Publications
2023
Scholarly publications
Zou, Y., van Breukelen, B., Pronker, M., Reiding, K., & Heck, A. J. R. (2023). Proteogenomic Features of the Highly Polymorphic Histidine-rich Glycoprotein Arose Late in Evolution. Molecular and Cellular Proteomics, 22(7), [100585]. https://doi.org/10.1016/j.mcpro.2023.100585
Li, B., Altelaar, M., & van Breukelen, B. (2023). Identification of Protein Complexes by Integrating Protein Abundance and Interaction Features Using a Deep Learning Strategy. International Journal of Molecular Sciences, 24(9). https://doi.org/10.3390/ijms24097884
2020
Scholarly publications
Bexkens, M. L., van Gestel, R. A., van Breukelen, B., Urbanus, R. T., Brouwers, J. F., Nieuwland, R., Tielens, A. G. M., & van Hellemond, J. J. (2020). Schistosoma mansoni infection affects the proteome and lipidome of circulating extracellular vesicles in the host. Molecular and Biochemical Parasitology, 238, [111296]. https://doi.org/10.1016/j.molbiopara.2020.111296
2015
Scholarly publications
Peng, M., Aye, T. T., Snel, B., Van Breukelen, B., Scholten, A., & Heck, A. J. R. (2015). Spatial Organization in Protein Kinase A Signaling Emerged at the Base of Animal Evolution. Journal of Proteome Research, 14(7), 2976-2987. https://doi.org/10.1021/acs.jproteome.5b00370
Giansanti, P., Aye, T. T., van den Toorn, H., Peng, M., van Breukelen, B., & Heck, A. J. R. (2015). An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas. Cell Reports [E], 11(11), 1834-1843. https://doi.org/10.1016/j.celrep.2015.05.029
2014
Scholarly publications
Guerreiro, A. C. L., Benevento, M., Lehmann, R., van Breukelen, B., Post, H., Giansanti, P., Altelaar, A., Axmann, I. M., & Heck, A. J. R. (2014). Daily rhythms in the cyanobacterium synechococcus elongatus probed by high-resolution mass spectrometry-based proteomics reveals a small defined set of cyclic proteins. Molecular & Cellular Proteomics, 13(8), 2042-2055. https://doi.org/10.1074/mcp.M113.035840
Walzer, M., Pernas, L. E., Nasso, S., Bittremieux, W., Nahnsen, S., Kelchtermans, P., Pichler, P., van den Toorn, H. W. P., Staes, A., Vandenbussche, J., Mazanek, M., Taus, T., Scheltema, R. A., Kelstrup, C. D., Gatto, L., van Breukelen, B., Aiche, S., Valkenborg, D., Laukens, K., ... Martens, L. (2014). qcML: an exchange format for quality control metrics from mass spectrometry experiments. Molecular & Cellular Proteomics, 13(8), 1905-13. https://doi.org/10.1074/mcp.M113.035907
Liu, F., van Breukelen, B., & Heck, A. J. R. (2014). Facilitating protein disulfide mapping by a combination of pepsin digestion, electron transfer higher energy dissociation (EThcD), and a dedicated search algorithm SlinkS. Molecular & Cellular Proteomics, 13(10), 2776-86. https://doi.org/10.1074/mcp.O114.039057
Binai, N. A., Bisschops, M. M. M., van Breukelen, B., Mohammed, S., Loeff, L., Pronk, J. T., Heck, A. J. R., Daran-Lapujade, P., & Slijper, M. (2014). Proteome adaptation of Saccharomyces cerevisiae to severe calorie restriction in Retentostat cultures. Journal of Proteome Research, 13(8), 3542-3553. https://doi.org/10.1021/pr5003388
Smit, M. A., Maddalo, G., Greig, K., Raaijmakers, L. M., Possik, P. A., van Breukelen, B., Cappadona, S., Heck, A. J., Altelaar, A., & Peeper, D. S. (2014). ROCK1 is a potential combinatorial drug target for BRAF mutant melanoma. Molecular Systems Biology [E], 10(12), 772. https://doi.org/10.15252/msb.20145450
