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Prof. dr. A.F.M. (Maarten) Altelaar

Professor 
Science
Pharmaceutical sciences
Biomolecular Mass Spectrometry and Proteomics
Biomolecular Mass Spectrometry and Proteomics

Prof. dr. A.F.M. (Maarten) Altelaar

Professor
Biomolecular Mass Spectrometry and Proteomics
m.altelaar@uu.nl
Profile Publications Activities Prizes Research Teaching Ancillary activities Contact
Profile Publications Activities Prizes Research Teaching Ancillary activities Contact
Research areas

Highlighted publications

Rontogianni, S., Synadaki, E., Li, B., Liefaard, M. C., Lips, E. H., Wesseling, J., Wu, W., & Altelaar, M. (2019). Proteomic profiling of extracellular vesicles allows for human breast cancer subtyping. Communications Biology, 2, Article 325. https://doi.org/10.1038/s42003-019-0570-8
Altelaar, A. F. M., Munoz-Peralta, J., & Heck, A. J. R. (2013). Next-generation proteomics: towards an integrative view of proteome dynamics. Nature Reviews. Genetics, 14, 35-48. https://doi.org/10.1038/nrg3356
Frese, C. K., Mikhaylova, M., Stucchi, R., Gautier, V., Liu, Q., Mohammed, S., Heck, A. J. R., Altelaar, A. F. M., & Hoogenraad, C. C. (2017). Quantitative Map of Proteome Dynamics during Neuronal Differentiation. Cell Reports, 18(6), 1527-1542. https://doi.org/10.1016/j.celrep.2017.01.025
Schmidlin, T., Debets, D. O., van Gelder, C. A. G. H., Stecker, K. E., Rontogianni, S., van den Eshof, B. L., Kemper, K., Lips, E. H., van den Biggelaar, M., Peeper, D. S., Heck, A. J. R., & Altelaar, M. (2019). High-Throughput Assessment of Kinome-wide Activation States. Cell Systems, 9(4), 366-374. https://doi.org/10.1016/j.cels.2019.08.005
Valverde, J. M., Dubra, G., Phillips, M., Haider, A., Elena-Real, C., Fournet, A., Alghoul, E., Chahar, D., Andrés-Sanchez, N., Paloni, M., Bernadó, P., van Mierlo, G., Vermeulen, M., van den Toorn, H., Heck, A. J. R., Constantinou, A., Barducci, A., Ghosh, K., Sibille, N., ... Altelaar, M. (2023). A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation. Nature Communications, 14(1), 1-23. Article 6316. https://doi.org/10.1038/s41467-023-42049-0
https://dspace.library.uu.nl/bitstream/handle/1874/434421/s41467-023-42049-0.pdf?sequence=1
Debets, D. O., Stecker, K. E., Piskopou, A., Liefaard, M. C., Wesseling, J., Sonke, G. S., Lips, E. H., & Altelaar, M. (2023). Deep (phospho)proteomics profiling of pre- treatment needle biopsies identifies signatures of treatment resistance in HER2+ breast cancer. Cell Reports Medicine, 4(10), 1-13. Article 101203. https://doi.org/10.1016/j.xcrm.2023.101203
https://dspace.library.uu.nl/bitstream/handle/1874/434422/1-s2.0-S2666379123003701-main.pdf?sequence=1

Publications

2024

Scholarly publications

Rai, D., Song, Y., Hua, S., Stecker, K., Monster, J. L., Yin, V., Stucchi, R., Xu, Y., Zhang, Y., Chen, F., Katrukha, E. A., Altelaar, M., Heck, A. J. R., Wieczorek, M., Jiang, K., & Akhmanova, A. (2024). CAMSAPs and nucleation-promoting factors control microtubule release from γ-TuRC. Nature Cell Biology, 26(3), 404-420. https://doi.org/10.1038/s41556-024-01366-2
Veth, T. S., Nouwen, L. V., Zwaagstra, M., Lyoo, H., Wierenga, K. A., Westendorp, B., Altelaar, M. A. F. M., Berkers, C., van Kuppeveld, F. J. M., & Heck, A. J. R. (2024). Assessment of Kinome-wide Activity Remodeling Upon Picornavirus Infection. Molecular and Cellular Proteomics, 100757. Advance online publication. https://doi.org/10.1016/j.mcpro.2024.100757
Ibáñez-Molero, S., Pruijs, J. T. M., Atmopawiro, A., Wang, F., Terry, A. M., Altelaar, M., Peeper, D. S., & Stecker, K. E. (2024). Phosphoprotein dynamics of interacting T cells and tumor cells by HySic. Cell Reports, 43(1), Article 113598. https://doi.org/10.1016/j.celrep.2023.113598
https://dspace.library.uu.nl/bitstream/handle/1874/435829/mmc4.pdf?sequence=1
Mayayo-Peralta, I., Debets, D. O., Prekovic, S., Schuurman, K., Beerthuijzen, S., Almekinders, M., Sanders, J., Moelans, C. B., Saleiro, S., Wesseling, J., van Diest, P. J., Henrique, R., Jerónimo, C., Altelaar, M., & Zwart, W. (2024). Proteomics on malignant pleural effusions reveals ERα loss in metastatic breast cancer associates with SGK1–NDRG1 deregulation. Molecular Oncology, 18(1), 156-169. https://doi.org/10.1002/1878-0261.13540
https://dspace.library.uu.nl/bitstream/handle/1874/434538/Molecular_Oncology_-_2023_-_Mayayo_Peralta_-_Proteomics_on_malignant_pleural_effusions_reveals_ER_loss_in_metastatic.pdf?sequence=1

2023

Scholarly publications

Hoefsmit, E. P., Völlmy, F., Rozeman, E. A., Reijers, I. L. M., Versluis, J. M., Hoekman, L., van Akkooi, A. C. J., Long, G. V., Schadendorf, D., Dummer, R., Altelaar, M., & Blank, C. U. (2023). Systemic LRG1 Expression in Melanoma is Associated with Disease Progression and Recurrence. Cancer research communications, 3(4), 672-683. https://doi.org/10.1158/2767-9764.CRC-23-0015
https://dspace.library.uu.nl/bitstream/handle/1874/435854/crc-23-0015.pdf?sequence=1
Bhin, J., Yemelyanenko, J., Chao, X., Klarenbeek, S., Opdam, M., Malka, Y., Hoekman, L., Kruger, D., Bleijerveld, O., Brambillasca, C. S., Sprengers, J., Siteur, B., Annunziato, S., van Haren, M. J., Martin, N. I., van de Ven, M., Peters, D., Agami, R., Linn, S. C., ... Wessels, L. F. A. (2023). MYC is a clinically significant driver of mTOR inhibitor resistance in breast cancer. Journal of Experimental Medicine, 220(11), Article e20211743. https://doi.org/10.1084/jem.20211743
Mayayo-Peralta, I., Gregoricchio, S., Schuurman, K., Yavuz, S., Zaalberg, A., Kojic, A., Abbott, N., Geverts, B., Beerthuijzen, S., Siefert, J., Severson, T. M., van Baalen, M., Hoekman, L., Lieftink, C., Altelaar, M., Beijersbergen, R. L., Houtsmuller, A. B., Prekovic, S., & Zwart, W. (2023). PAXIP1 and STAG2 converge to maintain 3D genome architecture and facilitate promoter/enhancer contacts to enable stress hormone-dependent transcription. Nucleic Acids Research, 51(18), 9576-9593. https://doi.org/10.1093/nar/gkad267
https://dspace.library.uu.nl/bitstream/handle/1874/434537/gkad267.pdf?sequence=1
Prekovic, S., Chalkiadakis, T., Roest, M., Roden, D., Lutz, C., Schuurman, K., Opdam, M., Hoekman, L., Abbott, N., Tesselaar, T., Wajahat, M., Dwyer, A. R., Mayayo-Peralta, I., Gomez, G., Altelaar, M., Beijersbergen, R., Győrffy, B., Young, L., Linn, S., ... Zwart, W. (2023). Luminal breast cancer identity is determined by loss of glucocorticoid receptor activity. EMBO Molecular Medicine, 15(12), Article e17737. https://doi.org/10.15252/emmm.202317737
Debets, D. O., Stecker, K. E., Piskopou, A., Liefaard, M. C., Wesseling, J., Sonke, G. S., Lips, E. H., & Altelaar, M. (2023). Deep (phospho)proteomics profiling of pre- treatment needle biopsies identifies signatures of treatment resistance in HER2+ breast cancer. Cell Reports Medicine, 4(10), 1-13. Article 101203. https://doi.org/10.1016/j.xcrm.2023.101203
https://dspace.library.uu.nl/bitstream/handle/1874/434422/1-s2.0-S2666379123003701-main.pdf?sequence=1
Valverde, J. M., Dubra, G., Phillips, M., Haider, A., Elena-Real, C., Fournet, A., Alghoul, E., Chahar, D., Andrés-Sanchez, N., Paloni, M., Bernadó, P., van Mierlo, G., Vermeulen, M., van den Toorn, H., Heck, A. J. R., Constantinou, A., Barducci, A., Ghosh, K., Sibille, N., ... Altelaar, M. (2023). A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation. Nature Communications, 14(1), 1-23. Article 6316. https://doi.org/10.1038/s41467-023-42049-0
https://dspace.library.uu.nl/bitstream/handle/1874/434421/s41467-023-42049-0.pdf?sequence=1
Yalçin, Z., Koot, D., Bezstarosti, K., Salas-Lloret, D., Bleijerveld, O. B., Boersma, V., Falcone, M., González-Prieto, R., Altelaar, M., Demmers, J. A. A., & Jacobs, J. J. L. (2023). Ubiquitinome Profiling Reveals in Vivo UBE2D3 Targets and Implicates UBE2D3 in Protein Quality Control. Molecular and Cellular Proteomics, 22(6), Article 100548. https://doi.org/10.1016/j.mcpro.2023.100548
Man, J. H. K., van Gelder, C. A. G. H., Breur, M., Molenaar, D., Abbink, T., Altelaar, M., Bugiani, M., & van der Knaap, M. S. (2023). Regional vulnerability of brain white matter in vanishing white matter. Acta neuropathologica communications, 11(1), 1-14. Article 103. https://doi.org/10.1186/s40478-023-01599-6
https://dspace.library.uu.nl/bitstream/handle/1874/434419/s40478-023-01599-6.pdf?sequence=1
Wang, F., Veth, T., Kuipers, M., Altelaar, M., & Stecker, K. E. (2023). Optimized Suspension Trapping Method for Phosphoproteomics Sample Preparation. Analytical Chemistry, 95(25), 9471-9479. https://doi.org/10.1021/acs.analchem.3c00324
Gan, C., Wang, J., Wang, Y., Martínez-Chávez, A., Hillebrand, M., de Vries, N., Beukers, J., Lebre, M. C., Wagenaar, E., Rosing, H., Klarenbeek, S., Bleijerveld, O. B., Song, J. Y., Altelaar, M., Beijnen, J. H., & Schinkel, A. H. (2023). Natural deletion of mouse carboxylesterases Ces1c/d/e impacts drug metabolism and metabolic syndrome development. Biomedicine and Pharmacotherapy, 164, Article 114956. https://doi.org/10.1016/j.biopha.2023.114956
Veth, T. S., Francavilla, C., Heck, A. J. R., & Altelaar, M. (2023). Elucidating Fibroblast Growth Factor-induced kinome dynamics using targeted mass spectrometry and dynamic modeling. Molecular and Cellular Proteomics, 22(8), Article 100594. https://doi.org/10.1016/j.mcpro.2023.100594
Lyu, J., Torchia, C., Post, H., Moran Torres, J. P., Altelaar, A. F. M., de Cock, H., & Wösten, H. A. B. (2023). The α-(1,3)-glucan synthase gene agsE impacts the secretome of Aspergillus niger. Antonie van Leeuwenhoek, 116(9), 867-882. https://doi.org/10.1007/s10482-023-01853-w
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), Article 7884. https://doi.org/10.3390/ijms24097884
Lyu, J., Tegelaar, M., Post, H., Moran Torres, J., Torchia, C., Altelaar, A. F. M., Bleichrodt, R.-J., de Cock, H., Lugones, L. G., & Wösten, H. A. B. (2023). Heterogeneity in Spore Aggregation and Germination Results in Different Sized, Cooperative Microcolonies in an Aspergillus niger Culture. mBio, 14(1), 1-20. Article e0087022. https://doi.org/10.1128/mbio.00870-22

