Dr. L. (Luitzen) de Jong
Faculty of Science
Swammerdam Institute for Life Sciences
Visiting address
- Science Park 904
Postal address
- Postbus 94215
1090 GE Amsterdam
Contact details
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Publications
- refereed (41)
- academic (9)
- professional (3)
- popular scientific (1)
- other output (1)
- recognitions (3)
- supervised theses (6)
2021
de Jong, L., Roseboom, W., & Kramer, G. (2021). A composite filter for low FDR of protein-protein interactions detected by in vivo cross-linking. Journal of Proteomics, 230, [103987]. https://doi.org/10.1016/j.jprot.2020.103987 [details]- de Jong, L., Roseboom, W., & Kramer, G. (2021). Towards low false discovery rate estimation for protein-protein interactions detected by chemical cross-linking. Biochimica et Biophysica Acta. Proteins and Proteomics, 1869(7), [140655]. https://doi.org/10.1016/j.bbapap.2021.140655 [details]
2018
- Roseboom, W., Nazir, M. G., Meiresonne, N. Y., Mohammadi, T., Verheul, J., Buncherd, H., Bonvin, A. M. J. J., de Koning, L. J., de Koster, C. G., De Jong, L., & Den Blaauwen, T. (2018). Mapping the Contact Sites of the Escherichia coli Division-Initiating Proteins FtsZ and ZapA by BAMG Cross-Linking and Site-Directed Mutagenesis. International Journal of Molecular Sciences, 19(10), [2928]. https://doi.org/10.3390/ijms19102928 [details]
2017
- de Jong, L., de Koning, E. A., Roseboom, W., Buncherd, H., Wanner, M. J., Dapic, I., Jansen, P. J., van Maarseveen, J. H., Corthals, G. L., Lewis, P. J., Hamoen, L. W., & de Koster, C. G. (2017). In-Culture Cross-Linking of Bacterial Cells Reveals Large-Scale Dynamic Protein-Protein Interactions at the Peptide Level. Journal of Proteome Research, 16(7), 2457-2471. https://doi.org/10.1021/acs.jproteome.7b00068 [details]
2016
- Buncherd, H., Roseboom, W., Chokchaichamnankit, D., Sawangareetrakul, P., Phongdara, A., Srisomsap, C., de Jong, L., & Svasti, J. (2016). β-Elimination coupled with strong cation-exchange chromatography for phosphopeptide analysis. Rapid Communications in Mass Spectrometry, 30(14), 1695-1704. https://doi.org/10.1002/rcm.7606
2015
- Glas, M., van den Berg van Saparoea, H. B., McLaughlin, S. H., Roseboom, W., Liu, F., Koningstein, G. M., Fish, A., den Blaauwen, T., Heck, A. J. R., de Jong, L., Bitter, W., de Esch, I. J. P., & Luirink, J. (2015). The Soluble Periplasmic Domains of Escherichia coli Cell Division Proteins FtsQ/FtsB/FtsL form a Trimeric Complex with Sub-micromolar Affinity. The Journal of Biological Chemistry, 290(35), 21498-21509. https://doi.org/10.1074/jbc.M115.654756 [details]
2012
- Buncherd, H., Nessen, M. A., Nouse, N., Stelder, S. K., Roseboom, W., Dekker, H. L., Arents, J. C., Smeenk, L. E., Wanner, M. J., van Maarseveen, J. H., Yang, X., Lewis, P. J., de Koning, L. J., de Koster, C. G., & de Jong, L. (2012). Selective enrichment and identification of cross-linked peptides to study 3-D structures of protein complexes by mass spectrometry. Journal of Proteomics, 75(7), 2205-2215. https://doi.org/10.1016/j.jprot.2012.01.025 [details]
2011
- Kramer, G., Kasper, P. T., de Jong, L., & de Koster, C. G. (2011). Quantitation of newly synthesized proteins by pulse labeling with azidohomoalanine. In K. Gevaert, & J. Vandekerckhove (Eds.), Gel-free proteomics: methods and protocols (pp. 169-181). (Methods in molecular biology; No. 753). [S.l.]: Humana Press. https://doi.org/10.1007/978-1-61779-148-2_12 [details]
2010
