A full list of my publications can be found at my ResearcherID.
Publications
2018
Scholarly publications
Bockelmann, S., Mina, J. G. M., Korneev, S., Hassan, D. G., Mueller, D., Hilderink, A., Vlieg, H. C., Raijmakers, R., Heck, A. J. R., Haberkant, P., & Holthuis, J. C. M. (2018). A search for ceramide binding proteins using bifunctional lipid analogs yields CERT-related protein StarD7. Journal of Lipid Research, 59(3), 515-530. https://doi.org/10.1194/jlr.M082354
2014
Scholarly publications
Assohou-Luty, C., Raijmakers, R., Benckhuijsen, W. E., Stammen-Vogelzangs, J., De Ru, A., Van Veelen, P. A., Franken, K. L. M. C., Drijfhout, J. W., & Pruijn, G. J. M. (2014). The human peptidylarginine deiminases type 2 and type 4 have distinct substrate specificities. Biochimica et Biophysica Acta - Proteins and Proteomics, 1844(4), 829-836. https://doi.org/10.1016/j.bbapap.2014.02.019
Raijmakers, R., Olsen, J. V., Aebersold, R., & Heck, A. J. R. (2014). PRIME-XS, a European infrastructure for proteomics. Molecular & Cellular Proteomics, 13(8), 1901-4. https://doi.org/10.1074/mcp.E114.040162
2013
Scholarly publications
Haberkant, P., Raijmakers, R., Wildwater, M., Sachsenheimer, T., Brügger, B., Maeda, K., Houweling, M., Gavin, A-C., Schultz, C., van Meer, G., Heck, A. J. R., & Holthuis, J. C. M. (2013). Bifunktionalisierte Fettsäuren zur Visualisierung und Identifizierung von Protein-Lipid-Interaktionen in lebenden Zellen. Angewandte Chemie, 125(14), 4125-4130. https://doi.org/10.1002/ange.201210178
Van Beers, J. J. B. C., Zendman, A. J. W., Raijmakers, R., Stammen-Vogelzangs, J., & Pruijn, G. J. M. (2013). Peptidylarginine deiminase expression and activity in PAD2 knock-out and PAD4-low mice. Biochimie, 95(2), 299-308. https://doi.org/10.1016/j.biochi.2012.09.029
Moscarello, M. A., Lei, H., Mastronardi, F. G., Winer, S., Tsui, H., Li, Z., Ackerley, C., Zhang, L., Raijmakers, R., & Wood, D. D. (2013). Inhibition of peptidyl-arginine deiminases reverses protein- hypercitrullination and disease in mouse models of multiple sclerosis. DMM Disease Models and Mechanisms, 6(2), 467-478. https://doi.org/10.1242/dmm.010520
Haberkant, P., Raijmakers, R., Wildwater, M., Sachsenheimer, T., Brügger, B., Maeda, K., Houweling, M., Gavin, A-C., Schultz, C., van Meer, G., Heck, A. J. R., & Holthuis, J. C. M. (2013). In vivo profiling and visualization of cellular protein–lipid interactions using bifunctional fatty acids. Angewandte Chemie-International Edition, 52, 4033-4038. https://doi.org/10.1002/anie.201210178
2012
Scholarly publications
Kovanich, D., Cappadona, S., Raijmakers, R., Mohammed, S., Scholten, A., & Heck, A. J. R. (2012). Applications of stable isotope dimethyl labeling in quantitative proteomics. Analytical and Bioanalytical Chemistry, 404(4), 991-1009. https://doi.org/10.1007/s00216-012-6070-z
Polat, A. N., Kraiczek, K., Heck, A. J. R., Raijmakers, R., & Mohammed, S. (2012). Fully automated isotopic dimethyl labeling and phosphopeptide enrichment using a microfluidic HPLC phosphochip. Analytical and Bioanalytical Chemistry, 404, 2507-2512. https://doi.org/10.1007/s00216-012-6395-7
Raijmakers, R., Beers, J. J. B. C., El-Azzouny, M., Visser, N. F. C., Bozic, B., Pruijn, G. J. M., & Heck, A. J. R. (2012). Elevated levels of fibrinogen-derived endogenous citrullinated peptides in synovial fluid of rheumatoid arthritis patients. Arthritis Research & Therapy, 14.