2022

Scholarly publications

Morthorst, S. K., Nielsen, C., Farinelli, P., Anvarian, Z., Rasmussen, C. B. R., Serra-Marques, A., Grigoriev, I., Altelaar, M., Fürstenberg, N., Ludwig, A., Akhmanova, A., Christensen, S. T., & Pedersen, L. B. (2022). Angiomotin isoform 2 promotes binding of PALS1 to KIF13B at primary cilia and regulates ciliary length and signaling. Journal of Cell Science, 135(12), 1-10. Article jcs259471. https://doi.org/10.1242/jcs.259471
Linder, S., Hoogstraat, M., Stelloo, S., Eickhoff, N., Schuurman, K., de Barros, H., Alkemade, M., Bekers, E. M., Severson, T. M., Sanders, J., Huang, C. C. F., Morova, T., Altintas, U. B., Hoekman, L., Kim, Y., Baca, S. C., Sjöström, M., Zaalberg, A., Hintzen, D. C., ... Zwart, W. (2022). Drug-Induced Epigenomic Plasticity Reprograms Circadian Rhythm Regulation to Drive Prostate Cancer toward Androgen Independence. Cancer Discovery, 12(9), 2074-2097. https://doi.org/10.1158/2159-8290.CD-21-0576
van Ruiten, M. S., van Gent, D., Sedeño Cacciatore, Á., Fauster, A., Willems, L., Hekkelman, M. L., Hoekman, L., Altelaar, M., Haarhuis, J. H. I., Brummelkamp, T. R., de Wit, E., & Rowland, B. D. (2022). The cohesin acetylation cycle controls chromatin loop length through a PDS5A brake mechanism. Nature Structural and Molecular Biology, 29(6), 586-591. https://doi.org/10.1038/s41594-022-00773-z
Zhang, Z., Kong, X., Ligtenberg, M. A., van Hal-van Veen, S. E., Visser, N. L., de Bruijn, B., Stecker, K., van der Helm, P. W., Kuilman, T., Hoefsmit, E. P., Vredevoogd, D. W., Apriamashvili, G., Baars, B., Voest, E. E., Klarenbeek, S., Altelaar, M., & Peeper, D. S. (2022). RNF31 inhibition sensitizes tumors to bystander killing by innate and adaptive immune cells. Cell Reports Medicine, 3(6), Article 100655. https://doi.org/10.1016/j.xcrm.2022.100655
Man, J. H. K., van Gelder, C. A. G. H., Breur, M., Okkes, D., Molenaar, D., van der Sluis, S., Abbink, T., Altelaar, M., van der Knaap, M. S., & Bugiani, M. (2022). Cortical Pathology in Vanishing White Matter. Cells, 11(22), 1-19. Article 3581. https://doi.org/10.3390/cells11223581
Soares Lindoso, R., Yousef Yengej, F. A., Völlmy, F., Altelaar, M., Juncosa, E. M., Tsikari, T., Ammerlaan, C. M. E., van Balkom, B., Rookmaaker, M. B., Verhaar, M. C., & Masereeuw, R. (2022). Differentiated kidney tubular cell-derived extracellular vesicles enhance maturation of tubuloids. Journal of Nanobiotechnology, 20(1), 1-15. Article 326. https://doi.org/10.1186/s12951-022-01506-6
Willekers, S., Tessadori, F., van der Vaart, B., Henning, H. H., Stucchi, R., Altelaar, M., Roelen, B. A. J., Akhmanova, A., & Bakkers, J. (2022). The centriolar satellite protein Cfap53 facilitates formation of the zygotic microtubule organizing center in the zebrafish embryo. Development (Cambridge, England), 149(16), 1-13. Article dev198762. https://doi.org/10.1242/dev.198762
Silva, J., Alkan, F., Ramalho, S., Snieckute, G., Prekovic, S., Garcia, A. K., Hernández-Pérez, S., Kammen, R. V. D., Barnum, D., Hoekman, L., Altelaar, M., Zwart, W., Suijkerbuijk, S. J. E., Bekker-Jensen, S., & Faller, W. J. (2022). Ribosome impairment regulates intestinal stem cell identity via ZAKɑ activation. Nature Communications, 13(1), 1-12. Article 4492. https://doi.org/10.1038/s41467-022-32220-4
van der Grein, S. G., Defourny, K. A. Y., Rabouw, H. H., Goerdayal, S. S., van Herwijnen, M. J. C., Wubbolts, R. W., Altelaar, M., van Kuppeveld, F. J. M., & Nolte-'t Hoen, E. N. M. (2022). The encephalomyocarditis virus Leader promotes the release of virions inside extracellular vesicles via the induction of secretory autophagy. Nature Communications, 13(1), 1-14. Article 3625. https://doi.org/10.1038/s41467-022-31181-y
Vargas-Diaz, D., & Altelaar, M. (2022). Automated High-Throughput Method for the Fast, Robust, and Reproducible Enrichment of Newly Synthesized Proteins. Journal of Proteome Research, 21(1), 189-199. https://doi.org/10.1021/acs.jproteome.1c00743
Kip, A. M., Valverde, J. M., Altelaar, M., Heeren, R. M. A., Hundscheid, I. H. R., Dejong, C. H. C., Olde Damink, S. W. M., Balluff, B., & Lenaerts, K. (2022). Combined Quantitative (Phospho)proteomics and Mass Spectrometry Imaging Reveal Temporal and Spatial Protein Changes in Human Intestinal Ischemia–Reperfusion. Journal of Proteome Research, 21(1), 49-66. https://doi.org/10.1021/acs.jproteome.1c00447
Pataskar, A., Champagne, J., Nagel, R., Kenski, J., Laos, M., Michaux, J., Pak, H. S., Bleijerveld, O. B., Mordente, K., Navarro, J. M., Blommaert, N., Nielsen, M. M., Lovecchio, D., Stone, E., Georgiou, G., de Gooijer, M. C., van Tellingen, O., Altelaar, M., Joosten, R. P., ... Agami, R. (2022). Tryptophan depletion results in tryptophan-to-phenylalanine substitutants. Nature, 603(7902), 721-727. https://doi.org/10.1038/s41586-022-04499-2
Apriamashvili, G., Vredevoogd, D. W., Krijgsman, O., Bleijerveld, O. B., Ligtenberg, M. A., de Bruijn, B., Boshuizen, J., Traets, J. J. H., D’Empaire Altimari, D., van Vliet, A., Lin, C. P., Visser, N. L., Londino, J. D., Sanchez-Hodge, R., Oswalt, L. E., Altinok, S., Schisler, J. C., Altelaar, M., & Peeper, D. S. (2022). Ubiquitin ligase STUB1 destabilizes IFNγ-receptor complex to suppress tumor IFNγ signaling. Nature Communications, 13(1), 1-16. Article 1923. https://doi.org/10.1038/s41467-022-29442-x
Castiglioni, V. G., Ramalho, J. J., Kroll, J. R., Stucchi, R., van Beuzekom, H., Schmidt, R., Altelaar, M., & Boxem, M. (2022). Identification and characterization of Crumbs polarity complex proteins in Caenorhabditis elegans. Journal of Biological Chemistry, 298(4), 1-16. Article 101786. https://doi.org/10.1016/j.jbc.2022.101786
Lindoso, R. S., Yengej, F. A. Y., Voellmy, F., Altelaar, M., Juncosa, E. M., Tsikari, T., Ammerlaan, C. M. E., Balkom, B. W. M. V., Verhaar, M. C., & Masereeuw, R. (2022). Differentiated kidney tubular cell-derived extracellular vesicles enhance maturation of tubuloids. (pp. 1-31). bioRxiv. https://doi.org/10.1101/2022.02.08.479621
https://dspace.library.uu.nl/bitstream/handle/1874/420003/2022.02.08.479621v1.full.pdf?sequence=1