- Kramer, G., Sprenger, R. R., Nessen, M. A., Roseboom, W., Speijer, D., de Jong, L., Teixeira de Mattos, M. J., Back, J. W., & de Koster, C. G. (2010). Proteome-wide alterations in Escherichia coli translation rates upon anaerobiosis. Molecular & Cellular Proteomics, 9(11), 2508-2516. https://doi.org/10.1074/mcp.M110.001826
2009
- Kramer, G., Sprenger, R. R., Back, J. W., Dekker, H. L., Nessen, M. A., van Maarseveen, J. H., ... de Koster, C. G. (2009). Identification and quantitation of newly synthesized proteins in Escherichia coli by enrichment of azidohomoalanine-labeled peptides with diagonal chromatography. Molecular & Cellular Proteomics, 8(7), 1599-1611. https://doi.org/10.1074/mcp.M800392-MCP200 [details]
- Nessen, M. A., Kramer, G., Back, J. W., Baskin, J. M., Smeenk, L. E. J., de Koning, L. J., ... de Koster, C. G. (2009). Selective enrichment of azide-containing peptides from complex mixtures. Journal of Proteome Research, 8(7), 3702-3711. https://doi.org/10.1021/pr900257z [details]
2008
- Popolo, L., Ragni, E., Carotti, C., Palomares, O., Aardema, R., Back, J. W., ... de Koster, C. G. (2008). Disulfide bond structure and domain organization of yeast beta(1,3)-glucanosyltransferases involved in cell wall biogenesis. The Journal of Biological Chemistry, 283(27), 18553-18565. https://doi.org/10.1074/jbc.M801562200 [details]
2007
- Kasper, P. T., Back, J. W., Vitale, M. R., Hartog, A. F., Roseboom, W., de Koning, L. J., ... de Jong, L. (2007). An aptly positioned azido group in the spacer of a protein cross-linker for facile mapping of lysines in close proximity. ChemBioChem, 8(11), 1281-1292. https://doi.org/10.1002/cbic.200700150 [details]
- Yin, Q., de Groot, P. W. J., de Jong, L., Klis, F. M., & de Koster, C. G. (2007). Mass spectrometric quantitation of covalently bound cell wall proteins in Saccharomyces cerevisiae. FEMS Yeast Research, 7(6), 887-896. https://doi.org/10.1111/j.1567-1364.2007.00272.x [details]
2006
- de Koning, L. J., Kasper, P. T., Back, J. W., Nessen, M., Vanrobaeys, F., van Beeumen, J. J., ... de Jong, L. (2006). Computer-assisted mass spectrometric analysis of naturally occurring and artificially introduced cross-links in proteins and protein complexes. The FEBS Journal, 273, 281-291. [details]
2005
- Back, J. W., David, O. R. P., Kramer, G., Masson, G. S., Kasper, P. T., de Koning, L. J., ... de Koster, C. G. (2005). Mild and chemoselective peptide-bond cleavage of peptides and proteins at azido homoalanine. Angewandte Chemie, International Edition, 44, 7946-7950. https://doi.org/10.1002/anie.200502431 [details]
- Back, J. W., David, O. R. P., Kramer, G., Masson, G. S., de Jong, L., de Koning, L. J., ... de Koster, C. G. (2005). Selective and mild chemical protein cleavage. The FEBS Journal, 272, S1-151. [details]
- Yin, Q., de Groot, P. W. J., Dekker, H. L., de Jong, L., Klis, F. M., & de Koster, C. G. (2005). Comprehensive proteomic analysis of Saccharomyces cerevisiae cell walls: identification of protein glycosylphosphatidylinositol remnants or mild alkali-sensitive linkages. The Journal of Biological Chemistry, 280(21), 20894-20901. https://doi.org/10.1074/jbc.M500334200 [details]
2004
- Wong, H. Y., Burghoorn, J. A., van Leeuwen, M., de Ruiter, P. E., Schippers, E., Blok, L. J., ... Brinkmann, A. O. (2004). Phosphorylation of androgen receptor isoforms. Biochemical Journal, 383, 267-276. https://doi.org/10.1042/BJ20040683 [details]
