Publications
2023
Scholarly publications
Khmelinskaia, A., Bethel, N. P., Fatehi, F., Antanasijevic, A., Borst, A. J., Lai, S-H., Wang, J. Y. J., Mallik, B. B., Miranda, M. C., Watkins, A. M., Ogohara, C., Caldwell, S., Wu, M., Heck, A. J. R., Veesler, D., Ward, A. B., Baker, D., Twarock, R., & King, N. P. (2023). Local structural flexibility drives oligomorphism in computationally designed protein assemblies. bioRxiv. https://doi.org/10.1101/2023.10.18.562842
Muts, R. M., den Boer, M. A., Bardoel, B. W., Aerts, P. C., de Haas, C. J. C., Heck, A. J. R., Rooijakkers, S. H. M., & Heesterbeek, D. A. C. (2023). Artificial surface labelling of Escherichia coli with StrepTagII antigen to study how monoclonal antibodies drive complement-mediated killing. Scientific Reports, 13(1), 18836. https://doi.org/10.1038/s41598-023-46026-x
van Bergen, W., Fiala, J., Heck, AJ., & Baggelaar, M. (2023). Dual-Probe Activity-Based Protein Profiling Reveals Site-Specific Differences in Protein Binding of EGFR-Directed Drugs. bioRxiv, Article 562725. https://www.biorxiv.org/content/10.1101/2023.10.19.562725v1.full.pdf
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), Article 6316. https://doi.org/10.1038/s41467-023-42049-0
Hevler, J. F., & Heck, A. J. R. (2023). Higher-order structural organization of the mitochondrial proteome charted by in situ cross-linking mass spectrometry. Molecular and Cellular Proteomics, 22(11), Article 100657. https://doi.org/10.1016/j.mcpro.2023.100657
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, 59. https://doi.org/10.12688/openreseurope.15810.1
Yin, V., Devine, P. W. A., Saunders, J. C., Barendregt, A., Cusdin, F., Ristani, A., Hines, A., Shepherd, S., Dembek, M., Dobson, C. L., Snijder, J., Bond, N. J., & Heck, A. J. R. (2023). Stochastic assembly of biomacromolecular complexes: impact and implications on charge interpretation in native mass spectrometry. Chemical Science, 14(35), 9316-9327. https://doi.org/10.1039/d3sc03228k
Miao, B., Hu, Z., Mezzadra, R., Hoeijmakers, L., Fauster, A., Du, S., Yang, Z., Sator-Schmitt, M., Engel, H., Li, X., Broderick, C., Jin, G., Gomez-Eerland, R., Rozeman, L., Lei, X., Matsuo, H., Yang, C., Hofland, I., Peters, D., ... Sun, C. (2023). CMTM6 shapes antitumor T cell response through modulating protein expression of CD58 and PD-L1. Cancer Cell, 41(10), 1817-1828.e9. https://doi.org/10.1016/j.ccell.2023.08.008
Milenkovic, D., Misic, J., Hevler, J. F., Molinié, T., Chung, I., Atanassov, I., Li, X., Filograna, R., Mesaros, A., Mourier, A., Heck, A. J. R., Hirst, J., & Larsson, N-G. (2023). Preserved respiratory chain capacity and physiology in mice with profoundly reduced levels of mitochondrial respirasomes. Cell Metabolism, 35(10), 1799-1813. https://doi.org/10.1016/j.cmet.2023.07.015
Peng, W., den Boer, M. A., Tamara, S., Mokiem, N. J., van der Lans, S. P. A., Bondt, A., Schulte, D., Haas, P-J., Minnema, M. C., Rooijakkers, S. H. M., van Zuilen, A. D., Heck, A. J. R., & Snijder, J. (2023). Direct Mass Spectrometry-Based Detection and Antibody Sequencing of Monoclonal Gammopathy of Undetermined Significance from Patient Serum: A Case Study. Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.3c00330
Stip, M. C., Evers, M., Nederend, M., Chan, C., Reiding, K. R., Damen, M. J., Heck, A. J. R., Koustoulidou, S., Ramakers, R., Krijger, G. C., de Roos, R., Souteyrand, E., Cornel, A. M., Dierselhuis, M. P., Jansen, M., de Boer, M., Valerius, T., van Tetering, G., Leusen, J. H. W., & Meyer-Wentrup, F. (2023). IgA antibody immunotherapy targeting GD2 is effective in preclinical neuroblastoma models. Journal for ImmunoTherapy of Cancer, 11(7), Article 006948. https://doi.org/10.1136/jitc-2023-006948
Leung, M. R., Zeng, J., Wang, X., Roelofs, M. C., Huang, W., Zenezini Chiozzi, R., Hevler, J. F., Heck, A. J. R., Dutcher, S. K., Brown, A., Zhang, R., & Zeev-Ben-Mordehai, T. (2023). Structural specializations of the sperm tail. Cell. https://doi.org/10.1016/j.cell.2023.05.026
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
Mathew, A., Giskes, F., Lekkas, A., Greisch, J-F., Eijkel, G. B., Anthony, I. G. M., Fort, K., Heck, A. J. R., Papanastasiou, D., Makarov, A. A., Ellis, S. R., & Heeren, R. M. A. (2023). An Orbitrap/Time-of-Flight Mass Spectrometer for Photofragment Ion Imaging and High-Resolution Mass Analysis of Native Macromolecular Assemblies. Journal of the American Society for Mass Spectrometry, 34(7), 1359-1371. https://doi.org/10.1021/jasms.3c00053
van Els, C. A. C. M., van Veelen, P. A., Heck, A. J. R., & Meiring, H. D. (2023). Remembering Ad de Jong. Molecular and Cellular Proteomics, 22(6), Article 100568. https://doi.org/10.1016/j.mcpro.2023.100568
Deslignière, E., Rolland, A., Ebberink, E. H. T. M., Yin, V., & Heck, A. J. R. (2023). Orbitrap-Based Mass and Charge Analysis of Single Molecules. Accounts of Chemical Research, 56(12), 1458–1468. https://doi.org/10.1021/acs.accounts.3c00079
Zou, Y., van Breukelen, B., Pronker, M., Reiding, K., & Heck, A. J. R. (2023). Proteogenomic Features of the Highly Polymorphic Histidine-rich Glycoprotein Arose Late in Evolution. Molecular and Cellular Proteomics, 22(7), Article 100585. https://doi.org/10.1016/j.mcpro.2023.100585
Radić, L., Sliepen, K., Yin, V., Brinkkemper, M., Capella-Pujol, J., Schriek, A. I., Torres, J. L., Bangaru, S., Burger, J. A., Poniman, M., Bontjer, I., Bouhuijs, J. H., Gideonse, D., Eggink, D., Ward, A. B., Heck, A. J. R., Van Gils, M. J., Sanders, R. W., & Schinkel, J. (2023). Bispecific antibodies combine breadth, potency, and avidity of parental antibodies to neutralize sarbecoviruses. iScience, 26(4), 106540. https://doi.org/10.1016/j.isci.2023.106540
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. https://doi.org/10.12688/openreseurope.15810.1
Aguinagalde Salazar, L., den Boer, M. A., Castenmiller, S. M., Zwarthoff, S. A., de Haas, C., Aerts, P. C., Beurskens, F. J., Schuurman, J., Heck, A. J. R., van Kessel, K., & Rooijakkers, S. H. M. (2023). Promoting Fc-Fc interactions between anti-capsular antibodies provides strong immune protection against
Streptococcus pneumoniae. eLife, 12, Article e80669. https://doi.org/10.7554/eLife.80669
Jager, S., Cramer, D. A. T., & Heck, A. J. R. (2023). Normal Alpha-1-Antitrypsin Variants Display in Serum Allele-Specific Protein Levels. Journal of Proteome Research, 22(4), 1331-1338. https://doi.org/10.1021/acs.jproteome.2c00833
Subramaniam, G., Schleicher, K., Kovanich, D., Zerio, A., Folkmanaite, M., Chao, Y-C., Surdo, N. C., Koschinski, A., Hu, J., Scholten, A., Heck, A. J. R., Ercu, M., Sholokh, A., Chan Park, K., Klussmann, E., Meraviglia, V., Bellin, M., Zanivan, S., Hester, S., ... Zaccolo, M. (2023). Integrated Proteomics Unveils Nuclear PDE3A2 as a Regulator of Cardiac Myocyte Hypertrophy. Circulation Research, 132(7), 828-848. https://doi.org/10.1161/circresaha.122.321448
Chen, Y-H., Tian, W., Yasuda, M., Ye, Z., Song, M., Mandel, U., Kristensen, C., Povolo, L., Marques, A. R. A., Čaval, T., Heck, A. J. R., Sampaio, J. L., Johannes, L., Tsukimura, T., Desnick, R., Vakhrushev, S. Y., Yang, Z., & Clausen, H. (2023). A universal GlycoDesign for lysosomal replacement enzymes to improve circulation time and biodistribution. Frontiers in Bioengineering and Biotechnology, 11, Article 1128371. https://doi.org/10.3389/fbioe.2023.1128371
Cramer, D. A. T., Franc, V., Heidenreich, A-K., Hook, M., Adibzadeh, M., Reusch, D., Heck, A. J. R., & Haberger, M. (2023). Characterization of high-molecular weight by-products in the production of a trivalent bispecific 2+1 heterodimeric antibody. mAbs, 15(1), 1-13. Article 2175312. https://doi.org/10.1080/19420862.2023.2175312
Hevler, J. F., Albanese, P., Cabrera-Orefice, A., Potter, A., Jankevics, A., Misic, J., Scheltema, R. A., Brandt, U., Arnold, S., & Heck, A. J. R. (2023). MRPS36 provides a structural link in the eukaryotic 2-oxoglutarate dehydrogenase complex. Open Biology, 13(3), Article 220363. https://doi.org/10.1098/rsob.220363
Zhang, M., Chiozzi, R. Z., Bromfield, E. G., Heck, A. J., Helms, J. B., & Gadella, B. M. (2023). Characterization of acrosin and acrosin binding protein as novel CRISP2 interacting proteins in boar spermatozoa. Andrology, 11(7), 1460-1471. https://doi.org/10.1111/andr.13413
Gazi, I., Reiding, K. R., Groeneveld, A., Bastiaans, J., Huppertz, T., & Heck, A. J. R. (2023). Key changes in bovine milk immunoglobulin G during lactation: NeuAc sialylation is a hallmark of colostrum immunoglobulin G N-glycosylation. Glycobiology, 33(2), 115-125. https://doi.org/10.1093/glycob/cwad001
Mukherjee, S., Jankevics, A., Busch, F., Lubeck, M., Zou, Y., Kruppa, G., Heck, A. J. R., Scheltema, R. A., & Reiding, K. R. (2023). Oxonium Ion-Guided Optimization of Ion Mobility-Assisted Glycoproteomics on the timsTOF Pro. Molecular and Cellular Proteomics, 22(1), Article 100486. https://doi.org/10.1016/j.mcpro.2022.100486
van Bergen, W., Hevler, J. F., Wu, W., Baggelaar, M. P., & Heck, A. J. R. (2023). Site-specific Activity-based Protein Profiling Using Phosphonate Handles. Molecular and Cellular Proteomics, 22(1), 1-15. Article 100455. https://doi.org/10.1016/j.mcpro.2022.100455
