A full list of my publications can be found at my ResearcherID.
Publicaties
2025
Vakpublicaties
van Vlissingen, M. F., Heringa, J., Kok, R., Koureas, D., Lifang, L., & Raijmakers, R. (2025). Sustaining Dutch strength in European Life and Medical Science (LMS) research infrastructures: A collective perspective on the long-term sustainability of national participation in European LMS research infrastructures. Zenodo. [DOI]
2023
Wetenschappelijke publicaties
Mundt, F., Albrechtsen, N. J. W., Mann, S. P., Treit, P., Ghodgaonkar-Steger, M., O’Flaherty, M., Raijmakers, R., Vizcaíno, J. A., Heck, A. J. R., & Mann, M. (2023). Foresight in clinical proteomics: current status, ethical considerations, and future perspectives. Open Research Europe, 3, Article 59. [DOI] [Repository]
2018
Wetenschappelijke publicaties
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. [DOI] [Repository]
2014
Wetenschappelijke publicaties
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. [DOI]
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. [DOI]
2013
Wetenschappelijke publicaties
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. [DOI]
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. [DOI]
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. [DOI]
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. [DOI]
2012
Wetenschappelijke publicaties
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. [DOI]
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. [DOI]
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
Wetenschappelijke publicaties
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. [DOI]
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., 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. [DOI]
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
Wetenschappelijke publicaties
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
Wetenschappelijke publicaties
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
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
Wetenschappelijke publicaties
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. [DOI]
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. [DOI]
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
Wetenschappelijke publicaties
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, Article R12. [DOI]
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. [DOI]
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. [DOI]
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. [DOI]
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. [DOI]
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. [DOI]
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. [DOI]
2006
Wetenschappelijke publicaties
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. [DOI]
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. [DOI]
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. [DOI]
2005
Wetenschappelijke publicaties
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. [DOI]
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. [DOI]
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. [DOI]
2004
Wetenschappelijke publicaties
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. [DOI]
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. [DOI]
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. [DOI]
2003
Wetenschappelijke publicaties
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. [DOI]
2002
Wetenschappelijke publicaties
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. [DOI]
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. [DOI]
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. [DOI]
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. [DOI]
2001
Wetenschappelijke publicaties
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. [DOI]
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. [DOI]
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. [DOI]