2021

Scholarly publications

Varderidou-Minasian, S., Verheijen, B. M., Harschnitz, O., Kling, S., Karst, H., van der Pol, W. L., Pasterkamp, R. J., & Altelaar, M. (2021). Spinal Muscular Atrophy Patient iPSC-Derived Motor Neurons Display Altered Proteomes at Early Stages of Differentiation. ACS Omega, 6(51), 35375-35388. https://doi.org/10.1021/acsomega.1c04688
Mayayo-Peralta, I., Faggion, B., Hoekman, L., Morris, B., Lieftink, C., Goldsbrough, I., Buluwela, L., Siefert, J. C., Post, H., Altelaar, M., Beijersbergen, R., Ali, S., Zwart, W., & Prekovic, S. (2021). Ribociclib Induces Broad Chemotherapy Resistance and EGFR Dependency in ESR1 Wildtype and Mutant Breast Cancer. Cancers, 13(24), 1-15. Article 6314. https://doi.org/10.3390/cancers13246314
Filez, M., Caratelli, C., Rivera-Torrente, M., Muniz-Miranda, F., Hoek, M., Altelaar, M., Heck, A. J. R., Van Speybroeck, V., & Weckhuysen, B. M. (2021). Elucidation of the pre-nucleation phase directing metal-organic framework formation. Cell Reports Physical Science, 2(12), 1-16. Article 100680. https://doi.org/10.1016/j.xcrp.2021.100680
Martín-Alonso, M., Iqbal, S., Vornewald, P. M., Lindholm, H. T., Damen, M. J., Martínez, F., Hoel, S., Díez-Sánchez, A., Altelaar, M., Katajisto, P., Arroyo, A. G., & Oudhoff, M. J. (2021). Smooth muscle-specific MMP17 (MT4-MMP) regulates the intestinal stem cell niche and regeneration after damage. Nature Communications, 12(1), 1-17. Article 6741. https://doi.org/10.1038/s41467-021-26904-6
Champagne, J., Pataskar, A., Blommaert, N., Nagel, R., Wernaart, D., Ramalho, S., Kenski, J., Bleijerveld, O. B., Zaal, E. A., Berkers, C. R., Altelaar, M., Peeper, D. S., Faller, W. J., & Agami, R. (2021). Oncogene-dependent sloppiness in mRNA translation. Molecular Cell, 81(22), 4709-4721. https://doi.org/10.1016/j.molcel.2021.09.002
Van Gelder, C. A. G. H., & Altelaar, M. (2021). Neuroproteomics of the synapse: Subcellular quantification of protein networks and signaling dynamics. Molecular and Cellular Proteomics, 20, 1-18. Article 100087. https://doi.org/10.1016/J.MCPRO.2021.100087
Sato, K., Martin-Pintado, N., Post, H., Altelaar, M., & Knipscheer, P. (2021). Multistep mechanism of G-quadruplex resolution during DNA replication. Science advances, 7(39), 1-17. Article eabf8653. https://doi.org/10.1126/sciadv.abf8653
Li, L., Ugalde, A. P., Scheele, C. L. G. J., Dieter, S. M., Nagel, R., Ma, J., Pataskar, A., Korkmaz, G., Elkon, R., Chien, M.-P., You, L., Su, P.-R., Bleijerveld, O. B., Altelaar, M., Momchev, L., Manber, Z., Han, R., van Breugel, P. C., Lopes, R., ... Agami, R. (2021). A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis. Genome Biology, 22(1), 1-28. Article 54. https://doi.org/10.1186/s13059-021-02272-8
de Krijger, I., Föhr, B., Pérez, S. H., Vincendeau, E., Serrat, J., Thouin, A. M., Susvirkar, V., Lescale, C., Paniagua, I., Hoekman, L., Kaur, S., Altelaar, M., Deriano, L., Faesen, A. C., & Jacobs, J. J. L. (2021). MAD2L2 dimerization and TRIP13 control shieldin activity in DNA repair. Nature Communications, 12(1), Article 5421. https://doi.org/10.1038/s41467-021-25724-y
Lindhout, F. W., Portegies, S., Kooistra, R., Herstel, L. J., Stucchi, R., Hummel, J. J. A., Scheefhals, N., Katrukha, E. A., Altelaar, M., MacGillavry, H. D., Wierenga, C. J., & Hoogenraad, C. C. (2021). Centrosome-mediated microtubule remodeling during axon formation in human iPSC-derived neurons. EMBO Journal, 40(10), 1-17. Article e106798. https://doi.org/10.15252/embj.2020106798
Remmelzwaal, S., Geisler, F., Stucchi, R., van der Horst, S., Pasolli, M., Kroll, J. R., Jarosinska, O. D., Akhmanova, A., Richardson, C. A., Altelaar, M., Leube, R. E., Ramalho, J. J., & Boxem, M. (2021). BBLN-1 is essential for intermediate filament organization and apical membrane morphology. Current Biology, 31(11), 2334-2346.e9. https://doi.org/10.1016/j.cub.2021.03.069
van der Zwet, J. C. G., Buijs-Gladdines, J. G. C. A. M., Cordo’, V., Debets, D. O., Smits, W. K., Chen, Z., Dylus, J., Zaman, G. J. R., Altelaar, M., Oshima, K., Bornhauser, B., Bourquin, J. P., Cools, J., Ferrando, A. A., Vormoor, J., Pieters, R., Vormoor, B., & Meijerink, J. P. P. (2021). MAPK-ERK is a central pathway in T-cell acute lymphoblastic leukemia that drives steroid resistance. Leukemia, 35(12), 3394-3405. https://doi.org/10.1038/s41375-021-01291-5
Buijs, R. R., Hummel, J. J. A., Burute, M., Pan, X., Cao, Y., Stucchi, R., Altelaar, M., Akhmanova, A., Kapitein, L. C., & Hoogenraad, C. C. (2021). WDR47 protects neuronal microtubule minus ends from katanin-mediated severing. Cell Reports, 36(2), 1-e7. Article 109371. https://doi.org/10.1016/j.celrep.2021.109371
Prekovic, S., Schuurman, K., Mayayo-Peralta, I., Manjón, A. G., Buijs, M., Yavuz, S., Wellenstein, M. D., Barrera, A., Monkhorst, K., Huber, A., Morris, B., Lieftink, C., Chalkiadakis, T., Alkan, F., Silva, J., Győrffy, B., Hoekman, L., van den Broek, B., Teunissen, H., ... Zwart, W. (2021). Glucocorticoid receptor triggers a reversible drug-tolerant dormancy state with acquired therapeutic vulnerabilities in lung cancer. Nature Communications, 12(1), 1-18. Article 4360. https://doi.org/10.1038/s41467-021-24537-3
Li, B., Kong, X., Post, H., Raaijmakers, L., Peeper, D. S., & Altelaar, M. (2021). Proteomics and Phosphoproteomics Profiling of Drug-Addicted BRAFi-Resistant Melanoma Cells. Journal of Proteome Research, 20(9), 4381-4392. https://doi.org/10.1021/acs.jproteome.1c00331
Jamalpoor, A., van Gelder, C. A. G. H., Yousef Yengej, F. A., Zaal, E. A., Berlingerio, S. P., Veys, K. R., Pou Casellas, C., Voskuil, K., Essa, K., Ammerlaan, C. M. E., Rega, L. R., van der Welle, R. E. N., Lilien, M. R., Rookmaaker, M. B., Clevers, H., Klumperman, J., Levtchenko, E., Berkers, C. R., Verhaar, M. C., ... Janssen, M. J. (2021). Cysteamine–bicalutamide combination therapy corrects proximal tubule phenotype in cystinosis. EMBO Molecular Medicine, 13(7), 1-20. Article e13067. https://doi.org/10.15252/emmm.202013067
Zahavi, E. E., Hummel, J. J. A., Han, Y., Bar, C., Stucchi, R., Altelaar, M., & Hoogenraad, C. C. (2021). Combined kinesin-1 and kinesin-3 activity drives axonal trafficking of TrkB receptors in Rab6 carriers. Developmental Cell, 56(4), 494-508.E7. https://doi.org/10.1016/j.devcel.2021.01.010
Lema A, S., Klemenčič, M., Völlmy, F., Altelaar, M., & Funk, C. (2021). The Role of Pseudo-Orthocaspase (SyOC) of Synechocystis sp. PCC 6803 in Attenuating the Effect of Oxidative Stress. Frontiers in Microbiology, 12, 1-13. Article 634366. https://doi.org/10.3389/fmicb.2021.634366
Brunner, A. M., Lössl, P., Geurink, P. P., Ovaa, H., Albanese, P., Altelaar, A. F. M., Heck, A. J. R., & Scheltema, R. A. (2021). Quantifying Positional Isomers (QPI) by top-down mass spectrometry. Molecular and Cellular Proteomics, 20, 1-11. Article 100070. https://doi.org/10.1016/J.MCPRO.2021.100070
Bartok, O., Pataskar, A., Nagel, R., Laos, M., Goldfarb, E., Hayoun, D., Levy, R., Körner, P.-R., Kreuger, I. Z. M., Champagne, J., Zaal, E. A., Bleijerveld, O. B., Huang, X., Kenski, J., Wargo, J., Brandis, A., Levin, Y., Mizrahi, O., Alon, M., ... Agami, R. (2021). Anti-tumour immunity induces aberrant peptide presentation in melanoma. Nature, 590(7845), 332–337. https://doi.org/10.1038/s41586-020-03054-1