Dingess, K. A., Hoek, M., van Rijswijk, D. M. H., Tamara, S., den Boer, M. A., Veth, T., Damen, M. J. A., Barendregt, A., Romijn, M., Juncker, H. G., van Keulen, B. J., Vidarsson, G., van Goudoever, J. B., Bondt, A., & Heck, A. J. R. (2023). Identification of common and distinct origins of human serum and breastmilk IgA1 by mass spectrometry-based clonal profiling. Cellular and Molecular Immunology, 20(1), 26-37. https://doi.org/10.1038/s41423-022-00954-2
2022
Scholarly publications
Hevler, J. F., Albanese, P., Cabrera-Orefice, A., Potter, A., Jankevics, A., Misic, J., Scheltema, R. A., Brandt, U., Arnold, S., & Heck, A. J. R. (2022, Oct 8). MRPS36 provides a missing link in the eukaryotic 2-oxoglutarate dehydrogenase complex for recruitment of E3 to the E2 core. https://doi.org/10.1101/2022.10.08.511390
González-García, P., Díaz-Casado, M. E., Hidalgo-Gutiérrez, A., Jiménez-Sánchez, L., Bakkali, M., Barriocanal-Casado, E., Escames, G., Chiozzi, R. Z., Völlmy, F., Zaal, E. A., Berkers, C. R., Heck, A. J. R., & López, L. C. (2022). The Q-junction and the inflammatory response are critical pathological and therapeutic factors in CoQ deficiency. Redox Biology, 55, Article 102403. https://doi.org/10.1016/j.redox.2022.102403
Doorduijn, D. J., Lukassen, M. V., van 't Wout, M. F. L., Franc, V., Ruyken, M., Bardoel, B. W., Heck, A. J. R., & Rooijakkers, S. H. M. (2022). Soluble MAC is primarily released from MAC-resistant bacteria that potently convert complement component C5. eLife, 11, Article e77503. https://doi.org/10.7554/eLife.77503
Cramer, D. A. T., Franc, V., Caval, T., & Heck, A. J. R. (2022). Charting the Proteoform Landscape of Serum Proteins in Individual Donors by High-Resolution Native Mass Spectrometry. Analytical Chemistry, 94(37), 12732-12741. https://doi.org/10.1021/acs.analchem.2c02215
Chataigner, L. M. P., Gogou, C., den Boer, M. A., Frias, C. P., Thies-Weesie, D. M. E., Granneman, J. C. M., Heck, A. J. R., Meijer, D. H., & Janssen, B. J. C. (2022). Structural insights into the contactin 1 - neurofascin 155 adhesion complex. Nature Communications, 13(1), Article 6607. https://doi.org/10.1038/s41467-022-34302-9
van Rijswijck, D. M. H., Bondt, A., Hoek, M., van der Straten, K., Caniels, T. G., Poniman, M., Eggink, D., Reusken, C., de Bree, G. J., Sanders, R. W., van Gils, M. J., & Heck, A. J. R. (2022). Discriminating cross-reactivity in polyclonal IgG1 responses against SARS-CoV-2 variants of concern. Nature Communications, 13(1), Article 6103. https://doi.org/10.1038/s41467-022-33899-1
Fischer, E. S., Yu, C. W. H., Hevler, J. F., McLaughlin, S. H., Maslen, S. L., Heck, A. J. R., Freund, S. M. V., & Barford, D. (2022). Juxtaposition of Bub1 and Cdc20 on phosphorylated Mad1 during catalytic mitotic checkpoint complex assembly. Nature Communications, 13(1), Article 6381. https://doi.org/10.1038/s41467-022-34058-2
Brinkkemper, M., Veth, T. S., Brouwer, P. J. M., Turner, H., Poniman, M., Burger, J. A., Bouhuijs, J. H., Olijhoek, W., Bontjer, I., Snitselaar, J. L., Caniels, T. G., van der Linden, C. A., Ravichandran, R., Villaudy, J., van der Velden, Y. U., Sliepen, K., van Gils, M. J., Ward, A. B., King, N. P., ... Sanders, R. W. (2022). Co-display of diverse spike proteins on nanoparticles broadens sarbecovirus neutralizing antibody responses. iScience, 25(12), 1-22. Article 105649. https://doi.org/10.1016/j.isci.2022.105649
Ebberink, E. H. T. M., Ruisinger, A., Nuebel, M., Thomann, M., & Heck, A. J. R. (2022). Assessing production variability in empty and filled adeno-associated viruses by single molecule mass analyses. Molecular Therapy - Methods and Clinical Development, 27, 491-501. https://doi.org/10.1016/j.omtm.2022.11.003
Corbeski, I., Guo, X., Eckhardt, B. V., Fasci, D., Wiegant, W., Graewert, M. A., Vreeken, K., Wienk, H., Svergun, D. I., Heck, A. J. R., van Attikum, H., Boelens, R., Sixma, T. K., Mattiroli, F., & van Ingen, H. (2022). Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF. Science advances, 8(30), Article eabo0517. https://doi.org/10.1126/sciadv.abo0517
Gazi, I., Franc, V., Tamara, S., van Gool, M. P., Huppertz, T., & Heck, A. J. R. (2022). Identifying glycation hot-spots in bovine milk proteins during production and storage of skim milk powder. International Dairy Journal, 129, 1-10. Article 105340. https://doi.org/10.1016/j.idairyj.2022.105340
Leijten, N. M., Heck, A. J. R., & Lemeer, S. (2022). Histidine phosphorylation in human cells; a needle or phantom in the haystack? Nature Methods, 19(7), 827-828. https://doi.org/10.1038/s41592-022-01524-0
de Graaf, S. C., Hoek, M., Tamara, S., & Heck, A. J. R. (2022). A perspective toward mass spectrometry-based de novo sequencing of endogenous antibodies. mAbs, 14(1), 1-17. Article 2079449. https://doi.org/10.1080/19420862.2022.2079449
van Gorp, P. R. R., Zhang, J., Liu, J., Tsonaka, R., Mei, H., Dekker, S. O., Bart, C. I., De Coster, T., Post, H., Heck, A. J. R., Schalij, M. J., Atsma, D. E., Pijnappels, D. A., & de Vries, A. A. F. (2022). Sbk2, a Newly Discovered Atrium-Enriched Regulator of Sarcomere Integrity. Circulation Research, 131(1), 24-41. https://doi.org/10.1161/CIRCRESAHA.121.319300
Galhuber, M., Michenthaler, H., Heininger, C., Reinisch, I., Nössing, C., Krstic, J., Kupper, N., Moyschewitz, E., Auer, M., Heitzer, E., Ulz, P., Birner-Gruenberger, R., Liesinger, L., Lenihan-Geels, G. N., Oster, M., Spreitzer, E., Zenezini Chiozzi, R., Schulz, T. J., Schupp, M., ... Prokesch, A. (2022). Complementary omics strategies to dissect p53 signaling networks under nutrient stress. Cellular and Molecular Life Sciences, 79(6), 1-22. Article 326. https://doi.org/10.1007/s00018-022-04345-8
Jager, S., Cramer, D. A. T., Hoek, M., Mokiem, N. J., van Keulen, B. J., van Goudoever, J. B., Dingess, K. A., & Heck, A. J. R. (2022). Proteoform Profiles Reveal That Alpha-1-Antitrypsin in Human Serum and Milk Is Derived From a Common Source. Frontiers in Molecular Biosciences, 9, 1-10. Article 858856. https://doi.org/10.3389/fmolb.2022.858856
Wörner, T. P., Aizikov, K., Snijder, J., Fort, K. L., Makarov, A. A., & Heck, A. J. R. (2022). Frequency chasing of individual megadalton ions in an Orbitrap analyser improves precision of analysis in single-molecule mass spectrometry. Nature Chemistry, 14(5), 515-522. https://doi.org/10.1038/s41557-022-00897-1
Kooijman, S., Vrieling, H., Verhagen, L., de Ridder, J., de Haan, A., van Riet, E., Heck, A. J. R., Kersten, G. F. A., Pennings, J. L. A., Metz, B., & Meiring, H. D. (2022). Aluminum Hydroxide And Aluminum Phosphate Adjuvants Elicit A Different Innate Immune Response. Journal of Pharmaceutical Sciences, 111(4), 982-990. https://doi.org/10.1016/j.xphs.2022.01.014
Luijkx, Y. M. C. A., Henselijn, A. J., Bosman, G. P., Cramer, D. A. T., Giesbers, K. C. A. P., van 't Veld, E. M., Boons, G-J., Heck, A. J. R., Reiding, K. R., Strijbis, K., & Wennekes, T. (2022). Detection of Bacterial α-l-Fucosidases with an Ortho-Quinone Methide-Based Probe and Mapping of the Probe-Protein Adducts. Molecules (Basel, Switzerland), 27(5), 1-15. Article 1615. https://doi.org/10.3390/molecules27051615
van Kampen, M. D., Kuipers-De Wilt, L. H. A. M., van Egmond, M. L., Reinders-Blankert, P., van den Bremer, E. T. J., Wang, G., Heck, A. J. R., Parren, P. W. H. I., Beurskens, F. J., Schuurman, J., & de Jong, R. N. (2022). Biophysical characterization and stability of modified IgG1 antibodies with different hexamerization propensities. Journal of Pharmaceutical Sciences, 111(6), 1587-1598. https://doi.org/10.1016/j.xphs.2022.02.016
Zhang, M., Chiozzi, R. Z., Skerrett-Byrne, D. A., Veenendaal, T., University, U. M. C. U., Heck, A. J. R., Nixon, B., Helms, J. B., Gadella, B. M., & Bromfield, E. G. (2022). High Resolution Proteomic Analysis of Subcellular Fractionated Boar Spermatozoa Provides Comprehensive Insights Into Perinuclear Theca-Residing Proteins. Frontiers in Cell and Developmental Biology, 10, 1-18. Article 836208. https://doi.org/10.3389/fcell.2022.836208
Krstic, J., Reinisch, I., Schindlmaier, K., Galhuber, M., Riahi, Z., Berger, N., Kupper, N., Moyschewitz, E., Auer, M., Michenthaler, H., Nössing, C., Depaoli, M. R., Ramadani-Muja, J., Usluer, S., Stryeck, S., Pichler, M., Rinner, B., Deutsch, A. J. A., Reinisch, A., ... Prokesch, A. (2022). Fasting improves therapeutic response in hepatocellular carcinoma through p53-dependent metabolic synergism. Science advances, 8(3), 1-19. Article eabh2635. https://doi.org/10.1126/sciadv.abh2635
Klykov, O., Kopylov, M., Carragher, B., Heck, A. J. R., Noble, A. J., & Scheltema, R. A. (2022). Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology. Molecular Cell, 82(2), 285-303. https://doi.org/10.1016/j.molcel.2021.12.027
Wörner, T. P., Snijder, J., Friese, O., Powers, T., & Heck, A. J. R. (2022). Assessment of genome packaging in AAVs using Orbitrap-based charge-detection mass spectrometry. Molecular Therapy - Methods and Clinical Development, 24, 40-47. https://doi.org/10.1016/j.omtm.2021.11.013