- de Groot, P. W. J., de Boer, A. D., Cunningham, J., Dekker, H. L., de Jong, L., Hellingwerf, K. J., ... Klis, F. M. (2004). Proteomic analysis of Candida albicans cell walls reveals covalently bound carbohydrate-active enzymes and adhesins. Eukaryotic Cell, 3, 955-965. https://doi.org/10.1128/EC.3.4.955-965.2004 [details]
2003
- Back, J. W., de Jong, L., Muijsers, A. O., & de Koster, C. G. (2003). Chemical cross-linking and mass spectrometry for protein structural modelling. Journal of Molecular Biology, 331, 303-313. https://doi.org/10.1016/S0022-2836(03)00721-6 [details]
2002
- Back, J. W., Artal Sanz, M., de Jong, L., van der Spek, J. C., & Muijsers, A. O. (2002). A structure for the yeast prohibitin complex: Structure prediction and evidence from chemical crosslinking and mass spectrometry. Protein Science, 11, 2471-2478. https://doi.org/10.1110/ps.0212602 [details]
2001
- Back, J. W., Hartog, A. F., Dekker, H. L., Muijsers, A. O., de Koning, L. J., & de Jong, L. (2001). A new crosslinker for mass spectrometric analysis of the quaternary structure of protein complexes. Journal of the American Society for Mass Spectrometry, 12, 222-227. https://doi.org/10.1016/S1044-0305(00)00212-9 [details]
2000
- Nijtmans, L. G. J., de Jong, L., Artal Sanz, M., Coates, P. J., Berden, J. A., Back, J. W., ... Grivell, L. A. (2000). Prohibitins act as a membrane-bound chaperone for the stabilization of mitochondrial proteins. EMBO Journal, 19, 2444-2451. https://doi.org/10.1093/emboj/19.11.2444 [details]
1999
- Mattern, K. A., van der Kraan, I., Schul, W., de Jong, L., & van Driel, R. (1999). Spatial organization of four hnRNP proteins in relation to sites of transcription, to nuclear speckles and to each other in interphase nuclei and nuclear matrices of HeLa cells. Experimental Cell Research, 246, 961-470. [details]
- Schul, W., Adelaar, B., de Jong, L., & van Driel, R. (1999). Coiled bodies are predisposed to a spatial association with genes that contain snoRNA sequences in their introns. Journal of Cellular Biochemistry, 75, 393-403. [details]
- Schul, W., van der Kraan, I., Matera, A. G., van Driel, R., & de Jong, L. (1999). Nuclear domains enriched in RNA 3' processing factors associate with coiled bodies and histone genes in a cell cycle-dependent manner. Molecular Biology of the Cell, 10, 3815-3824. https://doi.org/10.1091/mbc.10.11.3815 [details]
1998
- Schul, W., de Jong, L., & van Driel, R. (1998). Nuclear neighbours: the spatial and functional organization of genes and nuclear domains. Journal of Cellular Biochemistry, 70, 159-171. https://doi.org/10.1002/(SICI)1097-4644(19980801)70:2<159::AID-JCB2>3.0.CO;2-N
- Schul, W., van Driel, R., & de Jong, L. (1998). A subset of poly(A) polymerase is concentrated at sites of RNA synthesis and is associated with domains enriched in splicing factors and poly(A) RNA. Experimental Cell Research, 238, 1-12. https://doi.org/10.1006/excr.1997.3808
- Schul, W., van Driel, R., & de Jong, L. (1998). Coiled bodies and U2 snRNA genes adjacent to coiled bodies are enriched in factors required for snRNA transcription. Molecular Biology of the Cell, 9, 1025-1036. https://doi.org/10.1091/mbc.9.5.1025
- van Driel, R., Otte, A. P., de Jong, L., Stap, J., & Aten, J. A. (1998). Mapping of DNA replication sites in situ by fluorescence microscopy. Methods in Cell Biology, 53, 455-469. [details]
1997
- Grande, M. A., van der Kraan, I., de Jong, L., & van Driel, R. (1997). Nuclear distribution of transcription factors in relation to sites of transcription and RNA polymerase II. Journal of Cell Science, (110), 1781-1791. [details]