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
Schoffelen, S., van Eldijk, M. B., Rooijakkers, B., Raijmakers, R., Heck, A. J. R., & van Hest, J. C. M. (2011). Metal-free and pH-controlled introduction of azides in proteins. Chemical Science, 2(4), 701-705. https://doi.org/10.1039/c0sc00562b
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
Snijder, J., Rose, R. J., Raijmakers, R., & Heck, A. J. R. (2011). Site-specific methionine oxidation in calmodulin affects structural integrity and interaction with Ca2+/calmodulin-dependent protein kinase II. Journal of Structural Biology, 174(1), 187-195.
van den Toorn, H. W. P., Munoz, 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.
van Dooren, S. H., Raijmakers, R., Pluk, H., Lokate, A. M. C., Koemans, T. S., Spanjers, R. E., Heck, A. J. R., Boelens, W. C., van Venrooij, W. J., & Pruijn, G. J. M. (2011). Oxidative stress-induced modifications of histidyl-tRNA synthetase affect its tRNA aminoacylation activity but not its immunoreactivity. Biochemistry and Cell Biology, 89(6), 545-553.
Di Palma, S., Raijmakers, R., Heck, A. J. R., & Mohammed, S. (2011). Evaluation of the deuterium isotope effect in zwitterionic hydrophilic interaction liquid chromatography separations for implementation in a quantitative proteomic approach. Analytical Chemistry, 83(21), 8352-8356.
2010
Scholarly publications
van Beers, J. B. C., Raijmakers, R., Alexander, L-E., Stammen-Vogelzangs, J., Lokate, A. M. C., Heck, A. J. R., Schasfoort, R. B. M., & Pruijn, G. J. M. (2010). Mapping of citrullinated fibrinogen B-cell epitopes in rheumatoid arthritis by imaging surface plasmon resonance. Arthritis Research & Therapy, 12(6).
Pelletier, S., Schuurman, K. G., Berkers, C. R., Ovaa, H., Heck, A. J. R., & Raijmakers, R. (2010). Quantifying cross-tissue diversity in proteasome complexes by mass spectrometry. Molecular BioSystems, 6, 1450-1453.
Staals, R. H. J., Bronkhorst, A. W., Schilders, G., Slomovic, S., Schuster, G., Heck, A. J. R., Raijmakers, R., & Pruijn, G. J. M. (2010). Dis3-like 1: a novel exoribonuclease associated with the human exosome. EMBO Journal, 29(14), 2358-2367.
Raijmakers, R., Kraiczek, K., de Jong, A. P., Mohammed, S., & Heck, A. J. R. (2010). Exploring the human leukocyte phosphoproteome using a microfluidic reversed-phase-TiO2-reversed-phase high-performance liquid chromatography phosphochip coupled to a quadrupole time-of-flight mass spectrometer. Analytical Chemistry, 82(3), 824-832.
Raijmakers, R., Pelletier, S., Gouw, J. W., Rumpel, K., Heck, A. J. R., & Dadvar, P. (2010). Target profiling of a small library of phosphodiesterase 5 (PDE5) inhibitors using chemical proteomics. ChemMedChem, 5, 1927-1936.
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.
Raijmakers, R., Neerincx, P. B. T., Mohammed, S., & Heck, A. J. R. (2010). Cleavage specificities of the brother and sister proteases Lys-C and Lys-N. Chemical Communications, 46, 8827-8829.
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.
Dadvar, P., Kovanich, D., Folkers, G. E., Rumpel, K., Raijmakers, R., & Heck, A. J. R. (2009). Phosphatidylethanolamine-binding proteins, including RKIP, exhibit affinity for phosphodiesterase-5 inhibitors. ChemBioChem, (10), 2654-2662.
Synowsky, S. A., van Wijk, M., Raijmakers, R., & Heck, A. J. R. (2009). Comparative multiplexed mass spectrometric analyses of endogenously expressed yeast nuclear and cytoplasmic exosomes. Journal of Molecular Biology, (385), 1300-1313.
Raijmakers, R., Heck, A. J. R., & Mohammed, S. (2009). Assessing biological variation and protein processing in primary human leukocytes by automated multiplex stable isotope labeling coupled to 2 dimensional peptide separation. Molecular BioSystems, (5), 992-1003.
Boersema, P. J., Raijmakers, R., Lemeer, S. M., Mohammed, S., & Heck, A. J. R. (2009). Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nature Protocols, (4), 484-494.
2008
Scholarly publications
Wood, D. D., Ackerley, C. A., Brand, B. V. D., Zhang, L., Raijmakers, R., Mastronardi, F. G., & Moscarello, M. A. (2008). Myelin localization of peptidylarginine deiminases 2 and 4: Comparison of PAD2 and PAD4 activities. Laboratory Investigation, 88(4), 354-364. https://doi.org/10.1038/labinvest.3700748
Musse, A. A., Polverini, E., Raijmakers, R., & Harauz, G. (2008). Kinetics of human peptidylarginine deiminase 2 (hPAD2) - Reduction of Ca2+ dependence by phospholipids and assessment of proposed inhibition by paclitaxel side chains. Biochemistry and Cell Biology, 86(5), 437-447. https://doi.org/10.1139/O08-124
Raijmakers, R., Berkers, C. R., de Jong, G. J., Ovaa, H., Heck, A. J. R., & Mohammed, S. (2008). Automated online sequential isotope labeling for protein quantitation applied to proteasome tissue specific diversity. Molecular & Cellular Proteomics, 7, 1755-1762.