Boer, M. A. D., Lai, S-H., Xue, X., Kampen, M. D. V., Bleijlevens, B., & Heck, A. J. R. (2022). Comparative Analysis of Antibodies and Heavily Glycosylated Macromolecular Immune Complexes by Size-Exclusion Chromatography Multi-Angle Light Scattering, Native Charge Detection Mass Spectrometry, and Mass Photometry. Analytical Chemistry, 94(2), 892-900. https://doi.org/10.1021/acs.analchem.1c03656
Tamara, S., den Boer, M. A., & Heck, A. J. R. (2022). High-Resolution Native Mass Spectrometry. Chemical Reviews, 122(8), 7269–7326. https://doi.org/10.1021/acs.chemrev.1c00212
van Bergen, W., Heck, A. J. R., & Baggelaar, M. P. (2022). Recent advancements in mass spectrometry-based tools to investigate newly synthesized proteins. Current Opinion in Chemical Biology, 66, Article 102074. https://doi.org/10.1016/j.cbpa.2021.07.001
2021
Scholarly publications
Rose, R. J., & Heck, A. J. R. (2021). Methods | Mass spectrometry of native complexes. In Encyclopedia of Biological Chemistry: Third Edition (Vol. 3, pp. 780-785). Elsevier. https://doi.org/10.1016/B978-0-12-819460-7.00586-7
Mathew, A., Buijs, R., Eijkel, G. B., Giskes, F., Dyachenko, A., van der Horst, J., Byelov, D., Spaanderman, D-J., Heck, A. J. R., Porta Siegel, T., Ellis, S. R., & Heeren, R. M. A. (2021). Ion Imaging of Native Protein Complexes Using Orthogonal Time-of-Flight Mass Spectrometry and a Timepix Detector. Journal of the American Society for Mass Spectrometry, 32(2), 569-580. https://doi.org/10.1021/jasms.0c00412
Leung, M. R., Chiozzi, R. Z., Roelofs, M. C., Hevler, J. F., Ravi, R. T., Maitan, P., Zhang, M., Henning, H., Bromfield, E. G., Howes, S. C., Gadella, B. M., Heck, A. J. R., & Zeev-Ben-Mordehai, T. (2021). In-cell structures of a conserved supramolecular array at the mitochondria-cytoskeleton interface in mammalian sperm. (pp. 1-17). bioRxiv. https://doi.org/10.1101/2021.02.16.431372
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
Almendral, J. M., Asokan, A., Berns, K. I., Chapman, M., Chatterjee, S., Chiorini, J., Flotte, T., Gao, G., Grimm, D., Hauswirth, W., Heilbronn, R., Kleinschmidt, J., Kotin, R., Lisowski, L., Logan, G., Alexander, I., Long, J., Lyumkis, D., Nathwani, A., ... Wilson, J. (2021). TRIBUTE TO MAVIS AGBANDJE-MCKENNA A Beautiful Mind and the Heart of an Explorer. Human Gene Therapy, 32(7-8), 321-326. https://doi.org/10.1089/hum.2021.29158.mam
Harding, R. J., Deme, J. C., Hevler, J. F., Tamara, S., Lemak, A., Cantle, J. P., Szewczyk, M. M., Begeja, N., Goss, S., Zuo, X., Loppnau, P., Seitova, A., Hutchinson, A., Fan, L., Truant, R., Schapira, M., Carroll, J. B., Heck, A. J. R., Lea, S. M., & Arrowsmith, C. H. (2021). Huntingtin structure is orchestrated by HAP40 and shows a polyglutamine expansion-specific interaction with exon 1. Communications Biology, 4, 1-16. Article 1374. https://doi.org/10.1038/s42003-021-02895-4
Bondt, A., Dingess, K. A., Hoek, M., van Rijswijck, D. M. H., & Heck, A. J. R. (2021). A Direct MS-Based Approach to Profile Human Milk Secretory Immunoglobulin A (IgA1) Reveals Donor-Specific Clonal Repertoires With High Longitudinal Stability. Frontiers in Immunology, 12, 1-11. Article 789748. https://doi.org/10.3389/fimmu.2021.789748
Mukherjee, S., Sanchez-Bernabeu, A., Demmers, L. C., Wu, W., & Heck, A. J. R. (2021). The HLA Ligandome Comprises a Limited Repertoire of O-GlcNAcylated Antigens Preferentially Associated With HLA-B*07:02. Frontiers in Immunology, 12, 1-10. Article 796584. https://doi.org/10.3389/fimmu.2021.796584
Yin, V., Lai, S-H., Caniels, T. G., Brouwer, P. J. M., Brinkkemper, M., Aldon, Y., Liu, H., Yuan, M., Wilson, I. A., Sanders, R. W., van Gils, M. J., & Heck, A. J. R. (2021). Probing Affinity, Avidity, Anticooperativity, and Competition in Antibody and Receptor Binding to the SARS-CoV-2 Spike by Single Particle Mass Analyses. ACS Central Science, 7(11), 1863-1873. https://doi.org/10.1021/acscentsci.1c00804
Greisch, J-F., den Boer, M. A., Lai, S-H., Gallagher, K., Bondt, A., Commandeur, J., & Heck, A. J. R. (2021). Extending Native Top-Down Electron Capture Dissociation to MDa Immunoglobulin Complexes Provides Useful Sequence Tags Covering Their Critical Variable Complementarity-Determining Regions. Analytical Chemistry, 93(48), 16068-16075. https://doi.org/10.1021/acs.analchem.1c03740
Leung, M. R., Zenezini Chiozzi, R., Roelofs, M. C., Hevler, J. F., Ravi, R. T., Maitan, P., Zhang, M., Henning, H., Bromfield, E. G., Howes, S. C., Gadella, B. M., Heck, A. J. R., & Zeev-Ben-Mordehai, T. (2021). In-cell structures of conserved supramolecular protein arrays at the mitochondria-cytoskeleton interface in mammalian sperm. Proceedings of the National Academy of Sciences of the United States of America, 118(45), 1-10. Article e2110996118. https://doi.org/10.1073/pnas.2110996118
Lai, S-H., Tamara, S., & Heck, A. J. R. (2021). Single-particle mass analysis of intact ribosomes by mass photometry and Orbitrap-based charge detection mass spectrometry. iScience, 24(11), 1-18. Article 103211. https://doi.org/10.1016/j.isci.2021.103211
Menny, A., Lukassen, M. V., Couves, E. C., Franc, V., Heck, A. J. R., & Bubeck, D. (2021). Structural basis of soluble membrane attack complex packaging for clearance. Nature Communications, 12(1), 1-11. Article 6086. https://doi.org/10.1038/s41467-021-26366-w
Lone, A. M., Giansanti, P., Jørgensen, M. J., Gjerga, E., Dugourd, A., Scholten, A., Saez-Rodriguez, J., Heck, A. J. R., & Taskén, K. (2021). Systems approach reveals distinct and shared signaling networks of the four PGE2 receptors in T cells. Science Signaling, 14(703), 1-20. Article eabc8579. https://doi.org/10.1126/scisignal.abc8579
Bondt, A., Hoek, M., Tamara, S., de Graaf, B., Peng, W., Schulte, D., van Rijswijck, D. M. H., den Boer, M. A., Greisch, J-F., Varkila, M. R. J., Snijder, J., Cremer, O. L., Bonten, M. J. M., & Heck, A. J. R. (2021). Human plasma IgG1 repertoires are simple, unique, and dynamic. Cell Systems, 12(12), 1131-1143.e5. https://doi.org/10.1016/j.cels.2021.08.008
FEBS Journal Editorial Team (2021). Editor Profile: Albert Heck. The FEBS journal, 288(18), 5228-5230. https://doi.org/10.1111/febs.15888
Hevler, J. F., Zenezeni Chiozzi, R., Cabrera-Orefice, A., Brandt, U., Arnold, S., & Heck, A. J. R. (2021). Molecular characterization of a complex of apoptosis-inducing factor 1 with cytochrome c oxidase of the mitochondrial respiratory chain. Proceedings of the National Academy of Sciences of the United States of America, 118(39), 1-10. Article e2106950118. https://doi.org/10.1073/pnas.2106950118
Reiding, K. R., Lin, Y-H., van Alphen, F. P. J., Meijer, A. B., & Heck, A. J. R. (2021). Neutrophil azurophilic granule glycoproteins are distinctively decorated by atypical pauci- and phosphomannose glycans. Communications Biology, 4(1), 1-13. Article 1012. https://doi.org/10.1038/s42003-021-02555-7
van Schaick, G., Domínguez-Vega, E., Gstöttner, C., van den Berg-Verleg, J. H., Schouten, O., Akeroyd, M., Olsthoorn, M. M. A., Wuhrer, M., Heck, A. J. R., Abello, N., & Franc, V. (2021). Native Structural and Functional Proteoform Characterization of the Prolyl-Alanyl-Specific Endoprotease EndoPro from Aspergillus niger. Journal of Proteome Research, 20(10), 4875–4885. https://doi.org/10.1021/acs.jproteome.1c00663
Hoek, M., Demmers, L. C., Wu, W., & Heck, A. J. R. (2021). Allotype-Specific Glycosylation and Cellular Localization of Human Leukocyte Antigen Class I Proteins. Journal of Proteome Research, 20(9), 4518-4528. https://doi.org/10.1021/acs.jproteome.1c00466
Dingess, K. A., Gazi, I., van den Toorn, H. W. P., Mank, M., Stahl, B., Reiding, K. R., & Heck, A. J. R. (2021). Monitoring Human Milk β-Casein Phosphorylation and O-Glycosylation Over Lactation Reveals Distinct Differences between the Proteome and Endogenous Peptidome. International Journal of Molecular Sciences, 22(15), Article 8140. https://doi.org/10.3390/ijms22158140
Kieper, S. N., Almendros, C., Haagsma, A. C., Barendregt, A., Heck, A. J. R., & Brouns, S. J. J. (2021). Cas4-Cas1 Is a Protospacer Adjacent Motif-Processing Factor Mediating Half-Site Spacer Integration During CRISPR Adaptation. CRISPR Journal, 4(4), 536-548. https://doi.org/10.1089/crispr.2021.0011
Lukassen, M. V., Franc, V., Hevler, J. F., & Heck, A. J. R. (2021). Similarities and differences in the structures and proteoform profiles of the complement proteins C6 and C7. Proteomics, 21(21-22), 1-11. Article 2000310. https://doi.org/10.1002/pmic.202000310
Dingess, K. A., van Dam, P., Zhu, J., Mank, M., Knipping, K., Heck, A. J. R., & Stahl, B. (2021). Optimization of a human milk-directed quantitative sIgA ELISA method substantiated by mass spectrometry. Analytical and Bioanalytical Chemistry, 413(20), 5037-5049. https://doi.org/10.1007/s00216-021-03468-4
Chiang, D. Y., Lahiri, S., Wang, G., Karch, J., Wang, M. C., Jung, S. Y., Heck, A. J. R., Scholten, A., & Wehrens, X. H. T. (2021). Phosphorylation-Dependent Interactome of Ryanodine Receptor Type 2 in the Heart. Proteomes, 9(2), 1-15. Article 27. https://doi.org/10.3390/proteomes9020027