2020

Scholarly publications

Jamalpoor, A., van Gelder, C. A. G. H., Yousef Yengej, F. A., Zaal, E. A., Berlingerio, S. P., Veys, K. R., Pou Casellas, C., Voskuil, K., Essa, K., Ammerlaan, C., Rega, L. R., van der Welle, R., Lilien, M. R., Rookmaaker, M. B., Clevers, H. C., Klumperman, J., Levtchenko, E., Berkers, C. R., Verhaar, M. C., ... Janssen, M. J. (2020). Cysteamine-bicalutamide combination treatment restores alpha-ketoglutarate and corrects proximal tubule phenotype in cystinosis. (pp. 1-53). bioRxiv. https://doi.org/10.1101/2020.02.10.941799
Vredevoogd, D. W., Kuilman, T., Ligtenberg, M. A., Boshuizen, J., Stecker, K. E., de Bruijn, B., Krijgsman, O., Huang, X., Kenski, J. C. N., Lacroix, R., Mezzadra, R., Gomez-Eerland, R., Yildiz, M., Dagidir, I., Apriamashvili, G., Zandhuis, N., van der Noort, V., Visser, N. L., Blank, C. U., ... Peeper, D. S. (2020). Correction: Augmenting Immunotherapy Impact by Lowering Tumor TNF Cytotoxicity Threshold. Cell, 180(2), 404-405. https://doi.org/10.1016/j.cell.2020.01.005
Pancholi, S., Ribas, R., Simigdala, N., Schuster, E., Nikitorowicz-Buniak, J., Ressa, A., Gao, Q., Leal, M. F., Bhamra, A., Thornhill, A., Morisset, L., Montaudon, E., Sourd, L., Fitzpatrick, M., Altelaar, M., Johnston, S. R., Marangoni, E., Dowsett, M., & Martin, L.-A. (2020). Tumour kinome re-wiring governs resistance to palbociclib in oestrogen receptor positive breast cancers, highlighting new therapeutic modalities. Oncogene, 39(25), 4781-4797. https://doi.org/10.1038/s41388-020-1284-6
Aher, A., Rai, D., Schaedel, L., Gaillard, J., John, K., Liu, Q., Altelaar, M., Blanchoin, L., Thery, M., & Akhmanova, A. (2020). CLASP Mediates Microtubule Repair by Restricting Lattice Damage and Regulating Tubulin Incorporation. Current Biology, 30(11), 2175-2183. Article e6. https://doi.org/10.1016/j.cub.2020.03.070
Varderidou-Minasian, S., Hinz, L., Hagemans, D., Posthuma, D., Altelaar, M., & Heine, V. M. (2020). Quantitative proteomic analysis of Rett iPSC-derived neuronal progenitors. Molecular Autism, 11(1), Article 38. https://doi.org/10.1186/s13229-020-00344-3
van Gelder, C. A. G. H., Penning, R., Veth, T. S., Catsburg, L. A. E., Hoogenraad, C. C., MacGillavry, H. D., & Altelaar, M. (2020). Temporal Quantitative Proteomics of mGluR-induced Protein Translation and Phosphorylation in Neurons. Molecular and Cellular Proteomics, 19(12), 1952-1967. https://doi.org/10.1074/mcp.RA120.002199
Varderidou-Minasian, S., Verheijen, B. M., Schätzle, P., Hoogenraad, C. C., Pasterkamp, R. J., & Altelaar, M. (2020). Deciphering the Proteome Dynamics during Development of Neurons Derived from Induced Pluripotent Stem Cells. Journal of Proteome Research, 19( 6), 2391-2403. https://doi.org/10.1021/acs.jproteome.0c00070
Lindhout, F. W., Kooistra, R., Portegies, S., Herstel, L. J., Stucchi, R., Snoek, B. L., Altelaar, M., MacGillavry, H. D., Wierenga, C. J., & Hoogenraad, C. C. (2020). Quantitative mapping of transcriptome and proteome dynamics during polarization of human iPSC-derived neurons. eLife, 9. https://doi.org/10.7554/eLife.58124
He, L., Kooistra, R., Das, R., Oudejans, E., van Leen, E., Ziegler, J., Portegies, S., de Haan, B., Altena, A. V. R., Stucchi, R., Altelaar, A. F. M., Wieser, S., Krieg, M., Hoogenraad, C. C., & Harterink, M. (2020). Cortical anchoring of the microtubule cytoskeleton is essential for neuron polarity. eLife, 9, Article e55111. https://doi.org/10.7554/eLife.55111
Cao, Y., Lipka, J., Stucchi, R., Burute, M., Pan, X., Portegies, S., Tas, R., Willems, J., Will, L., MacGillavry, H., Altelaar, M., Kapitein, L. C., Harterink, M., & Hoogenraad, C. C. (2020). Microtubule Minus-End Binding Protein CAMSAP2 and Kinesin-14 Motor KIFC3 Control Dendritic Microtubule Organization. Current Biology, 30(5), 899-908.e6. https://doi.org/10.1016/j.cub.2019.12.056
Schmidlin, T., & Altelaar, M. (2020). Effects of electron-transfer/higher-energy collisional dissociation (EThcD) on phosphopeptide analysis by data-independent acquisition. International Journal of Mass Spectrometry, 452, 1-9. Article 116336. https://doi.org/10.1016/j.ijms.2020.116336
Ferrari, L., Stucchi, R., Konstantoulea, K., van de Kamp, G., Kos, R., Geerts, W. J. C., van Bezouwen, L. S., Förster, F. G., Altelaar, M., Hoogenraad, C. C., & Rüdiger, S. G. D. (2020). Arginine π-stacking drives binding to fibrils of the Alzheimer protein Tau. Nature Communications, 11(1), 1-13. Article 571. https://doi.org/10.1038/s41467-019-13745-7
Rontogianni, S., Iskit, S., van Doorn, S., Peeper, D. S., & Altelaar, M. (2020). Combined EGFR and ROCK inhibition in TNBC leads to cell death via impaired autophagic flux. Molecular and Cellular Proteomics, 19(2), 261-277. https://doi.org/10.1074/mcp.RA119.001800

2019

Scholarly publications

Ferrari, L., Stucci, R., Konstantoulea, A., van, D. K. G., Kos, R., Geerts, WJ., Forster, FG., Altelaar, M., Hoogenraad, C., & Rudiger, SG. (2019, Jan). Fibril formation rewires interactome of the Alzheimer protein Tau by π-stacking. https://doi.org/10.1101/522284
Kierkels, G. J. J., Scheper, W., Meringa, A. D., Johanna, I., Beringer, D. X., Janssen, A., Schiffler, M., Aarts-Riemens, T., Kramer, L., Straetemans, T., Heijhuurs, S., Leusen, J. H. W., San José, E., Fuchs, K., Griffioen, M., Falkenburg, J. H., Bongiovanni, L., de Bruin, A., Vargas-Diaz, D., ... Kuball, J. (2019). Identification of a tumor-specific allo-HLA-restricted γδTCR. Blood advances, 3(19), 2870-2882. https://doi.org/10.1182/bloodadvances.2019032409
Schmidlin, T., Debets, D. O., van Gelder, C. A. G. H., Stecker, K. E., Rontogianni, S., van den Eshof, B. L., Kemper, K., Lips, E. H., van den Biggelaar, M., Peeper, D. S., Heck, A. J. R., & Altelaar, M. (2019). High-Throughput Assessment of Kinome-wide Activation States. Cell Systems, 9(4), 366-374. https://doi.org/10.1016/j.cels.2019.08.005
Rontogianni, S., Synadaki, E., Li, B., Liefaard, M. C., Lips, E. H., Wesseling, J., Wu, W., & Altelaar, M. (2019). Proteomic profiling of extracellular vesicles allows for human breast cancer subtyping. Communications Biology, 2, Article 325. https://doi.org/10.1038/s42003-019-0570-8
Fréal, A., Rai, D., Tas, R. P., Pan, X., Katrukha, E. A., van de Willige, D., Stucchi, R., Aher, A., Yang, C., Altelaar, A. F. M., Vocking, K., Post, J. A., Harterink, M., Kapitein, L. C., Akhmanova, A., & Hoogenraad, C. C. (2019). Feedback-Driven Assembly of the Axon Initial Segment. Neuron, 104(2), P305-321.E8. https://doi.org/10.1016/j.neuron.2019.07.029
Bastos, A. E. P., Costa, P. F., Varderidou-Minasian, S., Altelaar, M., & Lima, P. A. (2019). Feeding cycle alters the biophysics and molecular expression of voltage-gated Na+ currents in rat hippocampal CA1 neurones. European Journal of Neuroscience, 49(11), 1418-1435. https://doi.org/10.1111/ejn.14331
Farías, G. G., Fréal, A., Tortosa, E., Stucchi, R., Pan, X., Portegies, S., Will, L., Altelaar, M., & Hoogenraad, C. C. (2019). Feedback-Driven Mechanisms between Microtubules and the Endoplasmic Reticulum Instruct Neuronal Polarity. Neuron, 102(1), 184-201.e8. https://doi.org/10.1016/j.neuron.2019.01.030
Hooikaas, P. J., Martin, M., Mühlethaler, T., Kuijntjes, G. J., Peeters, C. A. E., Katrukha, E. A., Ferrari, L., Stucchi, R., Verhagen, D. G. F., Van Riel, W. E., Grigoriev, I., Altelaar, A. F. M., Hoogenraad, C. C., Rüdiger, S. G. D., Steinmetz, M. O., Kapitein, L. C., & Akhmanova, A. (2019). MAP7 family proteins regulate kinesin-1 recruitment and activation. Journal of Cell Biology, 218(4), 1298-1318. https://doi.org/10.1083/jcb.201808065
Vlaming, H., McLean, C. M., Korthout, T., Alemdehy, M. F., Hendriks, S., Lancini, C., Palit, S., Klarenbeek, S., Kwesi-Maliepaard, E. M., Molenaar, T. M., Hoekman, L., Schmidlin, T. T., Altelaar, AF. M., van Welsem, T., Dannenberg, J. H., Jacobs, H., & van Leeuwen, F. (2019). Conserved crosstalk between histone deacetylation and H3K79 methylation generates DOT1L-dose dependency in HDAC1-deficient thymic lymphoma. EMBO Journal, 38(14), Article e101564. https://doi.org/10.15252/embj.2019101564
Adamopoulos, A., Landskron, L., Heidebrecht, T., Tsakou, F., Bleijerveld, O. B., Altelaar, M., Nieuwenhuis, J., Celie, P. H. N., Brummelkamp, T. R., & Perrakis, A. (2019). Crystal structure of the tubulin tyrosine carboxypeptidase complex VASH1–SVBP. Nature Structural and Molecular Biology, 26(7), 567-570. https://doi.org/10.1038/s41594-019-0254-6
Vredevoogd, D. W., Kuilman, T., Ligtenberg, M. A., Boshuizen, J., Stecker, K. E., de Bruijn, B., Krijgsman, O., Huang, X., Kenski, J. C. N., Lacroix, R., Mezzadra, R., Gomez-Eerland, R., Yildiz, M., Dagidir, I., Apriamashvili, G., Zandhuis, N., van der Noort, V., Visser, N. L., Blank, C. U., ... Peeper, D. S. (2019). Augmenting Immunotherapy Impact by Lowering Tumor TNF Cytotoxicity Threshold. Cell, 178(3), 585-599.e15. https://doi.org/10.1016/j.cell.2019.06.014
Lindhout, F. W., Cao, Y., Kevenaar, J. T., Bodzęta, A., Stucchi, R., Boumpoutsari, M. M., Katrukha, E. A., Altelaar, M., MacGillavry, H. D., & Hoogenraad, C. C. (2019). VAP-SCRN1 interaction regulates dynamic endoplasmic reticulum remodeling and presynaptic function. EMBO Journal, 38(20), Article e101345. https://doi.org/10.15252/embj.2018101345
Ressa, A., Fitzpatrick, M., Van den Toorn, H., Heck, A. J. R., & Altelaar, M. (2019). PaDuA: a Python library for high-throughput (phospho)proteomic data analysis. Journal of Proteome Research, 18, 576-584. https://doi.org/10.1021/acs.jproteome.8b00576
Aerts, D., van den Bergh, S. G., Post, H., Altelaar, M. A. F., Arentshorst, M., Ram, A. F. J., Ohm, R. A., & Wösten, H. A. B. (2019). FlbA-Regulated Gene rpnR Is Involved in Stress Resistance and Impacts Protein Secretion when Aspergillus niger Is Grown on Xylose. Applied and Environmental Microbiology, 85(2), 1-12. Article e02282-18. https://doi.org/10.1128/AEM.02282-18
Baroni, L., Pollo-Oliveira, L., Heck, A. J., Altelaar, M., & Yatsuda, A. P. (2019). Actin from the apicomplexan Neospora caninum (NcACT) has different isoforms in 2D electrophoresis. Parasitology, 146(1), 33-41. https://doi.org/10.1017/S0031182018000872

