferases involved in cell wall biogenesis.

Popolo L, Ragni E, Carotti C, Palomares O, Aardema R, Back JW, Dekker HL, de Koning LJ, de Jong L, de Koster CG.

J Biol Chem. 2008 Jul 4;283(27):18553-65. doi: 10.1074/jbc.M801562200. Epub 2008 May 9.

31.

An aptly positioned azido group in the spacer of a protein cross-linker for facile mapping of lysines in close proximity.

Kasper PT, Back JW, Vitale M, Hartog AF, Roseboom W, de Koning LJ, van Maarseveen JH, Muijsers AO, de Koster CG, de Jong L.

Chembiochem. 2007 Jul 23;8(11):1281-92.

PMID:
17600791
32.

Computer-assisted mass spectrometric analysis of naturally occurring and artificially introduced cross-links in proteins and protein complexes.

de Koning LJ, Kasper PT, Back JW, Nessen MA, Vanrobaeys F, Van Beeumen J, Gherardi E, de Koster CG, de Jong L.

FEBS J. 2006 Jan;273(2):281-91.

33.

Mild and chemoselective peptide-bond cleavage of peptides and proteins at azido homoalanine.

Back JW, David O, Kramer G, Masson G, Kasper PT, de Koning LJ, de Jong L, van Maarseveen JH, de Koster CG.

Angew Chem Int Ed Engl. 2005 Dec 9;44(48):7946-50. No abstract available.

PMID:
16281315
34.

Modification of glutamine and lysine residues in holo and apo alpha-lactalbumin with microbial transglutaminase.

Nieuwenhuizen WF, Dekker HL, de Koning LJ, Gröneveld T, de Koster CG, de Jong GA.

J Agric Food Chem. 2003 Nov 19;51(24):7132-9.

PMID:
14611184
35.

A structure for the yeast prohibitin complex: Structure prediction and evidence from chemical crosslinking and mass spectrometry.

Back JW, Sanz MA, De Jong L, De Koning LJ, Nijtmans LG, De Koster CG, Grivell LA, Van Der Spek H, Muijsers AO.

Protein Sci. 2002 Oct;11(10):2471-8.

36.

Identification of cross-linked peptides for protein interaction studies using mass spectrometry and 18O labeling.

Back JW, Notenboom V, de Koning LJ, Muijsers AO, Sixma TK, de Koster CG, de Jong L.

Anal Chem. 2002 Sep 1;74(17):4417-22.

PMID:
12236350
37.

A new crosslinker for mass spectrometric analysis of the quaternary structure of protein complexes.

Back JW, Hartog AF, Dekker HL, Muijsers AO, de Koning LJ, de Jong L.

J Am Soc Mass Spectrom. 2001 Feb;12(2):222-7.

38.

The bimolecular hydrogen-deuterium exchange behavior of protonated alkyl dipeptides in the gas phase.

Gur EH, de Koning LJ, Nibbering NM.

J Am Soc Mass Spectrom. 1995 Jun;6(6):466-77. doi: 10.1016/1044-0305(95)00189-K.

PMID:
24214299
39.

On the stabilization of carbanions by adjacent phenyl, cyano, methoxy-carbonyl, and nitro groups in the gas phase.

Peerboom RA, de Koning LJ, Nibbering NM.

J Am Soc Mass Spectrom. 1994 Mar;5(3):159-68. doi: 10.1016/1044-0305(94)85029-1.

PMID:
24222545
40.

On the structure of protonated methane.

Heck AJ, de Koning LJ, Nibbering NM.

J Am Soc Mass Spectrom. 1991 Dec;2(6):453-8. doi: 10.1016/1044-0305(91)80030-B.

PMID:
24242765

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