Peng, M., Scholten, A., Heck, A. J. R., & van Breukelen, B. (2014). Identification of Enriched PTM Crosstalk Motifs from Large-Scale Experimental Data Sets. Journal of Proteome Research, 13(1), 249-259. https://doi.org/10.1021/pr4005579
2013
Scholarly publications
Low, T. Y., van Heesch, S. A. A. C., van den Toorn, H. W. P., Giansanti, P., Cristobal, A., Toonen, P., Schafer, S., Hübner, N., van Breukelen, B., Mohammed, S., Cuppen, E. P. J. G., & Heck, A. J. R. (2013). Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis. Cell Reports [E], 5(5), 1469-1478. https://doi.org/10.1016/j.celrep.2013.10.041
2012
Scholarly publications
Cote, R. G., Griss, J., Dianes, J. A., Wang, R., Wright, J. C., van den Toorn, H. W. P., van Breukelen, B., Heck, A. J. R., Hulstaert, N., Martens, L., Reisinger, F., Csordas, A., Ovelleiro, D., Perez-Rivevol, Y., Barsnes, H., Hermjakob, H., & Vizcaino, J. A. (2012). The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium. Molecular & Cellular Proteomics, 12, 1682-1689. https://doi.org/10.1074/mcp.O112.021543
Millioni, R., Tolin, S., Fadini, G. P., Falda, M., van Breukelen, B., Tessari, P., & Arrigoni, G. (2012). High confidence and sensitivity four-dimensional fractionation for human plasma proteome analysis. Amino Acids, 43(2), 2199-2202. https://doi.org/10.1007/s00726-012-1267-1
Peng, M., Ms. Taouatas, N., Cappadona, S., van Breukelen, B., Mohammed, S., Scholten, A., & Heck, A. J. R. (2012). Protease bias in absolute protein quantitation. Nature Methods, 9(6), 524-525. https://doi.org/10.1038/nmeth.2031
Cappadona, S., Baker, P. R., Cutillas, P., Heck, A. J. R., & van Breukelen, B. (2012). Current challenges in software solutions for mass spectrometry-based quantitative proteomics. Amino Acids, 43, 1087-1108. https://doi.org/10.1007/s00726-012-1289-8.
Altelaar, A. F. M., Navarro, D., Boekhorst, J., van Breukelen, B., Snel, B., Mohammed, S., & Heck, A. J. R. (2012). Database independent proteomics analysis of the ostrich and human proteome. Proceedings of the National Academy of Sciences of the United States of America, 109, 407-412.
Bleijerveld, O. B., Wijten, P., Cappadona, S., McClellan, E. A., Polat, A. N., Raijmakers, R., Sels, J. W., Colle, L. B., Grasso, S., van den Toorn, H. W. P., van Breukelen, B., Stubbs, A., Pasterkamp, G., Heck, A. J. R., Hoefer, I. E., & Scholten, A. (2012). Deep Proteome Profiling of Circulating Granulocytes Reveals Bactericidal/Permeability-Increasing Protein as a Biomarker for Severe Atherosclerotic Coronary Stenosis. Journal of Proteome Research, 11, 5235-5244. http://www.ncbi.nlm.nih.gov/pubmed/23020738
2011
Scholarly publications
Van Den Toorn, H. W. P., Muñoz, J., Mohammed, S., Raijmakers, R., Heck, A. J. R., & Van Breukelen, B. (2011). RockerBox: Analysis and filtering of massive proteomics search results. Journal of Proteome Research, 10(3), 1420-1424. https://doi.org/10.1021/pr1010185
De Graaf, E. L., Altelaar, A. F. M., Van Breukelen, B., Mohammed, S., & Heck, A. J. R. (2011). Improving SRM assay development: A global comparison between triple quadrupole, Ion trap, and higher energy CID peptide fragmentation spectra. Journal of Proteome Research, 10(9), 4334-4341. https://doi.org/10.1021/pr200156b
Boekhorst, J., Boersema, P. J., Tops, B. B. J., van Breukelen, B., Heck, A. J. R., & Snel, B. (2011). Evaluating experimental bias and completeness in comparative phosphoproteomics analysis. PLoS One, 6(8), 23276.