2018

Scholarly publications

Ressa, A., Bosdriesz, E., de Ligt, J., Mainardi, S., Maddalo, G., Prahallad, A., Jager, M., de la Fonteijne, L., Fitzpatrick, M. A., Groten, S., Altelaar, A. F. M., Bernards, R., Cuppen, E., Wessels, L. F. A., & Heck, A. J. R. (2018). A system-wide approach to monitor responses to synergistic BRAF and EGFR inhibition in colorectal cancer cells. bioRxiv. https://doi.org/10.1101/194845
Cunha-Ferreira, I., Chazeau, A., Buijs, R. R., Stucchi, R., Will, L., Pan, X., Adolfs, Y., van der Meer, C., Wolthuis, J. C., Kahn, O. I., Schätzle, P., Altelaar, M., Pasterkamp, R. J., Kapitein, L. C., & Hoogenraad, C. C. (2018). The HAUS Complex Is a Key Regulator of Non-centrosomal Microtubule Organization during Neuronal Development. Cell Reports, 24(4), 791-800. https://doi.org/10.1016/j.celrep.2018.06.093
Spel, L., Nieuwenhuis, J., Haarsma, R., Stickel, E., Bleijerveld, O. B., Altelaar, M., Boelens, J. J., Brummelkamp, T. R., Nierkens, S., & Boes, M. (2018). Nedd4 Binding Protein 1 (N4BP1) and TNFAIP3 Interacting Protein 1 (TNIP1) control MHC-1 display in neuroblastoma. Cancer Research, 78(23), 6621–6631. https://doi.org/10.1158/0008-5472.CAN-18-0545
Stucchi, R., Plucińska, G., Hummel, J. J. A., Zahavi, E. E., Guerra San Juan, I., Klykov, O., Scheltema, R. A., Altelaar, A. F. M., & Hoogenraad, C. C. (2018). Regulation of KIF1A-Driven Dense Core Vesicle Transport: Ca2+/CaM Controls DCV Binding and Liprin-α/TANC2 Recruits DCVs to Postsynaptic Sites. Cell Reports, 24(3), 685-700. https://doi.org/10.1016/j.celrep.2018.06.071
Zagorac, I., Fernandez-Gaitero, S., Penning, R., Post, H., Bueno, M. J., Mouron, S., Manso, L., Morente, M. M., Alonso, S., Serra, V., Muñoz, J., Gómez-López, G., Lopez-Acosta, J. F., Jimenez-Renard, V., Gris-Oliver, A., Al-Shahrour, F., Piñeiro-Yañez, E., Montoya-Suarez, J. L., Apala, J. V., ... Quintela-Fandino, M. (2018). In vivo phosphoproteomics reveals kinase activity profiles that predict treatment outcome in triple-negative breast cancer. Nature Communications, 9(1), Article 3501. https://doi.org/10.1038/s41467-018-05742-z
Pontes, M. V. A., Patyshakuliyeva, A., Post, H., Jurak, E., Hildén, K. S., Altelaar, M., Heck, A., Kabel, M. A., de Vries, R. P., & Mäkelä, M. R. (2018). The physiology of Agaricus bisporus in semi-commercial compost cultivation appears to be highly conserved among unrelated isolates. Fungal Genetics and Biology, 112, 12-20. https://doi.org/10.1016/j.fgb.2017.12.004
Simonetta, M., de Krijger, I., Serrat, J., Moatti, N., Fortunato, D., Hoekman, L., Bleijerveld, O. B., Altelaar, A. F. M., & Jacobs, J. J. L. (2018). H4K20me2 distinguishes pre-replicative from post-replicative chromatin to appropriately direct DNA repair pathway choice by 53BP1-RIF1-MAD2L2. Cell Cycle, 17(1), 124-136. https://doi.org/10.1080/15384101.2017.1404210
Stelloo, S., Nevedomskaya, E., Kim, S.-Y., Hoekman, L., Bleijerveld, O. B., Mirza, T., Wessels, L. F. A., van Weerden, W. M., Altelaar, A. F. M., Bergman, A. M., & Zwart, W. (2018). Endogenous androgen receptor proteomic profiling reveals genomic subcomplex involved in prostate tumorigenesis. Oncogene, 37, 313–322. https://doi.org/10.1038/onc.2017.330

2017

Scholarly publications

Wisse, L. E., Penning, R., Zaal, E. A., van Berkel, C. G. M., ter Braak, T. J., Polder, E., Kenney, J. W., Proud, C. G., Berkers, C. R., Altelaar, M. A. F., Speijer, D., van der Knaap, M. S., & Abbink, T. E. M. (2017). Proteomic and metabolomic analyses of vanishing white matter mouse astrocytes reveal deregulation of ER functions. Frontiers in Cellular Neuroscience, 11, Article 411. https://doi.org/10.3389/fncel.2017.00411
Nieuwenhuis, J., Adamopoulos, A., Bleijerveld, O. B., Mazouzi, A., Stickel, E., Celie, P., Altelaar, M., Knipscheer, P., Perrakis, A., Blomen, V. A., & Brummelkamp, T. R. (2017). Vasohibins encode tubulin detyrosinating activity. Science, 358(6369), 1453-1456. https://doi.org/10.1126/science.aao5676
Brockmann, M., Blomen, V. A., Nieuwenhuis, J., Stickel, E., Raaben, M., Bleijerveld, O. B., Altelaar, A. F. M., Jae, L. T., & Brummelkamp, T. R. (2017). Genetic wiring maps of single-cell protein states reveal an off-switch for GPCR signalling. Nature, 546(7657), 307-311. https://doi.org/10.1038/nature22376
Niklasson, M., Maddalo, I., Sramkova, Z., Mutlu, E., Wee, S., Sekyrova, P., Schmidt, L., Fritz, N., Dehnisch, I., Kyriatzis, G., Krafcikova, M., Carson, B. B., Feenstra, J. M., Marinescu, V. D., Segerman, A., Haraldsson, M., Gustavsson, A. L., Hammarström, J. G. J., Jenmalm Jensen, A., ... Andang, M. (2017). Membrane-depolarizing channel blockers induce selective glioma cell death by impairing nutrient transport and unfolded protein/amino acid responses. Cancer Research, 77(7), 1741-1752. https://doi.org/10.1158/0008-5472.CAN-16-2274
Jiang, K., Rezabkova, L., Hua, S., Liu, Q., Capitani, G., Altelaar, M., Heck, A. J. R., Kammerer, R. A., Steinmetz, M. O., & Akhmanova, A. (2017). Microtubule minus-end regulation at spindle poles by an ASPM-katanin complex. Nature Cell Biology, 19(5), 480-492. https://doi.org/10.1038/ncb3511
Mäkelä, M. R., Bouzid, O., Ruiz-Robleto, J., Post, H., Peng, M., Heck, A., Altelaar, M., & de Vries, R. P. (2017). Cultivation of Podospora anserina on soybean hulls results in an efficient enzyme cocktail for plant biomass hydrolysis. New Biotechnology, 37(Part B), 162-171. https://doi.org/10.1016/j.nbt.2017.02.002
Vega, F. M., Gautier, V., Fernandez-Ponce, C. M., Extremera, M. J., Altelaar, A. F. M., Millan, J., Tellez, J. C., Hernandez-Campos, J. A., Conejero, R., Bolivar, J., Pardal, R., Garcia-Cózar, F. J., Aguado, E., Heck, A. J. R., & Duran-Ruiz, M. C. (2017). The atheroma plaque secretome stimulates the mobilization of endothelial progenitor cells ex vivo. Journal of Molecular and Cellular Cardiology, 105, 12-23. https://doi.org/10.1016/j.yjmcc.2017.02.001
Frese, C. K., Mikhaylova, M., Stucchi, R., Gautier, V., Liu, Q., Mohammed, S., Heck, A. J. R., Altelaar, A. F. M., & Hoogenraad, C. C. (2017). Quantitative Map of Proteome Dynamics during Neuronal Differentiation. Cell Reports, 18(6), 1527-1542. https://doi.org/10.1016/j.celrep.2017.01.025
Post, H., Penning, R., Fitzpatrick, M., Garrigues, L. B., Wu, W., Mac Gillavry, H. D., Hoogenraad, C. C., Heck, A. J. R., & Altelaar, A. F. M. (2017). Robust, Sensitive, and Automated Phosphopeptide Enrichment Optimized for Low Sample Amounts Applied to Primary Hippocampal Neurons. Journal of Proteome Research, 16(2), 728-737. https://doi.org/10.1021/acs.jproteome.6b00753
Tsiatsiani, L., Giansanti, P., Scheltema, R. A., van den Toorn, H., Overall, C. M., Altelaar, A. F. M., & Heck, A. J. R. (2017). Opposite Electron-Transfer Dissociation and Higher-Energy Collisional Dissociation Fragmentation Characteristics of Proteolytic K/R(X)n and (X)nK/R Peptides Provide Benefits for Peptide Sequencing in Proteomics and Phosphoproteomics. Journal of Proteome Research, 16(2), 852-861. https://doi.org/10.1021/acs.jproteome.6b00825
https://dspace.library.uu.nl/bitstream/handle/1874/396065/10.1021acs.jproteome.6b00825_Tsiatsiani_et_al_2017_JPR.pdf?sequence=1