2007
Scholarly publications
Schilders, G., Raijmakers, R., Malmegrim, K. C. R., Vande Walle, L., Saelens, X., Vree Egberts, W., van Venrooij, W. J., Vandenabeele, P., & Pruijn, G. J. M. (2007). Caspase-mediated cleavage of the exosome subunit PM/Scl-75 during apoptosis. Arthritis Research and Therapy, 9, [R12]. https://doi.org/10.1186/ar2119
Raijmakers, R., Zendman, A. J. W., Egberts, W. V., Vossenaar, E. R., Raats, J., Soede-Huijbregts, C., Rutjes, F. P. J. T., van Veelen, P. A., Drijfhout, J. W., & Pruijn, G. J. M. (2007). Methylation of Arginine Residues Interferes with Citrullination by Peptidylarginine Deiminases in vitro. Journal of Molecular Biology, 367(4), 1118-1129. https://doi.org/10.1016/j.jmb.2007.01.054
Mahler, M., Raijmakers, R., & Fritzler, M. J. (2007). Challenges and controversies in autoantibodies associated with systemic rheumatic diseases. Current Rheumatology Reviews, 3(1), 67-78. https://doi.org/10.2174/157339707779815722
Mahler, M., Raijmakers, R., & Fritzler, M. J. (2007). Challenges and controversies in autoantibodies associated with systemic rheumatic diseases. Current Rheumatology Reviews, 3(1), 67-78. https://doi.org/10.2174/157339707779815722
Mahler, M., & Raijmakers, R. (2007). Novel aspects of autoantibodies to the PM/Scl complex: Clinical, genetic and diagnostic insights. Autoimmunity Reviews, 6(7), 432-437. https://doi.org/10.1016/j.autrev.2007.01.013
Schilders, G., Egberts, W. V., Raijmakers, R., & Pruijn, G. J. M. (2007). C1D is a major autoantibody target in patients with the polymyositis-scleroderma overlap syndrome. Arthritis and Rheumatism, 56(7), 2449-2454. https://doi.org/10.1002/art.22710
Zendman, A. J. W., Raijmakers, R., Nijenhuis, S., Vossenaar, E. R., Tillaart, M. V. D., Chirivi, R. G. S., Raats, J. M. H., van Venrooij, W. J., Drijfhout, J. W., & Pruijn, G. J. M. (2007). ABAP: Antibody-based assay for peptidylarginine deiminase activity. Analytical Biochemistry, 369(2), 232-240. https://doi.org/10.1016/j.ab.2007.07.009
Kessenbrock, K., Raijmakers, R., Fritzler, M. J., & Mahler, M. (2007). Synthetic peptides: The future of patient management in systemic rheumatic diseases? Current Medicinal Chemistry, 14(26), 2831-2838. https://doi.org/10.2174/092986707782360150
2006
Scholarly publications
Raijmakers, R., Vogelzangs, J., Raats, J., Panzenbeck, M., Corby, M., Jiang, H., Thibodeau, M., Haynes, N., Van Venrooij, W. J., Pruijn, G. J. M., & Werneburg, B. (2006). Experimental autoimmune encephalomyelitis induction in peptidylarginine deiminase 2 knockout mice. Journal of Comparative Neurology, 498(2), 217-226. https://doi.org/10.1002/cne.21055
Schilders, G., van Dijk, E., Raijmakers, R., & Pruijn, G. J. M. (2006). Cell and Molecular Biology of the Exosome: How to Make or Break an RNA. International Review of Cytology, 251, 159-208. https://doi.org/10.1016/S0074-7696(06)51005-8
Mastronardi, F. G., Wood, D. D., Mei, J., Raijmakers, R., Tseveleki, V., Dosch, H. M., Probert, L., Casaccia-Bonnefil, P., & Moscarello, M. A. (2006). Increased citrullination of histone H3 in multiple sclerosis brain and animal models of demyelination: A role for tumor necrosis factor-induced peptidylarginine deiminase 4 translocation. Journal of Neuroscience, 26(44), 11387-11396. https://doi.org/10.1523/JNEUROSCI.3349-06.2006
2005
Scholarly publications
Schilders, G., Raijmakers, R., Raats, JMH., & Pruijn, G. J. M. (2005). MPP6 is an exosome-associated RNA-binding protein involved in 5.8S rRNA maturation. Nucleic Acids Research, 33(21), 6795-6804. https://doi.org/10.1093/nar/gki982
Mahler, M., Raijmakers, R., Dahnrich, C., Bluthner, M., & Fritzler, MJ. (2005). Clinical evaluation of autoantibodies to a novel PM/Scl peptide antigen. Arthritis Research & Therapy, 7(3), R704-R713. https://doi.org/10.1186/ar1729
Raijmakers, R., Vogelzangs, J., Croxford, JL., Wesseling, P., Van Venrooij, WJ., & Pruijn, GJM. (2005). Citrullination of central nervous system proteins during the development of experimental autoimmune encephalomyelitis. Journal of Comparative Neurology, 486(3), 243-253. https://doi.org/10.1002/cne.20529
2004
Scholarly publications
Raijmakers, R., Renz, M., Wiemann, C., Egberts, WV., Seelig, HP., van Venrooij, WJ., & Pruijn, GJM. (2004). PM-Scl-75 is the main autoantigen in patients with the polymyositis/scleroderma overlap syndrome. Arthritis and Rheumatism, 50(2), 565-569. https://doi.org/10.1002/art.20056
Raijmakers, R., Schilders, G., & Pruijn, G. J. M. (2004). The exosome, a molecular machine for controlled RNA degradation in both nucleus and cytoplasm. European Journal of Cell Biology, 83(5), 175-183.