- Mattern, K. A., Goethem, R. E. M., de Jong, L., & van Driel, R. (1997). The major internal nuclear matrix proteins are common to different human cell types. Journal of Cellular Biochemistry, (65), 42-52. [details]
- Stuurman, N., Floore, A., Middelkoop, E., van Driel, R., & de Jong, L. (1997). PML Shuttles between nuclear bodies and the cytoplasm. Molecular and Cellular Biology, (2), 137-150. [details]
- van Driel, R., Manders, E. M. M., de Jong, L., Stap, J., & Aten, J. A. (1997). Mapping of DNA replication sites in situ by fluorescence microscopy. Methods in Cell Biology, (53), 455-469. [details]
1996
- Grande, M. A., van der Kraan, K., van Steensel, B., Schul, W., de The, H., van der Voort, H. T. M., ... van Driel, R. (1996). PML-containing nuclear bodies: their spatial distribution in relation to other nuclear components. Journal of Cellular Biochemistry, 63, 280-291. https://doi.org/10.1002/(SICI)1097-4644(19961201)63:3<280::AID-JCB3>3.0.CO;2-T [details]
- Mattern, K. A., Humbel, B. M., Muijsers, A. O., de Jong, L., & van Driel, R. (1996). hnRNP proteins and B23 are the major proteins of the internal nuclear matrix of HeLa S3 cells. Journal of Cellular Biochemistry, 62, 275-289. https://doi.org/10.1002/(SICI)1097-4644(199608)62:2<275::AID-JCB15>3.0.CO;2-K [details]
- Schul, W., Groenhout, B., Koberna, K., Takagaki, Y., Jenny, A., Manders, E. M. M., ... de Jong, L. (1996). The RNA 3'cleavage factors CstF-64kD and CPSF 100 kDa are concentrated in nuclear domains closely associated with coiled bodies and newly synthesized RNA. EMBO Journal, 15, 2883-2892. [details]
- Wansink, D. G., Sibon, O. C. M., Cremers, F. F. M., van Driel, R., & de Jong, L. (1996). Ultrastructural localization of active genes in nuclei of A431 cells. Journal of Cellular Biochemistry, 62, 10-18. https://doi.org/10.1002/(SICI)1097-4644(199607)62:1<10::AID-JCB2>3.0.CO;2-4 [details]
- de Jong, L., Grande, M. A., Mattern, K. A., Schul, W., & van Driel, R. (1996). Nuclear domains involved in RNA synthesis, RNA processing and replication. Critical reviews in eukaryotic gene expression, 6, 215-246. [details]
2014
- Buncherd, H., Roseboom, W., Ghavim, B., Du, W., de Koning, L. J., de Koster, C. G., & de Jong, L. (2014). Isolation of cross-linked peptides by diagonal strong cation exchange chromatography for protein complex topology studies by peptide fragment fingerprinting from large sequence databases. Journal of Chromatography A, 1348, 34-46. https://doi.org/10.1016/j.chroma.2014.04.083 [details]
- Buncherd, H., Roseboom, W., de Koning, L. J., de Koster, C. G., & de Jong, L. (2014). A gas phase cleavage reaction of cross-linked peptides for protein complex topology studies by peptide fragment fingerprinting from large sequence database. Journal of Proteomics, 108, 65-77. https://doi.org/10.1016/j.jprot.2014.05.003 [details]
1997
- Mattern, K. A., van Driel, R., & de Jong, L. (1997). Composition and structure of the internal nuclear matrix. In G. Stein, R. C. Bird, J. Lian, & J. Stein (Eds.), Nuclear structure and gene expression (pp. 87-110). San Diego: Academic Press. [details]
- Wansink, D. G., de Jong, L., & van Driel, R. (1997). Transcription by RNA polymerase II and nuclear architecture. In G. Stein, R. C. Bird, J. Lian, & J. Stein (Eds.), Nuclear structure and gene expression (pp. 215-239). San Diego: Academic Press. [details]
1994
- Koken, M., Puvion-Dutilleul, F., Viron, A., Linares-Cruz, G., Stuurman, N., de Jong, L., ... De The, H. (1994). The t(15;17) translocation alters the structure of a nuclear body in a RA-reversible fashion. EMBO Journal, 13, 1073-1083. [details]