Cappadona, S., Munoz, J., Spee, W. P. E., Low, T. Y., Mohammed, S., van Breukelen, B., & Heck, A. J. R. (2011). Deconvolution of overlapping isotopic clusters improves quantification of stable isotope-labeled peptides. Journal of Proteomics, 74(10), 2204-2209.
Ahmad, I., Suits, F., Hoekman, B., Swertz, M. A., Byelas, H., Dijkstra, M., Hooft, R., Katsubo, D., van Breukelen, B., Bischoff, R., & Horvatovich, P. (2011). A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data. Bioinformatics, 27(8), 1176-1178.
2010
Scholarly publications
Helbig, A. O., Rosati, S., Pijnappel, W. W. M. P., van Breukelen, B., Timmers, H. T. M., Mohammed, S., Slijper, M., & Heck, A. J. R. (2010). Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels. BMC Genomics, 11(1). https://doi.org/10.1186/1471-2164-11-685
Van Breukelen, B., Georgiou, A., Drugan, M. M., Taouatas, N., Mohammed, S., & Heck, A. J. R. (2010). LysNDeNovo: An algorithm enabling de novo sequencing of Lys-N generated peptides fragmented by electron transfer dissociation. Proteomics, 10(6), 1196-1201. https://doi.org/10.1002/pmic.200900405
Boersema, P. J., Foong, L. Y., Ding, V. M., Lemeer, S., van Breukelen, B., Philp, R., Boekhorst, J., Snel, B., den Hertog, J., Choo, A. B., & Heck, A. J. (2010). In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling. Molecular & Cellular Proteomics, 9(1), 84-99. http://www.ncbi.nlm.nih.gov/pubmed/19770167
Helbig, A. O., Gauci, S., Raijmakers, R., van Breukelen, B., Slijper, M., Mohammed, S., & Heck, A. J. R. (2010). Profiling of N-acetylated protein termini provides in-depth insights into the N-terminal nature of the proteome. Molecular & Cellular Proteomics, 9, 928-939.
Barbu, I. M., Smith, D. F., van Breukelen, B., van der Burgt, Y. E. M., Duursma, M. C., Heck, A. J. R., Heeren, R. M. A., & Krijgsveld, J. (2010). On-the-fly targeted selection of labeled peptides in liquid chromatography/mass spectrometry based quantitative proteomics. Rapid Communications in Mass Spectrometry, 24, 239-241.
2009
Scholarly publications
Boersema, P., Foong, L. Y., Ding, V., Lemeer, S., Mohammed, S., Raijmakers, R., van Breukelen, B., Boekhorst, J., Choo, A. B. H., & Heck, A. J. R. (2009). Large Scale Multiplex Stable Isotope Dimethyl Labeling Applied to the Quantitative Analysis of Tyrosine Phosphorylation. Molecular & Cellular Proteomics, S47-S47. https://www.researchgate.net/publication/295938897_Large_Scale_Multiplex_Stable_Isotope_Dimethyl_Labeling_Applied_to_the_Quantitative_Analysis_of_Tyrosine_Phosphorylation
van Breukelen, B., van den Toorn, H. W. P., Drugan, M. M., & Heck, A. J. R. (2009). StatQuant: A post-quantification analysis toolbox for improving quantitative mass spectrometry. Bioinformatics, 25(11), 1472-1473. https://doi.org/10.1093/bioinformatics/btp181
2008
Scholarly publications
Boekhorst, J., van Breukelen, B., Heck, A. J. R., & Snel, B. (2008). Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes. Genome Biology, 9, R144.1-R144.9.
Gauci, S., van Breukelen, B., Lemeer, S. M., Krijgsveld, J., & Heck, A. J. R. (2008). A versatile peptide pI calculator for phosphorylated and N-terminal acetylated peptides experimentally tested using peptide isoelectric focusing. Proteomics, 8(23-24), 4898-4906.