Bauzá-Martinez, J., Heck, A. J. R., & Wu, W. (2021). HLA-B and cysteinylated ligands distinguish the antigen presentation landscape of extracellular vesicles. Communications Biology, 4(1), 1-11. Article 825. https://doi.org/10.1038/s42003-021-02364-y
Völlmy, F., van den Toorn, H., Zenezini Chiozzi, R., Zucchetti, O., Papi, A., Volta, C. A., Marracino, L., Vieceli Dalla Sega, F., Fortini, F., Demichev, V., Tober-Lau, P., Campo, G., Contoli, M., Ralser, M., Kurth, F., Spadaro, S., Rizzo, P., & Heck, A. J. (2021). A serum proteome signature to predict mortality in severe COVID-19 patients. Life Science Alliance, 4(9), 1-12. Article e202101099. https://doi.org/10.26508/LSA.202101099
https://dspace.library.uu.nl/bitstream/handle/1874/412548/e202101099.full.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/412548/e202101099.full.pdf?sequence=1
Hevler, J. F., Lukassen, M. V., Cabrera-Orefice, A., Arnold, S., Pronker, M. F., Franc, V., & Heck, A. J. R. (2021). Selective cross-linking of coinciding protein assemblies by in-gel cross-linking mass spectrometry. EMBO Journal, 40(4), 1-16. Article e106174. https://doi.org/10.15252/embj.2020106174
Armony, G., Heck, A. J. R., & Wu, W. (2021). Extracellular crosslinking mass spectrometry reveals HLA class I - HLA class II interactions on the cell surface. Molecular Immunology, 136, 16-25. https://doi.org/10.1016/j.molimm.2021.05.010
van Keulen, B. J., Romijn, M., Bondt, A., Dingess, K. A., Kontopodi, E., van der Straten, K., den Boer, M. A., Burger, J. A., Poniman, M., Bosch, B. J., Brouwer, P. J. M., de Groot, C. J. M., Hoek, M., Li, W., Pajkrt, D., Sanders, R. W., Schoonderwoerd, A., Tamara, S., Timmermans, R. A. H., ... van Goudoever, J. B. (2021). Human Milk from Previously COVID-19-Infected Mothers: The Effect of Pasteurization on Specific Antibodies and Neutralization Capacity. Nutrients, 13(5), 1-14. Article 1645. https://doi.org/10.3390/nu13051645
Demmers, L. C., Wu, W., & Heck, A. J. R. (2021). HLA class II presentation is specifically altered at elevated temperatures in the B-lymphoblastic cell line JY. Molecular and Cellular Proteomics, 20, Article 100089. https://doi.org/10.1016/j.mcpro.2021.100089
Čaval, T., Buettner, A., Haberger, M., Reusch, D., & Heck, A. J. R. (2021). Discrepancies between High-Resolution Native and Glycopeptide-Centric Mass Spectrometric Approaches: A Case Study into the Glycosylation of Erythropoietin Variants. Journal of the American Society for Mass Spectrometry, 32(8), 2099-2104. https://doi.org/10.1021/jasms.1c00060
Čaval, T., Lin, Y-H., Varkila, M., Reiding, K. R., Bonten, M. J. M., Cremer, O. L., Franc, V., & Heck, A. J. R. (2021). Glycoproteoform Profiles of Individual Patients' Plasma Alpha-1-Antichymotrypsin are Unique and Extensively Remodeled Following a Septic Episode. Frontiers in Immunology, 11, 1-14. Article 608466. https://doi.org/10.3389/fimmu.2020.608466
Cruz, A. R., Boer, M. A. D., Strasser, J., Zwarthoff, S. A., Beurskens, F. J., de Haas, C. J. C., Aerts, P. C., Wang, G., de Jong, R. N., Bagnoli, F., van Strijp, J. A. G., van Kessel, K. P. M., Schuurman, J., Preiner, J., Heck, A. J. R., & Rooijakkers, S. H. M. (2021). Staphylococcal protein A inhibits complement activation by interfering with IgG hexamer formation. Proceedings of the National Academy of Sciences of the United States of America, 118(7), 1-11. Article e2016772118. https://doi.org/10.1073/pnas.2016772118
Wargacki, A. J., Wörner, T. P., van de Waterbeemd, M., Ellis, D., Heck, A. J. R., & King, N. P. (2021). Complete and cooperative in vitro assembly of computationally designed self-assembling protein nanomaterials. Nature Communications, 12(1), 1-14. Article 883. https://doi.org/10.1038/s41467-021-21251-y
Zhu, J., Dingess, K. A., Mank, M., Stahl, B., & Heck, A. J. R. (2021). Personalized Profiling Reveals Donor- and Lactation-Specific Trends in the Human Milk Proteome and Peptidome. Journal of Nutrition, 151(4), 826-839. https://doi.org/10.1093/jn/nxaa445
Wörner, T. P., Bennett, A., Habka, S., Snijder, J., Friese, O., Powers, T., Agbandje-McKenna, M., & Heck, A. J. R. (2021). Adeno-associated virus capsid assembly is divergent and stochastic. Nature Communications, 12(1), 1-9. Article 1642. https://doi.org/10.1038/s41467-021-21935-5
Čaval, T., Hecht, E. S., Tang, W., Uy-Gomez, M., Nichols, A., Kil, Y. J., Sandoval, W., Bern, M., & Heck, A. J. R. (2021). The lysosomal endopeptidases Cathepsin D and L are selective and effective proteases for the middle-down characterization of antibodies. The FEBS journal, 288(18), 5389-5405. https://doi.org/10.1111/febs.15813
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
Greisch, J-F., den Boer, M. A., Beurskens, F., Schuurman, J., Tamara, S., Bondt, A., & Heck, A. J. R. (2021). Generating Informative Sequence Tags from Antigen-Binding Regions of Heavily Glycosylated IgA1 Antibodies by Native Top-Down Electron Capture Dissociation. Journal of the American Society for Mass Spectrometry, 32(6), 1326-1335. https://doi.org/10.1021/jasms.0c00461
Sturm, T., Sautter, B., Wörner, T. P., Stevanović, S., Rammensee, H-G., Planz, O., Heck, A. J. R., & Aebersold, R. (2021). Mild Acid Elution and MHC Immunoaffinity Chromatography Reveal Similar Albeit Not Identical Profiles of the HLA Class I Immunopeptidome. Journal of Proteome Research, 20(1), 289-304. https://doi.org/10.1021/acs.jproteome.0c00386
Wörner, T. P., Shamorkina, T. M., Snijder, J., & Heck, A. J. R. (2021). Mass Spectrometry-Based Structural Virology. Analytical Chemistry, 93(1), 620-640. https://doi.org/10.1021/acs.analchem.0c04339
Caval, T., Heck, A. J. R., & Reiding, K. R. (2021). Meta-heterogeneity: evaluating and describing the diversity in glycosylation between sites on the same glycoprotein. Molecular and Cellular Proteomics, 20, 1-14. Article 100010. https://doi.org/10.1074/mcp.R120.002093
2020
Scholarly publications
Greisch, J-F., van der Laarse, S. A. M., & Heck, A. J. R. (2020). Enhancing Top-Down Analysis Using Chromophore-Assisted Infrared Multiphoton Dissociation from (Phospho)peptides to Protein Assemblies. Analytical Chemistry, 92(23), 15506-15516. https://doi.org/10.1021/acs.analchem.0c03412
Luczak, E. D., Wu, Y., Granger, J. M., Joiner, M-L. A., Wilson, N. R., Gupta, A., Umapathi, P., Murphy, K. R., Reyes Gaido, O. E., Sabet, A., Corradini, E., Tseng, W-W., Wang, Y., Heck, A. J. R., Wei, A-C., Weiss, R. G., & Anderson, M. E. (2020). Mitochondrial CaMKII causes adverse metabolic reprogramming and dilated cardiomyopathy. Nature Communications, 11(1), Article 4416. https://doi.org/10.1038/s41467-020-18165-6
Zhao, Y., van Woudenbergh, E., Zhu, J., Heck, A. J. R., van Kessel, K. P. M., de Haas, C. J. C., Aerts, P. C., van Strijp, J. A. G., & McCarthy, A. J. (2020). The Orphan Immune Receptor LILRB3 Modulates Fc Receptor-Mediated Functions of Neutrophils. Journal of Immunology, 204(4), 954-966. https://doi.org/10.4049/jimmunol.1900852
Demmers, L. C., Kretzschmar, K., Van Hoeck, A., Bar-Epraïm, Y. E., van den Toorn, H. W. P., Koomen, M., van Son, G., van Gorp, J., Pronk, A., Smakman, N., Cuppen, E., Clevers, H., Heck, A. J. R., & Wu, W. (2020). Single-cell derived tumor organoids display diversity in HLA class I peptide presentation. Nature Communications, 11(1), Article 5338. https://doi.org/10.1038/s41467-020-19142-9
Wörner, T. P., Snijder, J., Bennett, A., Agbandje-McKenna, M., Makarov, A. A., & Heck, A. J. R. (2020). Resolving heterogeneous macromolecular assemblies by Orbitrap-based single-particle charge detection mass spectrometry. Nature Methods, 17(4), 395-398. https://doi.org/10.1038/s41592-020-0770-7
Neviani, V., van Deventer, S., Wörner, T. P., Xenaki, K. T., van de Waterbeemd, M., Rodenburg, R. N. P., Wortel, I. M. N., Kuiper, J. K., Huisman, S., Granneman, J., van Bergen En Henegouwen, P. M. P., Heck, A. J. R., van Spriel, A. B., & Gros, P. (2020). Site-specific functionality and tryptophan mimicry of lipidation in tetraspanin CD9. The FEBS journal, 287(24), 5323-5344. https://doi.org/10.1111/febs.15295
Wang, G., Chaihu, L., Tian, M., Shao, X., Dai, R., de Jong, R. N., Ugurlar, D., Gros, P., & Heck, A. J. R. (2020). Releasing Nonperipheral Subunits from Protein Complexes in the Gas Phase. Analytical Chemistry, 92(24), 15799–15805. https://doi.org/10.1021/acs.analchem.0c02845
den Boer, M. A., Greisch, J-F., Tamara, S., Bondt, A., & Heck, A. J. R. (2020). Selectivity over coverage in de novo sequencing of IgGs. Chemical Science, 11(43), 11886-11896. https://doi.org/10.1039/d0sc03438j
Leitner, A., Bonvin, A. M. J. J., Borchers, C. H., Chalkley, R. J., Chamot-Rooke, J., Combe, C. W., Cox, J., Dong, M-Q., Fischer, L., Götze, M., Gozzo, F. C., Heck, A. J. R., Hoopmann, M. R., Huang, L., Ishihama, Y., Jones, A. R., Kalisman, N., Kohlbacher, O., Mechtler, K., ... Rappsilber, J. (2020). Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry. Structure, 28(11), 1259-1268. https://doi.org/10.1016/j.str.2020.09.011