2016

Scholarly publications

Bouchet, B. P., Gough, R. E., Ammon, Y.-C., van de Willige, D., Post, H., Jacquemet, G., Altelaar, M., Heck, A. J., Goult, B. T., & Akhmanova, A. (2016). Talin-KANK1 interaction controls the recruitment of cortical microtubule stabilizing complexes to focal adhesions. (pp. 1-23). (eLife). eLife Sciences Publications. https://doi.org/10.7554/eLife.18124
Vlaming, H., Molenaar, T., van Welsem, T., Poramba-Liyanage, D., Smith, D., Velds, A., Hoekman, L., Korthout, T., Hendriks, S., Altelaar, A. F. M., & van Leeuwen, F. (2016). Direct screening for chromatin status on DNA barcodes in yeast delineates the regulome of H3K79 methylation by Dot1. eLife, 5(e18919), 1-22. https://doi.org/10.7554/eLife.18919
Isogai, T., Van Der Kammen, R., Bleijerveld, O. B., Goerdayal, S. S., Argenzio, E., Altelaar, A. F. M., & Innocenti, M. (2016). Quantitative Proteomics Illuminates a Functional Interaction between mDia2 and the Proteasome. Journal of Proteome Research, 15(12), 4624-4637. https://doi.org/10.1021/acs.jproteome.6b00718
Zuko, A., Oguro-Ando, A., Post, H., Taggenbrock, R. L. R. E., van Dijk, R. E., Altelaar, A. F. M., Heck, A. J. R., Petrenko, A. G., van der Zwaag, B., Shimoda, Y., Pasterkamp, R. J., & Burbach, J. P. H. (2016). Association of Cell Adhesion Molecules Contactin-6 and Latrophilin-1 Regulates Neuronal Apoptosis. Frontiers in Molecular Neuroscience, 9. https://doi.org/10.3389/fnmol.2016.00143
Groot Kormelink, T., Arkesteijn, G. J. A., van de Lest, C. H. A., Geerts, W. J. C., Goerdayal, S., Altelaar, M. A. F., Redegeld, F. A., Nolte-'t Hoen, E. N. M., & Wauben, M. H. M. (2016). Mast Cell Degranulation Is Accompanied by the Release of a Selective Subset of Extracellular Vesicles That Contain Mast Cell-Specific Proteases. Journal of Immunology, 197(8), 3382-3392. https://doi.org/10.4049/jimmunol.1600614
Wu, J., de Heus, C., Liu, Q., Bouchet, B. P., Noordstra, I., Jiang, K., Hua, S., Martin, M., Yang, C., Grigoriev, I., Katrukha, E. A., Altelaar, A. F. M., Hoogenraad, C. C., Qi, R. Z., Klumperman, J., & Akhmanova, A. (2016). Molecular Pathway of Microtubule Organization at the Golgi Apparatus. Developmental Cell, 39(1), 44–60. https://doi.org/10.1016/j.devcel.2016.08.009
Parreira, J. R., Bouraada, J., Fitzpatrick, M. A., Silvestre, S., Bernardes da Silva, A., Marques da Silva, J., Almeida, A. M., Fevereiro, P., Altelaar, A. F. M., & Araújo, S. S. (2016). Differential proteomics reveals the hallmarks of seed development in common bean (Phaseolus vulgaris L.). Journal of Proteomics, 143, 188-198. https://doi.org/10.1016/j.jprot.2016.03.002
Kemper, K., Krijgsman, O., Kong, X., Cornelissen-Steijger, P., Shahrabi, A., Weeber, F., van der Velden, D. L., Bleijerveld, O. B., Kuilman, T., Kluin, R. J. C., Sun, C., Voest, E. E., Ju, Y. S., Schumacher, T. N. M., Altelaar, A. F. M., McDermott, U., Adams, D. J., Blank, C. U., Haanen, J. B., & Peeper, D. S. (2016). BRAF(V600E) Kinase Domain Duplication Identified in Therapy-Refractory Melanoma Patient-Derived Xenografts. Cell Reports [E], 16(1), 263-277. https://doi.org/10.1016/j.celrep.2016.05.064
van Herwijnen, M. J. C., Zonneveld, M. I., Goerdayal, S., Nolte-'t Hoen, E. N. M., Garssen, J., Stahl, B., Altelaar, A. F. M., Redegeld, F. A., & Wauben, M. H. M. (2016). Comprehensive proteomic analysis of human milk-derived extracellular vesicles unveils a novel functional proteome distinct from other milk components. Molecular & Cellular Proteomics, 15(11), 3412-3423. https://doi.org/10.1074/mcp.M116.060426
Guerreiro, A. C. L., Penning, R., Raaijmakers, L. M., Axman, I. M., Heck, A. J. R., & Altelaar, A. F. M. (2016). Monitoring light/dark association dynamics of multi-protein complexes in cyanobacteria using size exclusion chromatography-based proteomics. Journal of Proteomics, 142, 33-44. https://doi.org/10.1016/j.jprot.2016.04.030
Schmidlin, T., Garrigues, L., Lane, C. S., Mulder, T. C., van Doorn, S., Post, H., de Graaf, E. L., Lemeer, S., Heck, A. J. R., & Altelaar, A. F. M. (2016). Assessment of SRM, MRM(3) and DIA for the targeted analysis of phosphorylation dynamics in non-small cell lung cancer. Proteomics, 16(15-16), 2193–2205. https://doi.org/10.1002/pmic.201500453

2015

Scholarly publications

Van Herwijnen, M., Zonneveld, M., Goerdayal, S., Altelaar, M., Hoen, E. N., Garssen, J., Redegeld, F., & Wauben, M. (2015). In-depth proteomics analysis of human breast milk-derived extracellular vesicles to reveal their origin and targets in the infant's developing immune system. Journal of Extracellular Vesicles, 4, 81. https://doi.org/10.3402/jev.v4.27783
Ameziane, N., May, P., Haitjema, A., Van De Vrugt, H. J., Van Rossum-Fikkert, S. E., Ristic, D., Williams, G. J., Balk, J., Rockx, D., Li, H., Rooimans, M. A., Oostra, A. B., Velleuer, E., Dietrich, R., Bleijerveld, O. B., Altelaar, M., Meijers-Heijboer, H., Joenje, H., Glusman, G., ... Dorsman, J. C. (2015). A novel Fanconi anaemia subtype associated with a dominant-negative mutation in RAD51. Nature Communications [E], 6, Article 8829. https://doi.org/10.1038/ncomms9829
Elkon, R., Loayza-Puch, F., Korkmaz, G., Lopes, R., Van Breugel, P. C., Bleijerveld, O. B., Altelaar, A. F. M., Wolf, E., Lorenzin, F., Eilers, M., & Agami, R. (2015). Myc coordinates transcription and translation to enhance transformation and suppress invasiveness. EMBO Reports, 16(12), 1723-1736. https://doi.org/10.15252/embr.201540717
van Beuningen, S. F. B., Will, L., Harterink, M., Chazeau, A., van Battum, E. Y., Frias, C. P., Franker, M. A. M., Katrukha, E. A., Stucchi, R., Vocking, K., Antunes, A. T., Slenders, L., Doulkeridou, S., Sillevis Smitt, P., Altelaar, A. F. M., Post, J. A., Akhmanova, A., Pasterkamp, R. J., Kapitein, L. C., ... Hoogenraad, C. C. (2015). TRIM46 Controls Neuronal Polarity and Axon Specification by Driving the Formation of Parallel Microtubule Arrays. Neuron, 88(6), 1208-1226. https://doi.org/10.1016/j.neuron.2015.11.012
Patyshakuliyeva, A., Harm, P., Zhou, M., Jurak, E., Heck, A. J. R., Hildén, K. S., Kabel, M. A., Mäkelä, M. R., Altelaar, M. A. F., & De Vries, R. P. (2015). Unraveling the abilities of agaricus bisporus to degrade plant biomass throughout its life cycle. Acta Microbiologica et Immunologica Hungarica, 62, 198. https://doi.org/10.1556/030.62.2015
De Graaf, E. L., Kaplon, J., Mohammed, S., Vereijken, L. A. M., Duarte, D. P., Redondo Gallego, L., Heck, A. J. R., Peeper, D. S., & Altelaar, A. F. M. (2015). Signal Transduction Reaction Monitoring Deciphers Site-Specific PI3K-mTOR/MAPK Pathway Dynamics in Oncogene-Induced Senescence. Journal of Proteome Research, 14(7), 2906-2914. https://doi.org/10.1021/acs.jproteome.5b00236
Raaijmakers, L. M., Giansanti, P., Possik, P. A., Mueller, J., Peeper, D. S., Heck, A. J. R., & Altelaar, A. F. M. (2015). PhosphoPath: Visualization of Phosphosite-centric Dynamics in Temporal Molecular Networks. Journal of Proteome Research, 14(10), 4332-4341. https://doi.org/10.1021/acs.jproteome.5b00529
Schmidlin, T., Boender, A. J., Frese, C. K., Heck, A. J. R., Adan, R. A. H., & Altelaar, A. F. M. (2015). Diet-Induced Neuropeptide Expression: Feasibility of Quantifying Extended and Highly Charged Endogenous Peptide Sequences by Selected Reaction Monitoring. Analytical Chemistry, 87(19), 9966-9973. https://doi.org/10.1021/acs.analchem.5b03334
Benoit, I., Zhou, M., Duarte, A. V., Downes, D. J., Todd, R. B., Kloezen, W., Post, H., Heck, A. J. R., Altelaar, A. F. M., & de Vries, R. P. (2015). Spatial differentiation of gene expression in Aspergillus niger colony grown for sugar beet pulp utilization. Scientific Reports, 5, Article 13592. https://doi.org/10.1038/srep13592
Gray, A. N., Egan, A. J. F., van 't Veer, I., Verheul, J., Colavin, A., Koumoutsi, A., Biboy, J., Altelaar, A. F. M., Damen, M. J., Huang, K. C., Simorre, J.-P., Breukink, E., den Blaauwen, T., Typas, A., Gross, C. A., & Vollmer, W. (2015). Coordination of peptidoglycan synthesis and outer membrane constriction during Escherichia coli cell division. eLife, 4. https://doi.org/10.7554/eLife.07118
Jansen, R. S., Addie, R., Merkx, R., Fish, A., Mahakena, S., Bleijerveld, O. B., Altelaar, M., IJlst, L., Wanders, R. J., Borst, P., & van de Wetering, K. (2015). N-lactoyl-amino acids are ubiquitous metabolites that originate from CNDP2-mediated reverse proteolysis of lactate and amino acids. Proceedings of the National Academy of Sciences of the United States of America, 112(21), 6601-6606. https://doi.org/10.1073/pnas.1424638112
Stulemeijer, I. J. E., De Vos, D., Van Harten, K., Joshi, O. K., Blomberg, O., Van Welsem, T., Terweij, M., Vlaming, H., De Graaf, E. L., Altelaar, A. F. M., Bakker, B. M., & Van Leeuwen, F. (2015). Dot1 histone methyltransferases share a distributive mechanism but have highly diverged catalytic properties. Scientific Reports, 5, Article 9824. https://doi.org/10.1038/srep09824
Patyshakuliyeva, A., Post, H., Zhou, M., Jurak, E., Heck, A. J. R., Hildén, K. S., Kabel, M. A., Mäkelä, M. R., Altelaar, M. A. F., & De Vries, R. P. (2015). Uncovering the abilities of Agaricus bisporus to degrade plant biomass throughout its life cycle. Environmental Microbiology, 17(8), 3098-3109. https://doi.org/10.1111/1462-2920.12967
Isogai, T., Van Der Kammen, R., Goerdayal, S. S., Heck, A. J. R., Altelaar, A. F. M., & Innocenti, M. (2015). Proteomic analyses uncover a new function and mode of action for mouse homolog of diaphanous 2 (mDia2). Molecular & Cellular Proteomics, 14(4), 1064-1078. https://doi.org/10.1074/mcp.M114.043885
Götzke, H., Muheim, C., Altelaar, A. F. M., Heck, A. J. R., Maddalo, G., & Daley, D. O. (2015). Identification of putative substrates for the periplasmic chaperone YfgM in Escherichia coli using quantitative proteomics. Molecular & Cellular Proteomics, 14(1), 216-226. https://doi.org/10.1074/mcp.M114.043216
Brunner, A. M., Lössl, P., Liu, F., Huguet, R., Mullen, C., Yamashita, M., Zabrouskov, V., Makarov, A., Altelaar, A. F. M., & Heck, A. J. R. (2015). Benchmarking multiple fragmentation methods on an orbitrap fusion for top-down phospho-proteoform characterization. Analytical Chemistry, 87(8), 4152-4158. https://doi.org/10.1021/acs.analchem.5b00162
Balluff, B., Frese, C. K., Maier, S. K., Schöne, C., Kuster, B., Schmitt, M., Aubele, M., Höfler, H., Deelder, A. M., Heck, A. J. R., Hogendoorn, P. C. W., Morreau, J., Altelaar, A. F. M., Walch, A., & McDonnell, L. A. (2015). De novo discovery of phenotypic intratumour heterogeneity using imaging mass spectrometry. Journal of Pathology, 235(1), 3-13. https://doi.org/10.1002/path.4436
Vogel, C. J., Smit, M. A., Maddalo, G., Possik, P. A., Sparidans, R. W., van der Burg, S. H., Verdegaal, E. M., Heck, A. J. R., Samatar, A. A., Beijnen, J. H., Altelaar, A. F. M., & Peeper, D. S. (2015). Cooperative induction of apoptosis in NRAS mutant melanoma by inhibition of MEK and ROCK. Pigment Cell and Melanoma Research, 28(3), 307-317. https://doi.org/10.1111/pcmr.12364