Pinkse, M. W. H., Mohammed, S., Gouw, J. W., van Breukelen, B., Vos, H. R., & Heck, A. J. R. (2008). Highly Robust, Automated, and Sensitive Online TiO2-Based Phosphoproteomics Applied To Study Endogenous Phosphorylation in Drosophila melanogaster. Journal of Proteome Research, 7, 687-697.
https://dspace.library.uu.nl/bitstream/handle/1874/26426/39_highly_Pinkse.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26426/39_highly_Pinkse.pdf?sequence=1
Mohammed, S., Lorenzen, K., Kerkhoven, R., van Breukelen, B., Vannini, A., Cramer, P., & Heck, A. J. R. (2008). ) Multiplexed proteomics mapping of yeast RNA polymerase II and III allows near-complete sequence coverage and reveals several novel phosphorylation sites. Analytical Chemistry, 80(10), 3584-3592.
Lemeer, S. M., Pinkse, M. W. H., Mohammed, S., van Breukelen, B., den Hertog, J., Slijper, M., & Heck, A. J. R. (2008). Online automated in vivo zebrafish phosphoproteomics: From large-scale analysis down to a single embryo. Journal of Proteome Research, 7(4), 1555-1564.
2007
Scholarly publications
de Groot, M. J. L., Daran-Lapujade, P., van Breukelen, B., Knijnenburg, T. A., Hulster, E. A. F., Reinders, M. J. T., Pronk, J. T., Heck, A. J. R., & Slijper, M. (2007). Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes. Microbiology, 153, 3864-3878.
https://dspace.library.uu.nl/bitstream/handle/1874/26402/14_quantitative_degroot.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26402/14_quantitative_degroot.pdf?sequence=1
Dormeyer, W., Mohammed, S., van Breukelen, B., Krijgsveld, J., & Heck, A. J. R. (2007). Targeted Analysis of Protein Termini. Journal of Proteome Research.
https://dspace.library.uu.nl/bitstream/handle/1874/26333/16_targeted_dormeyer.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26333/16_targeted_dormeyer.pdf?sequence=1
2006
Scholarly publications
de Jong, H. M., van Breukelen, B., Wittink, R. A., Menke, F. L. H., Weisbeek, P. J., & van den Ackerveken, A. F. J. M. (2006). Membrane-associated transcripts in Arabidopsis; their isolation and characterisation by DNA microarray analysis and bioinformatics. Plant Journal, 46(4), 708-721.
van Breukelen, B., Barendregt, A., Heck, A. J. R., & van den Heuvel, R. H. H. (2006). Resolving stoichiometries and oligomeric states of glutamate synthase protein complexes with curve fitting and simulation of electrospray mass spectra. Rapid Communications in Mass Spectrometry, 20, 2490-2496.
Scholten, A., Poh, M. K., van Veen, A. A. B., van Breukelen, B., Vos, M. A., & Heck, A. J. R. (2006). 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. Journal of Proteome Research, 5(6), 1435-1447.
2004
Scholarly publications
Stracker, T. H., Cassel, G. D., Ward, P., Loo, Y-M., van Breukelen, B., Carrington-Lawrence, S. D., Hamatake, R. K., van der Vliet, P. C., Weller, S. K., Melendy, T., & Weitzman, M. D. (2004). The Rep protein of Adeno-associated virus type 2 interacts with single-stranded DNA-binding proteins that enhance viral replication. Journal of Virology, 78(1), 441-453.
2003
Scholarly publications
Van Breukelen, B., Brenkman, A. B., Holthuizen, P. E., & Van der Vliet, P. C. (2003). Adenovirus type 5 DNA binding protein stimulates binding of DNA polymerase to the replication origin. Journal of Virology, 77(2), 915-922. https://doi.org/10.1128/JVI.77.2.915-922.2003
2000
Scholarly publications
van Breukelen, B., Kanellopoulos, P. N., Tucker, P. A., & van der Vliet, P. C. (2000). The formation of a flexible DNA-binding protein chain is required for efficient DNA unwinding and adenovirus DNA chain elongation. Journal of Biological Chemistry, 275(52), 40897-40903.