- Wansink, D. G., Manders, E. M. M., van der Kraan, I., Aten, J. A., van Driel, R., & de Jong, L. (1994). RNA polymerase II transcription is concentrated outside replication domains throughout S-phase. Journal of Cell Science, 107, 1449-1456. [details]
- Wansink, D. G., Motley, A. M., van Driel, R., & de Jong, L. (1994). Fluorescent labeling of nascent RNA in the cell nucleus using 5-Bromouridine 5'-Triphosphate. In J. E. Celis (Ed.), Cell Biology: A Laboratory Handbook (Vol. 3, pp. 368-374). London: Academic Press. [details]
- Wansink, D. G., Nelissen, R. L. H., & de Jong, L. (1994). In vitro splicing of pre-mRNA containing bromouridine. Mol. Biol. Rep., 19, 109-113. https://doi.org/10.1007/BF00997156 [details]
- Wansink, D. G., van Driel, R., & de Jong, L. (1994). Organization of (pre-)mRNA metabolism in the cell nucleus. Mol. Biol. Rep., 20, 45-55. https://doi.org/10.1007/BF00996353 [details]
2007
- de Jong, L., Kasper, P. T., Back, J. W., van Maarseveen, J. H., & de Koster, C. G. (2007). bis(sulfosuccinimidyl)-5-(3-azido-1-carboxypropylamino)-5-oxopentanoate (BACOX) and bis(succinimidyl)-2-azidoglutarate as cross-linkers for neurotensin derivatives.
2005
- de Jong, L., Kasper, P. T., Back, J. W., van Maarseveen, J. H., & de Koster, C. G. (2005). Novel cross-linkers for obtaining structure information on molecule complexes.
1996
- de Jong, L., & Westermann, T. S. (1996). Degeneration of the joint surfaces in a sample of 21 individuals of known age, sex and profession. Journal of Paleopathology, 7(2), 95-95. [details]
1998
- van Driel, R., Otte, A. P., & de Jong, L. (1998). Mens en genen deel 3: de kern van de zaak. Natuur & Techniek, 66, 73-82.
2013
- Borirak, O., Bekker, M., Rolfe, M. D., Dekker, H. L., de Jong, L., de Koster, C. G., ... Hellingwerf, K. J. (2013). Dynamic changes of the Escherichia coli transcriptome and proteome exerted by glucose repression. The FASEB Journal, 27(1 Supplement), [lb136]. [details]
Talk / presentation
- Nessen, M. (speaker), Kramer, G. (speaker), Back, J. W. (speaker), van Maarseveen, J. H. (speaker), de Koning, L. J. (speaker), de Jong, L. (speaker), Hiemstra, H. (speaker) & de Koster, C. G. (speaker) (2-11-2009). Selective enrichment of azide-labelled peptides for mass spectrometric analysis of cellular proteome dynamics., Annual Meeting NWO/CW and NVMS, Lunteren, the Netherlands.
- Nessen, M. (speaker), Hiemstra, H. (speaker), de Koster, C. G. (speaker), de Jong, L. (speaker) & van Maarseveen, J. H. (speaker) (19-10-2009). Selective capturing and analysis of azide-labelled biomolecules., Annual Meeting NWO/CW Studiegroup OS/SR/BMC, Lunteren, the Netherlands.
- Nessen, M. (speaker), Kramer, G. (speaker), Back, J. W. (speaker), van Maarseveen, J. H. (speaker), de Koning, L. J. (speaker), de Jong, L. (speaker), Hiemstra, H. (speaker) & de Koster, C. (speaker) (26-3-2009). Selective purification of azide-containing peptides from complex mixtures., Ned. Ver. voor Massaspectrometrie, Kerkrade, the Netherlands.
2013
2010
2008
2003
1998
- Schul, W. (1998). The spatial and functional organization of transcription and RNA processing in relation to nuclear domains. Amsterdam. [details]
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Ancillary activities
No ancillary activities
de Jong, L., Roseboom, W., & Kramer, G. (2021). A composite filter for low FDR of protein-protein interactions detected by in vivo cross-linking. Journal of Proteomics, 230, [103987].