2014

Scholarly publications

Castano-Cerezo, S., Bernal, V., Post, H., Fuhrer, T., Cappadona, S., Sanchez-Diaz, N. C., Sauer, U., Heck, A. J. R., Altelaar, A. F. M., & Canovas, M. (2014). Protein acetylation affects acetate metabolism, motility and acid stress response in Escherichia coli. Molecular Systems Biology [E], 10(11), Article 762. https://doi.org/10.15252/msb.20145227
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
de Graaf, E. L., Giansanti, P., Altelaar, A. F. M., & Heck, A. J. R. (2014). Single-step enrichment by Ti4+-IMAC and label-free quantitation enables in-depth monitoring of phosphorylation dynamics with high reproducibility and temporal resolution. Molecular & Cellular Proteomics, 13(9), 2426-2434. https://doi.org/10.1074/mcp.O113.036608
de Graaf, E. L., Kaplon, J., Zhou, H., Heck, A. J. R., Peeper, D. S., & Altelaar, A. F. M. (2014). Phosphoproteome dynamics in onset and maintenance of oncogene-induced senescence. Molecular & Cellular Proteomics, 13(8), 2089-2100. https://doi.org/10.1074/mcp.M113.035436
Klaubauf, S., Narang, H. M., Post, H., Zhou, M., Brunner, K., Mach-Aigner, A. R., Mach, R. L., Heck, A. J. R., Altelaar, A. F. M., & de Vries, R. P. (2014). Similar is not the same: Differences in the function of the (hemi-)cellulolytic regulator XlnR (Xlr1/Xyr1) in filamentous fungi. Fungal Genetics and Biology, 72, 73-81. https://doi.org/10.1016/j.fgb.2014.07.007
Vlaming, H., van Welsem, T., de Graaf, E. L., Ontoso, D., Altelaar, A. F. M., San-Segundo, P. A., Heck, A. J. R., & van Leeuwen, F. (2014). Flexibility in crosstalk between H2B ubiquitination and H3 methylation in vivo (Corrigendum). EMBO Reports, 15(11), 1220-1221. https://doi.org/10.15252/embr.201471110
Vlaming, H., van Welsem, T., de Graaf, E. L., Ontoso, D., Altelaar, A. F. M., San-Segundo, P. A., Heck, A. J. R., & van Leeuwen, F. (2014). Flexibility in crosstalk between H2B ubiquitination and H3 methylation in vivo. EMBO Reports, 15(10), 1077-84. https://doi.org/10.15252/embr.201438793
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
Jiang, K., Hua, S., Mohan, R., Grigoriev, I., Yau, K. W., Liu, Q., Katrukha, E. A., Altelaar, A. F. M., Heck, A. J. R., Hoogenraad, C. C., & Akhmanova, A. (2014). Microtubule minus-end stabilization by polymerization-driven CAMSAP deposition. Developmental Cell, 28(3), 295-309. https://doi.org/10.1016/j.devcel.2014.01.001

2013

Scholarly publications

Ringrose, J. H., van den Toorn, H. W. P., Eitel, M., Post, H., Neerincx, P. B. T., Schierwater, B., Altelaar, A. F. M., & Heck, A. J. R. (2013). Deep proteome profiling of Trichoplax adhaerens reveals remarkable features at the origin of metazoan multicellularity. Nature Communications [E], 4, Article 1408. https://doi.org/10.1038/ncomms2424
Frese, C., Nolting, D., Altelaar, A. F. M., Griep-Raming, J., Mohammed, S., & Heck, A. J. R. (2013). Characterization of Electron Transfer Dissociation in the Orbitrap Velos HCD Cell. Journal of the American Society for Mass Spectrometry, 24(11), 1663-1670. https://doi.org/10.1007/s13361-013-0618-9
Altelaar, A. F. M., Munoz-Peralta, J., & Heck, A. J. R. (2013). Next-generation proteomics: towards an integrative view of proteome dynamics. Nature Reviews. Genetics, 14, 35-48. https://doi.org/10.1038/nrg3356
Jones, E. A., Schmitz, N., Waaijer, C. J. F., Frese, C., van Remoortere, A., van Zeijl, R. J. M., Heck, A. J. R., Hogendoorn, P. C. W., Deelder, A. M., Altelaar, A. F. M., Bovée, J. V. M. G., & McDonnell, L. A. (2013). Imaging Mass Spectrometry-based Molecular Histology Differentiates Microscopically Identical and Heterogeneous Tumors. Journal of Proteome Research, 12, 1847-1855. https://doi.org/10.1021/pr301190g
Altelaar, A. F. M., Frese, C. K., Preisinger, C., Hennrich, M. L., Schram, A. W., Timmers, H. T. M., Heck, A. J. R., & Mohammed, S. (2013). Benchmarking stable isotope labeling based quantitative proteomics. Journal of Proteomics, 88, 14-26. https://doi.org/10.1016/j.jprot.2012.10.009
Frese, C., Zhou, H., Taus, T., Altelaar, A. F. M., Mechtler, K., Heck, A. J. R., & Mohammed, S. (2013). Unambiguous Phosphosite Localization using Electron-Transfer/Higher-Energy Collision Dissociation (EThcD). Journal of Proteome Research, 12, 1520-1525. https://doi.org/10.1021/pr301130k
Meijer, L. A. T., Zhou, H., Chan, O. Y. A., Altelaar, A. F. M., Hennrich, M. L., Mohammed, S., Bos, J. L., & Heck, A. J. R. (2013). Quantitative global phosphoproteomics of human umbilical vein endothelial cells after activation of the Rap signaling pathway. Molecular BioSystems, 9, 732-749. https://doi.org/10.1039/c3mb25524g
Krijgsheld, P., Nitsche, B. M., Post, H., Levin, A. M., Muller, W. H., Heck, A. J. R., Ram, A. F., Altelaar, A. F. M., & Wösten, H. A. B. (2013). Deletion of flbA results in increased secretome complexity and reduced secretion heterogeneity in colonies of Aspergillus niger. Journal of Proteome Research, 12(4), 1808-1819. https://doi.org/10.1021/pr301154w
Frese, C., Boender, A. J., Mohammed, S., Heck, A. J. R., Adan, R. A. H., & Altelaar, A. F. M. (2013). Profiling of diet-induced neuropeptide changes in rat brain by quantitative mass spectrometry. Analytical Chemistry, 85(7), 4594-4604. https://doi.org/10.1021/ac400232y
Pollo-Oliveira, L., Post, H., Acencio, M. L., Lemke, N., van den Toorn, H. W. P., Tragante Do O, V., Heck, A. J. R., Altelaar, A. F. M., & Yatsuda, A. P. (2013). Unravelling the Neospora caninum secretome through the secreted fraction (ESA) and quantification of the discharged tachyzoite using high-resolution mass spectrometry-based proteomics. Parasites & Vectors, 6(1), 335. https://doi.org/10.1186/1756-3305-6-335
Pijnappel, W. W. M., Esch, D., Baltissen, M. P. A., Wu, G., Mischerikow, N., Bergsma, A., van der Wal, E., Han, D. W., vom Bruch, H., Moritz, S., Lijnzaad, P., Altelaar, A. F. M., Sameith, K., Zaehres, H., Heck, A. J. R., Holstege, F. C. P., Scholer, H. R., & Timmers, H. T. M. (2013). A central role for TFIID in the pluripotent transcription circuitry. Nature, 495, 516-519. https://doi.org/10.1038/nature11970
de Graaf, E. L., Vermeij, W. P., de Waard, M. C., Rijksen, Y., van der Pluijm, I., Hoogenraad, C. C., Hoeijmakers, J. H. J., Altelaar, A. F. M., & Heck, A. J. R. (2013). Spatio-temperal analysis of molecular determinants of neuronal degeneration in the aging mouse cerebellum. Molecular & Cellular Proteomics, 12(5), 1350-1362. https://doi.org/10.1074/mcp.M112.024950

2012

Scholarly publications

Krijgsheld, P., Altelaar, A. F. M., Post, H., Ringrose, J. H., Muller, W. H., Heck, A. J. R., & Wösten, H. A. B. (2012). Spatially resolving the secretome within the mycelium of the cell factory Aspergillus niger. Journal of Proteome Research, 11(5), 2807-2818.
Altelaar, A. F. M., & Heck, A. J. R. (2012). Trends in ultrasensitive proteomics. Current Opinion in Chemical Biology, 16, 206-213. https://doi.org/10.1016/j.cbpa.2011.12.011
Krijgsheld, P., Wosten, H. A. B., Altelaar, A. F. M., Post, H., Ringrose, J. H., Muller, W. H., & Heck, A. J. R. (2012). Spatially resolving the microtome within the mycelium of the cell factory Aspergillus niger. In onbekend
Frese, C. K., Altelaar, A. F. M., van den Toorn, H. W. P., Nolting, D., Griep-Raming, J., Heck, A. J. R., & Mohammed, S. (2012). Toward full peptide sequence coverage by dual fragmentation combining electron-transfer and higher-energy collision dissociation tandem mass spectrometry. Analytical Chemistry, 84, 9668-9673. https://doi.org/10.1021/ac3025366
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.

Other output

Krijgsheld, P., Wosten, H. A. B., Altelaar, A. F. M., Post, H., Ringrose, J. H., Muller, W. H., & Heck, A. J. R. (2012). Spatially resolving the microtome within the mycelium of the cell factory Aspergillus niger. Poster session presented at 11th European Conference on Fungal Genetics, Philipps-Universitaet Marburg, Germany.
Krijgsheld, P., Altelaar, A. F. M., Post, H., Ringrose, J. H., Muller, W. H., Heck, A. J. R., & Wösten, H. A. B. (2012). Spatially resolving the secretome within the mycelium of the cell factory Aspergillus niger. Abstract from Voorjaarsvergadering van de Nederlandse Vereniging voor Medische Microbiologie (NVMM) en de Koninklijke Nederlandse Vereniging voor Microbiologie (KNVM), Papendal.