Welting, TJM., Raijmakers, R., & Pruijn, G. J. M. (2004). Autoantigenicity of nucleolar complexes (vol 2, pg 313, 2003). Autoimmunity Reviews, 3(1), 88-89. https://doi.org/10.1016/S1568-9972(03)00141-1
Sambandam, T., Belousova, M., Accaviti-Loper, MA., Blanquicett, C., Guercello, V., Raijmakers, R., & Nicholas, AP. (2004). Increased peptidylarginine deiminase type II in hypoxic astrocytes. Biochemical and Biophysical Research Communications, 325(4), 1324-1329. https://doi.org/10.1016/j.bbrc.2004.10.173
2003
Scholarly publications
Raijmakers, R., Egberts, W. V., Van Venrooij, W. J., & Pruijn, G. J. M. (2003). The association of the human PM/Scl-75 autoantigen with the exosome is dependent on a newly identified N terminus. Journal of Biological Chemistry, 278(33), 30698-30704. https://doi.org/10.1074/jbc.M302488200
2002
Scholarly publications
Raijmakers, R., Noordman, Y. E., Van Venrooij, W. J., & Pruijn, G. J. M. (2002). Protein-protein interactions of hCsl4p with other human exosome subunits. Journal of Molecular Biology, 315(4), 809-818. https://doi.org/10.1006/jmbi.2001.5265
Raijmakers, R., Vree Egberts, W., Van Venrooij, W. J., & Pruijn, G. J. M. (2002). Protein-protein interactions between human exosome components support the assembly of RNase PH-type subunits into a six-membered PNPase-like ring. Journal of Molecular Biology, 323(4), 653-663. https://doi.org/10.1016/S0022-2836(02)00947-6
Mukherjee, D., Gao, M., O'Connor, J. P., Raijmakers, R., Pruijn, G., Lutz, C. S., & Wilusz, J. (2002). The mammalian exosome mediates the efficient degradation of mRNAs that contain AU-rich elements. EMBO Journal, 21(1-2), 165-174. https://doi.org/10.1093/emboj/21.1.165
Brouwer, R., Egberts, W. T. M. V., Hengstman, G. J. D., Raijmakers, R., Van Engelen, B. G. M., Seelig, H. P., Renz, M., Mierau, R., Genth, E., Pruijn, G. J. M., & Van Venrooij, W. J. (2002). Autoantibodies directed to novel components of the PM/Scl complex, the human exosome. Arthritis Research, 4(2), 134-138. https://doi.org/10.1186/ar389
2001
Scholarly publications
Brouwer, R., Allmang, C., Raijmakers, R., van Aarssen, Y., Vree Egberts, W., Petfalski, E., van Venrooij, WJ., Tollervey, D., & Pruijn, G. J. M. (2001). Three novel components of the human exosome. Journal of Biological Chemistry, 276(9), 6177-6184.
Fabini, G., Raijmakers, R., Hayer, S., Fouraux, MA., Pruijn, G. J. M., & Steiner, G. (2001). The heterogeneous nuclear ribonucleoproteins I and K interact with a subset of the Ro ribonucleoprotein-associated Y RNAs in vitro and in vivo. Journal of Biological Chemistry, 276(23), 20711-20718.
Chen, CY., Gherzi, R., Ong, SE., Chan, EKL., Raijmakers, R., Pruijn, G. J. M., Stoecklin, G., Moroni, C., Mann, M., & Karin, M. (2001). AU binding proteins recruit the exosome to degrade ARE-containing mRNAs. Cell, 107(4), 451-464.