Zhu, J., Lin, Y., Dingess, K. A., Mank, M., Stahl, B., & Heck, A. J. R. (2020). Quantitative Longitudinal Inventory of the N-Glycoproteome of Human Milk from a Single Donor Reveals the Highly Variable Repertoire and Dynamic Site-Specific Changes. Journal of Proteome Research, 19(5), 1941-1952. https://doi.org/10.1021/acs.jproteome.9b00753
Giansanti, P., Strating, J. R. P. M., Defourny, K. A. Y., Cesonyte, I., Bottino, A. M. S., Post, H., Viktorova, E. G., Ho, V. Q. T., Langereis, M. A., Belov, G. A., Nolte-'t Hoen, E. N. M., Heck, A. J. R., & van Kuppeveld, F. J. M. (2020). Dynamic remodelling of the human host cell proteome and phosphoproteome upon enterovirus infection. Nature Communications, 11(1), 1-12. Article 4332. https://doi.org/10.1038/s41467-020-18168-3
Mank, M., Hauner, H., Heck, A. J. R., & Stahl, B. (2020). Targeted LC-ESI-MS2 characterization of human milk oligosaccharide diversity at 6 to 16 weeks post-partum reveals clear staging effects and distinctive milk groups. Analytical and Bioanalytical Chemistry, 412, 6887–6907. https://doi.org/10.1007/s00216-020-02819-x
Campbell, H. M., Quick, A. P., Abu-Taha, I., Chiang, D. Y., Kramm, C. F., Word, T. A., Brandenburg, S., Hulsurkar, M., Alsina, K. M., Liu, H-B., Martin, B., Uhlenkamp, D., Moore, O. M., Lahiri, S. K., Corradini, E., Kamler, M., Heck, A. J. R., Lehnart, S. E., Dobrev, D., & Wehrens, X. H. T. (2020). Loss of SPEG Inhibitory Phosphorylation of RyR2 Promotes Atrial Fibrillation. Circulation, 142(12), 1159–1172. https://doi.org/10.1161/CIRCULATIONAHA.120.045791
Brücher, D., Franc, V., Smith, S. N., Heck, A. J. R., & Plückthun, A. (2020). Malignant tissues produce divergent antibody glycosylation of relevance for cancer gene therapy effectiveness. mAbs, 12(1), Article 1792084. https://doi.org/10.1080/19420862.2020.1792084
Steigenberger, B., van den Toorn, H., Bijl, E., Greisch, J-F., Räther, O., Lubeck, M., Pieters, R. J., Heck, A. J. R., & Scheltema, R. A. (2020). Benefits of Collisional Cross Section Assisted Precursor Selection (caps-PASEF) for Cross-linking Mass Spectrometry. Molecular and Cellular Proteomics, 19(10), 1677-1687. https://doi.org/10.1074/mcp.RA120.002094
Rabouw, H. H., Visser, L. J., Passchier, T. C., Langereis, M. A., Liu, F., Giansanti, P., van Vliet, A. L. W., Dekker, J. G., van der Grein, S. G., Saucedo, J. G., Anand, A. A., Trellet, M. E., Bonvin, A. M. J. J., Walter, P., Heck, A. J. R., de Groot, R. J., & van Kuppeveld, F. J. M. (2020). Inhibition of the integrated stress response by viral proteins that block p-eIF2-eIF2B association. Nature Microbiology, 5, 1361-1373. https://doi.org/10.1038/s41564-020-0759-0
Yuniati, L., Lauriola, A., Gerritsen, M., Abreu, S., Ni, E., Tesoriero, C., Onireti, J. O., Low, T. Y., Heck, A. J. R., Vettori, A., Cardozo, T., & Guardavaccaro, D. (2020). Ubiquitylation of the ER-Shaping Protein Lunapark via the CRL3KLHL12 Ubiquitin Ligase Complex. Cell Reports, 31(7), Article 107664. https://doi.org/10.1016/j.celrep.2020.107664
Tamara, S., Franc, V., & Heck, A. J. R. (2020). A wealth of genotype-specific proteoforms fine-tunes hemoglobin scavenging by haptoglobin. Proceedings of the National Academy of Sciences of the United States of America, 117(27), 15554–15564 . https://doi.org/10.1073/pnas.2002483117
Vyborova, A., Beringer, D. X., Fasci, D., Karaiskaki, F., van Diest, E., Kramer, L., de Haas, A., Sanders, J., Janssen, A., Straetemans, T., Olive, D., Leusen, J. H., Boutin, L., Nedellec, S., Schwartz, S. L., Wester, M. J., Lidke, K. A., Scotet, E., Lidke, D., ... Kuball, J. (2020). γ9δ2T cell diversity and the receptor interface with tumor cells. Journal of Clinical Investigation, 130(9), 4637-4651. https://doi.org/10.1172/JCI132489
Kleinpenning, F., Steigenberger, B., Wu, W., & Heck, A. J. R. (2020). Fishing for newly synthesized proteins with phosphonate-handles. Nature Communications, 11(1), Article 3244. https://doi.org/10.1038/s41467-020-17010-0
Beumer, J., Puschhof, J., Bauzá-Martinez, J., Martínez-Silgado, A., Elmentaite, R., James, K. R., Ross, A., Hendriks, D., Artegiani, B., Busslinger, G. A., Ponsioen, B., Andersson-Rolf, A., Saftien, A., Boot, C., Kretzschmar, K., Geurts, M. H., Bar-Ephraim, Y. E., Pleguezuelos-Manzano, C., Post, Y., ... Clevers, H. (2020). High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells. Cell, 181(6), 1291-1306. https://doi.org/10.1016/j.cell.2020.04.036
Montanari, R., Capelli, D., Yamamoto, K., Awaishima, H., Nishikata, K., Barendregt, A., Heck, A. J. R., Loiodice, F., Altieri, F., Paiardini, A., Grotessi, A., Pirone, L., Pedone, E. M., Peiretti, F., Brunel, J. M., Itoh, T., & Pochetti, G. (2020). Insights into PPARγ phosphorylation and its inhibition mechanism. Journal of Medicinal Chemistry, 63(9), 4811–4823. https://doi.org/10.1021/acs.jmedchem.0c00048
Steigenberger, B., Albanese, P., Heck, A. J. R., & Scheltema, R. A. (2020). To Cleave or Not To Cleave in XL-MS? Journal of the American Society for Mass Spectrometry, 31(2), 196-206. https://doi.org/10.1021/jasms.9b00085
van der Laarse, S. A. M., van Gelder, C. A. G. H., Bern, M., Akeroyd, M., Olsthoorn, M. M. A., & Heck, A. J. R. (2020). Targeting proline in (phospho)proteomics. The FEBS journal, 287(14), 2979-2997. https://doi.org/10.1111/febs.15190
De Leoz, M. L. A., Duewer, D. L., Fung, A., Liu, L., Yau, H. K., Potter, O., Staples, G. O., Furuki, K., Frenkel, R., Hu, Y., Sosic, Z., Zhang, P., Altmann, F., Gru Nwald-Grube, C., Shao, C., Zaia, J., Evers, W., Pengelley, S., Suckau, D., ... Haselberg, R. (2020). NIST Interlaboratory Study on Glycosylation Analysis of Monoclonal Antibodies: Comparison of Results from Diverse Analytical Methods. Molecular and Cellular Proteomics, 19(1), 11-30. https://doi.org/10.1074/mcp.RA119.001677
Klykov, O., van der Zwaan, C., Heck, A. J. R., Meijer, A. B., & Scheltema, R. A. (2020). Missing regions within the molecular architecture of human fibrin clots structurally resolved by XL-MS and integrative structural modeling. Proceedings of the National Academy of Sciences of the United States of America, 117(4), 1976-1987. https://doi.org/10.1073/pnas.1911785117
Vrieling, H., Kooijman, S., de Ridder, J., Thies-Weesie, D., Soema, P., Jiskoot, W., van Riet, E., Heck, A., Philipse, A., Kersten, G., Meiring, H., Pennings, J., & Metz, B. (2020). Activation of human monocytes by colloidal aluminium salts. Journal of Pharmaceutical Sciences, 109(1), 750–760. https://doi.org/10.1016/j.xphs.2019.08.014
2019
Scholarly publications
Liu, Z., Zhou, Y., Liu, J., Chen, J., Heck, A. J. R., & Wang, F. (2019). Reductive methylation labeling, from quantitative to structural proteomics. TrAC - Trends in Analytical Chemistry, 118, 771-778. https://doi.org/10.1016/j.trac.2019.07.009
Dondelinger, Y., Delanghe, T., Priem, D., Wynosky-Dolfi, M. A., Sorobetea, D., Rojas-Rivera, D., Giansanti, P., Roelandt, R., Gropengiesser, J., Ruckdeschel, K., Savvides, S. N., Heck, A. J. R., Vandenabeele, P., Brodsky, I. E., & Bertrand, M. J. M. (2019). Serine 25 phosphorylation inhibits RIPK1 kinase-dependent cell death in models of infection and inflammation. Nature Communications, 10(1), Article 1729. https://doi.org/10.1038/s41467-019-09690-0
Alsina, K. M., Hulsurkar, M., Brandenburg, S., Kownatzki-Danger, D., Lenz, C., Urlaub, H., Abu-Taha, I., Kamler, M., Chiang, D. Y., Lahiri, S. K., Reynolds, J. O., Quick, A. P., Scott, L., Word, T. A., Gelves, M. D., Heck, A. J. R., Li, N., Dobrev, D., Lehnart, S. E., & Wehrens, X. H. T. (2019). Loss of Protein Phosphatase 1 Regulatory Subunit PPP1R3A Promotes Atrial Fibrillation. Circulation, 140(8), 681-693. https://doi.org/10.1161/CIRCULATIONAHA.119.039642
Čaval, T., Zhu, J., & Heck, A. J. R. (2019). Simply Extending the Mass Range in Electron Transfer Higher Energy Collisional Dissociation Increases Confidence in N-Glycopeptide Identification. Analytical Chemistry, 91(16), 10401-10406. https://doi.org/10.1021/acs.analchem.9b02125
Yan, K., Yang, J., Zhang, Z., McLaughlin, S. H., Chang, L., Fasci, D., Ehrenhofer-Murray, A. E., Heck, A. J. R., & Barford, D. (2019). Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome. Nature, 574(7777), 278-282. https://doi.org/10.1038/s41586-019-1609-1
Strasser, J., de Jong, R. N., Beurskens, F. J., Wang, G., Heck, A. J. R., Schuurman, J., Parren, P. W. H. I., Hinterdorfer, P., & Preiner, J. (2019). Unraveling the Macromolecular Pathways of IgG Oligomerization and Complement Activation on Antigenic Surfaces. Nano Letters, 19(7), 4787-4796. https://doi.org/10.1021/acs.nanolett.9b02220
Lin, Y-H., Zhu, J., Meijer, S., Franc, V., & Heck, A. J. R. (2019). Glycoproteogenomics: A Frequent Gene Polymorphism Affects the Glycosylation Pattern of the Human Serum Fetuin/α-2-HS-Glycoprotein. Molecular and Cellular Proteomics, 18(8), 1479-1490. https://doi.org/10.1074/mcp.RA119.001411
Masson, G. R., Burke, J. E., Ahn, N. G., Anand, G. S., Borchers, C., Brier, S., Bou-Assaf, G. M., Engen, J. R., Englander, S. W., Faber, J., Garlish, R., Griffin, P. R., Gross, M. L., Guttman, M., Hamuro, Y., Heck, A. J. R., Houde, D., Iacob, R. E., Jørgensen, T. J. D., ... Rand, K. D. (2019). Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nature Methods, 16(7), 595-602. https://doi.org/10.1038/s41592-019-0459-y