2011

Scholarly publications

Bleijerveld, O. B., Brakenhoff, R. H., Schaaij-Visser, B. M., Damen, J. M. A., Altelaar, A. F. M., Heck, A. J. R., Leemans, C. R., & Slijper, M. (2011). Protein signatures associated with tumor cell dissemination in head and neck cancer. Journal of Proteomics, 74(4), 558-566. https://doi.org/10.1016/j.jprot.2011.01.008
de Vos, D., Frederiks, F., Terweij, M., Welsem, T., Verzijlbergen, K. F., Iachina, E., de Graaf, E. L., Altelaar, A. F. M., Oudgenoeg, G., Heck, A. J. R., Krijgsveld, J., Bakker, B. M., & van Leeuwen, F. (2011). Progressive methylation of ageing histones by Dot1 functions as a timer. EMBO Reports, 12(9), 956-962. https://doi.org/10.1038/embor.2011.131
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
Frese, C. K., Altelaar, A. F. M., Hennrich, M. L., Nolting, D., Zeller, M., Griep-Raming, J., Heck, A. J. R., & Mohammed, S. (2011). Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos. Journal of Proteome Research, 10(5), 2377-2388.
Wijte, D., van Baar, B. L. M., Heck, A. J. R., & Altelaar, A. F. M. (2011). Probing the proteome response to toluene exposure in the solvent tolerant pseudomonas putida S12. Journal of Proteome Research, 10(2), 394-403. https://doi.org/10.1021/pr100401n

2010

Scholarly publications

Hennrich, M. L., Mohammed, S., Altelaar, A. F. M., & Heck, A. J. R. (2010). Dimethyl isotope labeling assisted de novo peptide sequencing. Journal of the American Society for Mass Spectrometry, 12, 1957-1965.
Altelaar, A. F. M., & Piersma, S. R. (2010). Cellular imaging using matrix-enhanced and metal-assisted SIMS. Methods in Molecular Biology, 656, 197-208.
Mischerikow, N., van Nierop, P., Li, K. W., Bernstein, H. G., Smit, A. B., Heck, A. J. R., & Altelaar, A. F. M. (2010). Gaining efficiency by parallel quantification and identification of iTRAQ-labeled peptides using HCD and decision tree guided CID/ETD on an LTQ Orbitrap Orbitrap. Analyst, 135, 2643-2652.
Mischerikow, N., Altelaar, A. F. M., Navarro Herrero, J. D., Mohammed, S., & Heck, A. J. R. (2010). Comparative assessment of site assignments in CID and electron transfer dissociation spectra of phosphopeptides discloses limited relocation of phosphate groups. Molecular & Cellular Proteomics, 9, 2140-2148.

Other output

Krijgsheld, P., Ringrose, J. H., Altelaar, A. F. M., Heck, A. J. R., & Wösten, H. A. B. (2010). Secretome analysis of concentric zones of Aspergillus niger colonies. Poster session presented at 10th European Conference on Fungal Genetics, Noordwijkerhout (NH Conference Center Leeuwenhorst).

2009

Scholarly publications

Mischerikow, N., Spedale, G., Altelaar, A. F. M., Timmers, H. T. M., Pijnappel, W. W. M., & Heck, A. J. R. (2009). In-depth profiling of post-translational modifications on the related transcription factor complexes TFIID and SAGA. Journal of Proteome Research, 8(11), 5020-5030. http://www.ncbi.nlm.nih.gov/pubmed/19731963?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=1
Klerk, L. A., Altelaar, A. F. M., Froesch, M., McDonnell, L. A., & Heeren, R. M. A. (2009). Fast and automated large-area imaging MALDI mass spectrometry in microprobe and microscope mode. International Journal of Mass Spectrometry, (285), 19-25.
Ms. Taouatas, N., Altelaar, A. F. M., Drugan, M. M., Helbig, A. O., Mohammed, S., & Heck, A. J. R. (2009). Strong cation exchange-based fractionation of Lys-N-generated peptides facilitates the targeted analysis of post-translational modifications. Molecular & Cellular Proteomics, (8), 190-200.
Altelaar, A. F. M., & Heeren, R. M. A. (2009). Tissue analysis with high-resolution imaging mass spectrometry. Methods in Molecular Biology, (492), 295-308.
Boersema, P. J., Ms. Taouatas, N., Altelaar, A. F. M., Gouw, J. W., Ross, P. L., Pappin, D. J., Heck, A. J. R., & Mohammed, S. (2009). Straightforward and de novo peptide sequencing by MALDI-MS/MS using a Lys-N metalloendopeptidase. Molecular & Cellular Proteomics, (8), 650-660.
Altelaar, A. F. M., Mohammed, S., Brans, M. A., Adan, R. A. H., & Heck, A. J. R. (2009). Improved identification of endogenous peptides from murine nervous tissue by multiplexed peptide extraction methods and multiplexed mass spectrometric analysis. Journal of Proteome Research, 8(2), 870-876. http://www.ncbi.nlm.nih.gov/pubmed/19152261

2008

Scholarly publications

Broersen, A., Liere, R., Altelaar, A. F. M., Heeren, R. M. A., & McDonnell, L. A. (2008). Automated, Feature-Based Image Alignment for High-Resolution Imaging Mass Spectrometry of Large Biological Samples. Journal of the American Society for Mass Spectrometry, 19, 823-832.
van Werven, F. J., van Bakel, H. H. M. J., van Teeffelen, H. A. A. M., Altelaar, A. F. M., Groot Koerkamp, M. J. A., Heck, A. J. R., Holstege, F. C. P., & Timmers, H. T. M. (2008). Cooperative action of NC2 and Mot1p to regulate TATA-binding protein function across the genome. Genes and Development, 22, 2359-2369. https://doi.org/10.1101/gad.1682308

2007

Scholarly publications

Altelaar, A. F. M., Luxembourg, S. L., McDonnell, L. A., Piersma, S. R., & Heeren, R. M. A. (2007). Imaging mass spectrometry at cellular length scales. Nature Protocols, 2(5), 1185-1196. https://doi.org/10.1038/nprot.2007.117
Klinkert, I., McDonnell, L. A., Luxembourg, S. L., Altelaar, A. F. M., Amstalden, E. R., Piersma, S. R., & Heeren, R. M. A. (2007). Tools and strategies for visualization of large image datasets in high-resolution imaging mass spectrometry. Review of Scientific Instruments, 78, 053716-1-053716-10.
https://dspace.library.uu.nl/bitstream/handle/1874/26423/33_Klinkert_tools.pdf?sequence=1
Altelaar, A. F. M. (2007). Biomolecular Imaging Mass spectrometry, mapping molecular distributions in cells and tissue sections. [Doctoral thesis 1 (Research UU / Graduation UU), Utrecht University].
Altelaar, A. F. M., Taban, I., McDonnell, L. A., Verhaert, P. D. E. M., de Lange, R. P. J., Adan, R. A. H., Mooi, W. J., Heeren, R. M. A., & Piersma, S. R. (2007). High-resolution MALDI imaging mass spectrometry allows localization of peptide distributions at cellular length scales in pituitary tissue sections. International Journal of Mass Spectrometry, 260(2-3), 203-211.
https://dspace.library.uu.nl/bitstream/handle/1874/26329/36_Altelaar_high.pdf?sequence=1
Taban, I., Altelaar, A. F. M., van der Burgt, Y. E. M., McDonnell, L. A., & Heeren, R. M. A. (2007). Imaging of Peptides in the Rat Brain Using MALDI-FTICR Mass Spectrometry. Journal of the American Society for Mass Spectrometry, 18, 145-151.
https://dspace.library.uu.nl/bitstream/handle/1874/26379/10_imaging_taban.pdf?sequence=1

2006

Scholarly publications

Altelaar, A. F. M., Klinkert, I., Jalink, K., de Lange, R. P. J., Adan, R. A. H., Heeren, R. M. A., & Piersma, S. R. (2006). Gold-enhanced biomolecular surface imaging of cells and tissue by SIMS and MALDI mass spectrometry. Analytical Chemistry, 78(3), 734-742.
https://dspace.library.uu.nl/bitstream/handle/1874/19207/32_heeren%2520Gold.pdf?sequence=1
Heeren, R. M. A., McDonnell, L. A., Amstalden, E. R., Luxembourg, S. L., Altelaar, A. F. M., & Piersma, S. R. (2006). Why don’t biologists use SIMS? A critical evaluation of imaging MS. Applied Surface Science, 252, 6827-6835.
https://dspace.library.uu.nl/bitstream/handle/1874/19784/34_heeren%2520why.pdf?sequence=1
Altelaar, A. F. M., van Minnen, J., Heeren, R. M. A., & Piersma, S. R. (2006). The influence of the cholesterol microenvironment in tissue sections on molecular ionization efficiencies and distributions in ToF-SIMS. Applied Surface Science, 252, 6702-6705.
https://dspace.library.uu.nl/bitstream/handle/1874/19817/33_heeren%2520influence.pdf?sequence=1

2005

Scholarly publications

McDonnell, L. A., Piersma, S. R., Altelaar, A. F. M., Mize, T. H., Luxembourg, S. L., Verhaert, P. D. E. M., van Minnen, J., & Heeren, R. M. A. (2005). Subcellular imaging mass spectrometry of brain tissue. Journal of Mass Spectrometry, 40, 160-168.
Altelaar, A. F. M., van Minnen, J., Jiménez, C. R., Heeren, R. M. A., & Piersma, S. R. (2005). Direct molecular imaging of Lymnaea stagnalis nervous tissue at subcellular spatial resolution by mass spectrometry. Analytical Chemistry, 77, 735-741.

2002

Scholarly publications

Gimeno, R. A., Altelaar, A. F. M., Marcé, R. M., & Borrull, F. (2002). Determination of polycyclic aromatic hydrocarbons and polycylic aromatic sulfur heterocycles by high-performance liquid chromatography with fluorescence and atmospheric pressure chemical ionization mass spectrometry detection in seawater and sediment samples. Journal of Chromatography A, 958(1-2), 141-148. https://doi.org/10.1016/S0021-9673(02)00386-2

2000

Scholarly publications

Seifar, R. M., Altelaar, M. A. F., Dijkstra, R. J., Ariese, F., Brinkman, U. A. T., & Gooijer, C. (2000). Surface-enhanced resonance Raman spectroscopy as an identification tool in column liquid chromatography. Analytical Chemistry, 72(22), 5718-5724. https://doi.org/10.1021/ac000514g

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