Muha, V., Williamson, R., Hills, R., McNeilly, A. D., McWilliams, T. G., Alonso, J., Schimpl, M., Leney, A. C., Heck, A. J. R., Sutherland, C., Read, K. D., McCrimmon, R. J., Brooks, S. P., & van Aalten, D. M. F. (2019). Loss of CRMP2 O-GlcNAcylation leads to reduced novel object recognition performance in mice. Biology Open, 9(11), Article 190192. https://doi.org/10.1098/rsob.190192
Reiding, K. R., Franc, V., Huitema, M. G., Brouwer, E., Heeringa, P., & Heck, A. J. R. (2019). Neutrophil myeloperoxidase harbors distinct site-specific peculiarities in its glycosylation. Journal of Biological Chemistry, 294(52), 20233-20245. https://doi.org/10.1074/jbc.RA119.011098
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
Hoeksma, J., Misset, T., Wever, C., Kemmink, J., Kruijtzer, J., Versluis, K., Liskamp, R. M. J., Boons, G. J., Heck, A. J. R., Boekhout, T., & den Hertog, J. (2019). A new perspective on fungal metabolites: identification of bioactive compounds from fungi using zebrafish embryogenesis as read-out. Scientific Reports, 9(1), Article 17546. https://doi.org/10.1038/s41598-019-54127-9
Steigenberger, B., Pieters, R. J., Heck, A. J. R., & Scheltema, R. A. (2019). PhoX: An IMAC-Enrichable Cross-Linking Reagent. ACS Central Science, 5(9), 1514-1522. https://doi.org/10.1021/acscentsci.9b00416
van der Schoot, J. M. S., Fennemann, F. L., Valente, M., Dolen, Y., Hagemans, I. M., Becker, A. M. D., Le Gall, C. M., van Dalen, D., Cevirgel, A., van Bruggen, J. A. C., Engelfriet, M., Caval, T., Bentlage, A. E. H., Fransen, M. F., Nederend, M., Leusen, J. H. W., Heck, A. J. R., Vidarsson, G., Figdor, C. G., ... Scheeren, F. A. (2019). Functional diversification of hybridoma-produced antibodies by CRISPR/HDR genomic engineering. Science advances, 5(8), Article eaaw1822. https://doi.org/10.1126/sciadv.aaw1822
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
Greisch, J. F., Tamara, S., Scheltema, R. A., Maxwell, H. W. R., Fagerlund, R. D., Fineran, P. C., Tetter, S., Hilvert, D., & Heck, A. J. R. (2019). Expanding the mass range for UVPD-based native top-down mass spectrometry. Chemical Science, 10(30), 7163-7171. https://doi.org/10.1039/c9sc01857c
Iacobucci, C., Piotrowski, C., Aebersold, R., Amaral, B. C., Andrews, P. C., Bernfur, K., Borchers, C. H., Brodie, N. I., Bruce, J. E., Cao, Y., Chaignepain, S., Chavez, J. D., Claverol, S., Cox, J., Davis, T. N., Degliesposti, G., Dong, M-Q., Edinger, N., Emanuelsson, C., ... Sinz, A. (2019). The First Community-Wide, Comparative Cross-linking Mass Spectrometry Study. Analytical Chemistry, 91(11), 6953-6961. https://doi.org/10.1021/acs.analchem.9b00658
Tamara, S., Hoek, M., Scheltema, R. A., Leney, A. C., & Heck, A. J. R. (2019). A Colorful Pallet of B-Phycoerythrin Proteoforms Exposed by a Multimodal Mass Spectrometry Approach. Chem, 5(5), 1302-1317. https://doi.org/10.1016/j.chempr.2019.03.006
Potel, C. M., Lin, M-H., Prust, N., Van den Toorn, H., Heck, A. J. R., & Lemeer, S. (2019). Gaining confidence in the elusive histidine phosphoproteome. Analytical Chemistry, 91(9), 5542-5547. https://doi.org/10.1021/acs.analchem.9b00734
Santra, T., Herrero, A., Rodriguez, J., von Kriegsheim, A., Iglesias-Martinez, L. F., Schwarzl, T., Higgins, D., Aye, T-T., Heck, A. J. R., Calvo, F., Agudo-Ibáñez, L., Crespo, P., Matallanas, D., & Kolch, W. (2019). An Integrated Global Analysis of Compartmentalized HRAS Signaling. Cell Reports, 26(11), 3100-3115.e7. https://doi.org/10.1016/j.celrep.2019.02.038
Demmers, L. C., Heck, A. J. R., & Wu, W. (2019). Pre-fractionation Extends but also Creates a Bias in the Detectable HLA Class Ι Ligandom. Journal of Proteome Research, 18(4), 1634-1643. https://doi.org/10.1021/acs.jproteome.8b00821
van den Ham, H-J., Binai, N. A., Zaaraoui-Boutahar, F., Heck, A. J. R., & Andeweg, A. C. (2019). Proteomic Profiling of Mouse Helper T Cell Differentiation. Proteomics, 19(7), e1800045. https://doi.org/10.1002/pmic.201800045
Dingess, K. A., van den Toorn, H. W. P., Mank, M., Stahl, B., & Heck, A. J. R. (2019). Toward an efficient workflow for the analysis of the human milk peptidome. Analytical and Bioanalytical Chemistry, 411(7), 1351–1363. https://doi.org/10.1007/s00216-018-01566-4
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
Zhu, J., Garrigues, L., Van den Toorn, H., Stahl, B., & Heck, A. J. R. (2019). Discovery and quantification of non-human proteins in human milk. Journal of Proteome Research, 18(1), 225-238. https://doi.org/10.1021/acs.jproteome.8b00550
Mank, M., Welsch, P., Heck, A. J. R., & Stahl, B. (2019). Label-free targeted LC-ESI-MS analysis of human milk oligosaccharides (HMOS) and related human milk groups with enhanced structural selectivity. Analytical and Bioanalytical Chemistry, 411(1), 231–250. https://doi.org/10.1007/s00216-018-1434-7
Potel, C. M., Lemeer, S., & Heck, A. J. R. (2019). Phosphopeptide fragmentation and site localization by mass spectrometry; an update. Analytical Chemistry, 91, 126-141. https://doi.org/10.1021/acs.analchem.8b04746
Caval, T., Zhu, J., Tian, W., Remmelzwaal, S., Clausen, H., & Heck, A. J. R. (2019). Targeted analysis of lysosomal directed proteins and their sites of mannose-6-phosphate modification. Molecular & Cellular Proteomics, 18(1), 16-27. https://doi.org/10.1074/mcp.RA118.000967
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
Dyachenko, A., Tamara, S., & Heck, A. J. R. (2019). Distinct Stabilities of the Structurally Homologous Heptameric Co-Chaperonins GroES and gp31. Journal of the American Society for Mass Spectrometry, 30(1), 7-15. https://doi.org/10.1007/s13361-018-1910-5
Carrasco, K., Boufenzer, A., Jolly, L., Le Cordier, H., Wang, G., Heck, A. J., Cerwenka, A., Vinolo, E., Nazabal, A., Kriznik, A., Launay, P., Gibot, S., & Derive, M. (2019). TREM-1 multimerization is essential for its activation on monocytes and neutrophils. Cellular Immunology, 16, 460-472. https://doi.org/10.1038/s41423-018-0003-5
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
Antonova, S. V., Haffke, M., Corradini, E., Mikuciunas, M., Low, T. Y., Signor, L., van Es, R. M., Gupta, K., Scheer, E., Vos, H. R., Tora, L., Heck, A. J. R., Timmers, H. T. M., & Berger, I. (2018). Chaperonin CCT checkpoint function in basal transcription factor TFIID assembly. Nature Structural and Molecular Biology, 25, 1119-1127. https://doi.org/10.1038/s41594-018-0156-z
Reiding, K. R., Bondt, A., Franc, V., & Heck, A. J. R. (2018). The benefits of hybrid fragmentation methods for glycoproteomics. TrAC - Trends in Analytical Chemistry, 108, 260-268. https://doi.org/10.1016/j.trac.2018.09.007
Van De Waterbeemd, M., Tamara, S., Fort, K. L., Damoc, E., Franc, V., Bieri, P., Itten, M., Makarov, A., Ban, N., & Heck, A. J. R. (2018). Dissecting ribosomal particles throughout the kingdoms of life using advanced hybrid mass spectrometry methods. Nature Communications, 9(1), Article 2493. https://doi.org/10.1038/s41467-018-04853-x
Klykov, O., Steigenberger, B., Pektaş, S., Fasci, D., Heck, A. J. R., & Scheltema, R. A. (2018). Efficient and robust proteome-wide approaches for cross-linking mass spectrometry. Nature Protocols, 13, 2964–2990. https://doi.org/10.1038/s41596-018-0074-x
https://dspace.library.uu.nl/bitstream/handle/1874/373357/10.1038s41596_018_0074_x.pdf?sequence=3
https://dspace.library.uu.nl/bitstream/handle/1874/373357/10.1038s41596_018_0074_x.pdf?sequence=3
Lin, M-H., Potel, C. M., Tehrani, K. H. M. E., Heck, A. J. R., Martin, N. I., & Lemeer, S. (2018). A new tool to reveal bacterial signaling mechanisms in antibiotic treatment and resistance. Molecular and Cellular Proteomics, 17(12), 2496-2507. https://doi.org/10.1074/mcp.RA118.000880
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
Sostaric, N., O'Reilly, F. J., Giansanti, P., Heck, A. J. R., Gavin, A-C., & van Noort, V. (2018). Effects of acetylation and phosphorylation on subunit interactions in three large eukaryotic complexes. Molecular and Cellular Proteomics, 17(12). https://doi.org/10.1074/mcp.RA118.000892
Čaval, T., Tian, W., Yang, Z., Clausen, H., & Heck, A. J. R. (2018). Direct quality control of glycoengineered erythropoietin variants. Nature Communications, 9(1), Article 3342. https://doi.org/10.1038/s41467-018-05536-3
Fasci, D., van Ingen, H., Scheltema, R. A., & Heck, A. J. R. (2018). Histone interaction landscapes visualized by crosslinking mass spectrometry in intact cell nuclei. Molecular and Cellular Proteomics, 17(10), 2018-2033. https://doi.org/10.1074/mcp.RA118.000924
Lizatović, R., Assent, M., Barendregt, A., Dahlin, J., Bille, A., Satzinger, K., Tupina, D., Heck, A., Wennmalm, S., & André, I. (2018). A protein encapsulation system with Ca2+-controlled cargo loading and detachment. Angewandte Chemie-International Edition, 57(35), 11334-11338. https://doi.org/10.1002/anie.201806466
Lin, Y-H., Franc, V., & Heck, A. J. R. (2018). Similar albeit not the same; in-depth analysis of proteoforms of human serum, bovine serum and recombinant human fetuin. Journal of Proteome Research, 17(8), 2861-2869. https://doi.org/10.1021/acs.jproteome.8b00318
Magliozzi, R., Carrero, Z. I., Low, T. Y., Yuniati, L., Valdes-Quezada, C., Kruiswijk, F., van Wijk, K., Heck, A. J. R., Jackson, C. L., & Guardavaccaro, D. (2018). Inheritance of the Golgi Apparatus and Cytokinesis Are Controlled by Degradation of GBF1. Cell Reports, 23(11), 3381-3391.e4. https://doi.org/10.1016/j.celrep.2018.05.031
Potel, C. M., Fasci, D., & Heck, A. J. R. (2018). Mix and match of the tumor metastasis suppressor Nm23 protein isoforms in vitro and in vivo. The FEBS journal, 285(15), 2856-2868. https://doi.org/10.1111/febs.14525
Kooijman, S., Brummelman, J., van Els, C. A. C. M., Marino, F., Heck, A. J. R., van Riet, E., Metz, B., Kersten, G. F. A., Pennings, J. L. A., & Meiring, H. D. (2018). Vaccine antigens modulate the innate response of monocytes to Al(OH)3. PLoS One, 13(5), Article e0197885. https://doi.org/10.1371/journal.pone.0197885
Lill, J. R., van Veelen, P. A., Tenzer, S., Admon, A., Caron, E., Elias, J., Heck, A. J. R., Marcilla, M., Marino, F., Müller, M., Peters, B., Purcell, A. W., Sette, A., Sturm, T., Ternette, N., Vizcaíno, J. A., & Bassani-Sternberg, M. (2018). Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE). Proteomics, 18(12), Article e1800110. https://doi.org/10.1002/pmic.201800110
Sigmund, F., Massner, C., Erdmann, P., Stelzl, A., Rolbieski, H., Desai, M., Bricault, S., Wörner, T. P., Snijder, J., Geerlof, A., Fuchs, H., Hrabĕ de Angelis, M., Heck, A. J. R., Jasanoff, A., Ntziachristos, V., Plitzko, J., & Westmeyer, G. G. (2018). Bacterial encapsulins as orthogonal compartments for mammalian cell engineering. Nature Communications, 9(1), Article 1990. https://doi.org/10.1038/s41467-018-04227-3
van der Laarse, S. A. M., Leney, A. C., & Heck, A. J. R. (2018). Crosstalk between phosphorylation and O-GlcNAcylation: friend or foe. The FEBS journal, 285(17), 3152-3167. https://doi.org/10.1111/febs.14491
Wu, W., Zaal, E. A., Berkers, C. R., Lemeer, S., & Heck, A. J. R. (2018). CTGF/VEGFA-activated fibroblasts promote tumor migration through micro-environmental modulation. Molecular and Cellular Proteomics, 17(8), 1502-1514. https://doi.org/10.1074/mcp.RA118.000708
Chiang, D. Y., Alsina, K. M., Corradini, E., Fitzpatrick, M., Ni, L., Lahiri, S. K., Reynolds, J., Pan, X., Scott, L., Heck, A. J. R., & Wehrens, X. H. T. (2018). Rearrangement of the Protein Phosphatase 1 Interactome During Heart Failure Progression. Circulation, 138, 1569–1581. https://doi.org/10.1161/CIRCULATIONAHA.118.034361
Gerlach, J. P., Jordens, I., Tauriello, D. V. F., van 't Land-Kuper, I., Bugter, J. M., Noordstra, I., van der Kooij, J., Low, T. Y., Pimentel-Muiños, F. X., Xanthakis, D., Fenderico, N., Rabouille, C., Heck, A. J. R., Egan, D. A., & Maurice, M. M. (2018). TMEM59 potentiates Wnt signaling by promoting signalosome formation. Proceedings of the National Academy of Sciences of the United States of America, 115(17), E3996-E4005;. https://doi.org/10.1073/pnas.1721321115
Franc, V., Zhu, J., & Heck, A. J. R. (2018). Comprehensive Proteoform Characterization of Plasma Complement Component C8αβγ by Hybrid Mass Spectrometry Approaches. Journal of the American Society for Mass Spectrometry, 29(6), 1099-1110. https://doi.org/10.1007/s13361-018-1901-6
Halim, V. A., García-Santisteban, I., Warmerdam, D. O., van den Broek, B., Heck, A. J. R., Mohammed, S., & Medema, R. H. (2018). Doxorubicin-induced DNA damage causes extensive ubiquitination of ribosomal proteins associated with a decrease in protein translation. Molecular and Cellular Proteomics, 17(12), 2297-2308. https://doi.org/10.1074/mcp.RA118.000652
Potel, C. M., Lin, M-H., Heck, A. J. R., & Lemeer, S. (2018). Defeating major contaminants in Fe-IMAC phosphopeptide enrichment. Molecular and Cellular Proteomics, 17(5). https://doi.org/10.1074/mcp.TIR117.000518
Bern, M., Caval, T., Kil, Y. J., Tang, W., Becker, C., Carlson, E., Kletter, D., Sen, K. I., Galy, N., Hagemans, D., Franc, V., & Heck, A. J. R. (2018). Parsimonious Charge Deconvolution for Native Mass Spectrometry. Journal of Proteome Research, 17(3), 1216-1226. https://doi.org/10.1021/acs.jproteome.7b00839
Potel, C. M., Lin, M-H., Heck, A. J. R., & Lemeer, S. (2018). Widespread bacterial protein histidine phosphorylation revealed by mass spectrometry-based proteomics. Nature Methods, 15, 187-190. https://doi.org/10.1038/nmeth.4580
https://dspace.library.uu.nl/bitstream/handle/1874/362159/10.1038nmeth.4580_2018_Potel_et_al.pdf?sequence=3
https://dspace.library.uu.nl/bitstream/handle/1874/362159/10.1038nmeth.4580_2018_Potel_et_al.pdf?sequence=3
Huijbers, M. M. E., van Alen, I., Wu, J. W., Barendregt, A., Heck, A. J. R., & van Berkel, W. J. H. (2018). Functional Impact of the N-terminal Arm of Proline Dehydrogenase from Thermus thermophilus. Molecules, 23(1), Article 184. https://doi.org/10.3390/molecules23010184
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
Kooijman, S., Brummelman, J., van Els, C. A. C. M., Marino, F., Heck, A. J. R., Mommen, G. P. M., Metz, B., Kersten, G. F. A., Pennings, J. L. A., & Meiring, H. D. (2018). Novel identified aluminum hydroxide-induced pathways proof monocyte activation and pro-inflammatory preparedness. Journal of Proteomics, 175, 144-155. https://doi.org/10.1016/j.jprot.2017.12.021
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
Fort, K. L., Cramer, C. N., Voinov, V. G., Vasilev, Y. V., Lopez, N. I., Beckman, J. S., & Heck, A. J. R. (2018). Exploring ECD on a benchtop Q Exactive Orbitrap Mass Spectrometer. Journal of Proteome Research, 17(2), 926–933. https://doi.org/10.1021/acs.jproteome.7b00622
Liu, F., Lössl, P., Rabbitts, B. M., Balaban, R. S., & Heck, A. J. R. (2018). The interactome of intact mitochondria by cross-linking mass spectrometry provides evidence for co-existing respiratory supercomplexes. Molecular and Cellular Proteomics, 17(2), 216-232. https://doi.org/10.1074/mcp.RA117.000470
Shao, W., Pedrioli, P. G. A., Wolski, W., Scurtescu, C., Schmid, E., Vizcaíno, J. A., Courcelles, M., Schuster, H., Kowalewski, D., Marino, F., Arlehamn, C. S. L., Vaughan, K., Peters, B., Sette, A., Ottenhoff, T. H. M., Meijgaarden, K. E., Nieuwenhuizen, N., Kaufmann, S. H. E., Schlapbach, R., ... Caron, E. (2018). The SysteMHC Atlas project. Nucleic Acids Research, 46(D1), D1237–D1247. https://doi.org/10.1093/nar/gkx664
Leney, A. C., Tschanz, A., & Heck, A. J. R. (2018). Connecting color with assembly in the fluorescent B-phycoerythrin protein complex. The FEBS journal, 285(1), 178-187. https://doi.org/10.1111/febs.14331
Fort, K. L., van de Waterbeemd, M., Boll, D., Reinhardt-Szyba, M., Belov, M. E., Sasaki, E., Zschoche, R., Hilvert, D., Makarov, A. A., & Heck, A. J. R. (2018). Expanding the structural analysis capabilities on an Orbitrap-based mass spectrometer for large macromolecular complexes. The Analyst, 143(1), 100-105. https://doi.org/10.1039/c7an01629h
van Ooijen, M. P., Jong, V. L., Eijkemans, M. J. C., Heck, A. J. R., Andeweg, A. C., Binai, N. A., & van den Ham, H-J. (2018). Identification of differentially expressed peptides in high-throughput proteomics data. Briefings in Bioinformatics, 19(5), 971–981. https://doi.org/10.1093/bib/bbx031
2017
Scholarly publications
Fagerlund, R. D., Wilkinson, M. E., Klykov, O., Barendregt, A., Pearce, F. G., Kieper, S. N., Maxwell, H. W. R., Capolupo, A., Heck, A. J. R., Krause, K. L., Bostina, M., Scheltema, R. A., Staals, R. H. J., & Fineran, P. C. (2017). Spacer capture and integration by a type I-F Cas1-Cas2-3 CRISPR adaptation complex. Proceedings of the National Academy of Sciences of the United States of America, 114(26), 5122-5128. https://doi.org/10.1073/pnas.1618421114
Leney, A. C., Rafie, K., Van Aalten, D. M. F., & Heck, A. J. R. (2017). Direct Monitoring of Protein O-GlcNAcylation by High-Resolution Native Mass Spectrometry. ACS Chemical Biology, 12(8), 2078-2084. https://doi.org/10.1021/acschembio.7b00371
Vizcaíno, J. A., Walzer, M., Jiménez, R. C., Bittremieux, W., Bouyssié, D., Carapito, C., Corrales, F., Ferro, M., Heck, A. J. R., Horvatovich, P., Hubalek, M., Lane, L., Laukens, K., Levander, F., Lisacek, F., Novak, P., Palmblad, M., Piovesan, D., Pühler, A., ... Kohlbacher, O. (2017). A community proposal to integrate proteomics activities in ELIXIR. F1000Research, 6. https://doi.org/10.12688/f1000research.11751.1
Joshi, R. N., Binai, N. A., Marabita, F., Sui, Z., Altman, A., Heck, A. J. R., Tegnér, J., & Schmidt, A. (2017). Phosphoproteomics Reveals Regulatory T Cell-Mediated DEF6 Dephosphorylation That Affects Cytokine Expression in Human Conventional T Cells. Frontiers in Immunology, 8, Article 1163. https://doi.org/10.3389/fimmu.2017.01163
Leney, A. C., El Atmioui, D., Wu, W., Ovaa, H., & Heck, A. J. R. (2017). Elucidating crosstalk mechanisms between phosphorylation and O-GlcNAcylation. Proceedings of the National Academy of Sciences of the United States of America, 114(35), E7255-E7261. https://doi.org/10.1073/pnas.1620529114
Mezzadra, R., Sun, C., Jae, L. T., Gomez-Eerland, R., de Vries, E., Wu, W., Logtenberg, M. E. W., Slagter, M., Rozeman, E. A., Hofland, I., Broeks, A., Horlings, H. M., Wessels, L. F. A., Blank, C. U., Xiao, Y., Heck, A. J. R., Borst, J., Brummelkamp, T. R., & Schumacher, T. N. M. (2017). Identification of CMTM6 and CMTM4 as PD-L1 protein regulators. Nature, 549(7670), 106-110. https://doi.org/10.1038/nature23669
Tamara, S., Scheltema, R. A., Heck, A. J. R., & Leney, A. C. (2017). Phosphate Transfer in Activated Protein Complexes Reveals Interaction Sites. Angewandte Chemie-International Edition, 56(44), 13641-13644. https://doi.org/10.1002/anie.201706749
https://dspace.library.uu.nl/bitstream/handle/1874/357752/10.1002anie.201706749_Tamara_et_al._2017.pdf?sequence=3
https://dspace.library.uu.nl/bitstream/handle/1874/357752/10.1002anie.201706749_Tamara_et_al._2017.pdf?sequence=3
Liu, Q., Remmelzwaal, S., Heck, A. J. R., Akhmanova, A., & Liu, F. (2017). Facilitating identification of minimal protein binding domains by cross-linking mass spectrometry. Scientific Reports, 7(1), Article 13453. https://doi.org/10.1038/s41598-017-13663-y
Rodenburg, R. N. P., Snijder, J., van de Waterbeemd, M., Schouten, A., Granneman, J., Heck, A. J. R., & Gros, P. (2017). Stochastic palmitoylation of accessible cysteines in membrane proteins revealed by native mass spectrometry. Nature Communications, 8(1), Article 1280. https://doi.org/10.1038/s41467-017-01461-z
Leloup, N., Lössl, P., Meijer, D. H., Brennich, M., Heck, A. J. R., Thies-Weesie, D. M. E., & Janssen, B. J. C. (2017). Low pH-induced conformational change and dimerization of sortilin triggers endocytosed ligand release. Nature Communications, 8(1), 1708. https://doi.org/10.1038/s41467-017-01485-5
Tsiatsiani, L., Akeroyd, M., Olsthoorn, M., & Heck, A. J. R. (2017). The Aspergillus niger Prolyl endoprotease (An-PEP) for hydrogen-deuterium exchange mass spectrometry and protein structural studies. Analytical Chemistry, 89, 7966-7973. https://doi.org/10.1021/acs.analchem.7b01161
Montersino, S., Te Poele, E., Orru, R., Westphal, A. H., Barendregt, A., Heck, A. J. R., van der Geize, R., Dijkhuizen, L., Mattevi, A., & van Berkel, W. J. H. (2017). 3-Hydroxybenzoate 6-Hydroxylase from Rhodococcus jostii RHA1 Contains a Phosphatidylinositol Cofactor. Frontiers in Microbiology, 8, Article 1110. https://doi.org/10.3389/fmicb.2017.01110
Leestemaker, Y., de Jong, A., Witting, K. F., Penning, R., Schuurman, K., Rodenko, B., Zaal, E. A., van de Kooij, B., Laufer, S., Heck, A. J. R., Borst, J., Scheper, W., Berkers, C. R., & Ovaa, H. (2017). Proteasome Activation by Small Molecules. Cell Chemical Biology, 24(6), 725-736.e7. https://doi.org/10.1016/j.chembiol.2017.05.010
Liu, F., Lössl, P., Scheltema, R., Viner, R., & Heck, A. J. R. (2017). Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification. Nature Communications, 8, 1-8. Article 15473. https://doi.org/10.1038/ncomms15473
Yang, Y., Franc, V., & Heck, A. J. R. (2017). Glycoproteomics: A Balance between High-Throughput and In-Depth Analysis. Trends in Biotechnology, 35(7), 598-609. https://doi.org/10.1016/j.tibtech.2017.04.010
Tak, T., Wijten, P., Heeres, M., Pickkers, P., Scholten, A., Heck, A. J. R., Vrisekoop, N., Leenen, L. P., Borghans, J. E. A. M., Tesselaar, K., & Koenderman, L. (2017). Human CD62L(dim) Neutrophils Identified as a Separate Subset by Proteome Profiling and In Vivo Pulse-Chase Labelling. Blood, 129(26), 3476-3485. https://doi.org/10.1182/blood-2016-07-727669
Snijder, J., Radtke, K., Anderson, F., Scholtes, L., Corradini, E., Baines, J., Heck, A. J. R., Wuite, G. J. L., Sodeik, B., & Roos, W. H. (2017). The vertex specific proteins pUL17 and pUL25 mechanically reinforce Herpes Simplex Virus capsids. Journal of Virology, 91(10). https://doi.org/10.1128/JVI.00123-17
Wang, G., de Jong, R. N., van den Bremer, E. T. J., Parren, P. W. H. I., & Heck, A. J. R. (2017). Enhancing Accuracy in Molecular Weight Determination of Highly Heterogeneously Glycosylated Proteins by Native Tandem Mass Spectrometry. Analytical Chemistry, 89(9), 4793–4797. https://doi.org/10.1021/acs.analchem.6b05129
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
van de Waterbeemd, M., Llauró, A., Snijder, J., Valbuena, A., Rodríguez-Huete, A., Fuertes, M. A., de Pablo, P. J., Mateu, M. G., & Heck, A. J. R. (2017). Structural Analysis of a Temperature-Induced Transition in a Viral Capsid Probed by HDX-MS. Biophysical Journal, 112(6), 1157-1165. https://doi.org/10.1016/j.bpj.2017.02.003
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
van Riel, W. E., Rai, A., Bianchi, S., Katrukha, E. A., Liu, Q., Heck, A. J., Hoogenraad, C. C., Steinmetz, M. O., Kapitein, L. C., & Akhmanova, A. (2017). Kinesin-4 KIF21B is a potent microtubule pausing factor. eLife, 6, Article e24746. https://doi.org/10.7554/eLife.24746
Yang, Y., Wang, G., Song, T., Lebrilla, C. B., & Heck, A. J. R. (2017). Resolving the micro-heterogeneity and structural integrity of monoclonal antibodies by hybrid mass spectrometric approaches. mAbs, 1-8. https://doi.org/10.1080/19420862.2017.1290033
Mahmoudi, T., Boj, S. F., Hatzis, P., Li, V. S. W., Taouatas, N., Vries, R. G. J., Teunissen, H., Begthel, H., Korving, J., Mohammed, S., Heck, A. J. R., & Clevers, H. (2017). Correction: The Leukemia-Associated Mllt10/Af10-Dot1l Are Tcf4/β-Catenin Coactivators Essential for Intestinal Homeostasis. PLoS Biology, 15(2), Article 1002596. https://doi.org/10.1371/journal.pbio.1002596
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
Franc, V., Yang, Y., & Heck, A. J. R. (2017). Proteoform Profile Mapping of the Human Serum Complement Component C9 Revealing Unexpected New Features of N-, O-, and C-Glycosylation. Analytical Chemistry, 89(6), 3483–3491. https://doi.org/10.1021/acs.analchem.6b04527
Cristobal Gonzalez de Durana, A., Marino, F., Post, H., van den Toorn, H. W. P., Mohammed, S., & Heck, A. J. R. (2017). Toward an Optimized Workflow for Middle-Down Proteomics. Analytical Chemistry, 89(6), 3318-3325. https://doi.org/10.1021/acs.analchem.6b03756
Sasaki, E., Böhringer, D., van de Waterbeemd, M., Leibundgut, M., Zschoche, R., Heck, A. J. R., Ban, N., & Hilvert, D. (2017). Structure and assembly of scalable porous protein cages. Nature Communications, 8, Article 14663. https://doi.org/10.1038/ncomms14663
Snijder, J., Schuller, J. M., Wiegard, A., Lössl, P., Schmelling, N., Axmann, I. M., Plitzko, J. M., Förster, F., & Heck, A. J. R. (2017). Structures of the cyanobacterial circadian oscillator frozen in a fully assembled state. Science, 355(6330), 1181-1184. https://doi.org/10.1126/science.aag3218
De Nardis, C., Lössl, P., Van Den Biggelaar, M., Madoori, P. K., Leloup, N., Mertens, K., Heck, A. J. R., & Gros, P. (2017). Recombinant expression of the full-length ectodomain of LDL receptor-related protein 1 (LRP1) unravels phdependent conformational changes and the stoichiometry of binding with receptor-associated protein (RAP). Journal of Biological Chemistry, 292(3), 912-924. https://doi.org/10.1074/jbc.M116.758862
Lebesgue, N., Megyeri, M., Cristobal Gonzalez de Durana, A., Scholten, A., Chuartzman, S. G., Voichek, Y., Scheltema, R. A., Mohammed, S., Futerman, A. H., Schuldiner, M., Heck, A. J. R., & Lemeer, S. (2017). Combining Deep Sequencing, Proteomics, Phosphoproteomics, and Functional Screens To Discover Novel Regulators of Sphingolipid Homeostasis. Journal of Proteome Research, 16(2), 571-582. https://doi.org/10.1021/acs.jproteome.6b00691
van de Waterbeemd, M., Fort, K. L., Boll, D., Reinhardt-Szyba, M., Routh, A., Makarov, A., & Heck, A. J. R. (2017). High-fidelity mass analysis unveils heterogeneity in intact ribosomal particles. Nature Methods, 14, 283-286. https://doi.org/10.1038/nmeth.4147
https://dspace.library.uu.nl/bitstream/handle/1874/347942/10.1038nmeth.4147_2017_van_de_Waterbeemd.pdf?sequence=3
https://dspace.library.uu.nl/bitstream/handle/1874/347942/10.1038nmeth.4147_2017_van_de_Waterbeemd.pdf?sequence=3
Cristobal Gonzalez de Durana, A., van den Toorn, H. W. P., van de Wetering, M., Clevers, H., Heck, A. J. R., & Mohammed, S. (2017). Personalized Proteome Profiles of Healthy and Tumor Human Colon Organoids Reveal Both Individual Diversity and Basic Features of Colorectal Cancer. Cell Reports, 18(1), 263-274. https://doi.org/10.1016/j.celrep.2016.12.016
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
https://dspace.library.uu.nl/bitstream/handle/1874/396065/10.1021acs.jproteome.6b00825_Tsiatsiani_et_al_2017_JPR.pdf?sequence=1
Gagarinov, I. A., Li, T., Sastre Torano, J., Caval, T., Srivastava, A. D., Kruijtzer, J. A. W., Heck, A. J. R., & Boons, G-J. (2017). A Chemoenzymatic Approach for the Preparation of Asymmetric Bi-, Tri- and Tetra-Antennary N-Glycans from a Common Precursor. Journal of the American Chemical Society. https://doi.org/10.1021/jacs.6b12080
Loo, J. A., & Heck, A. J. R. (2017). Editorial and Review: 31st ASMS Asilomar Conference on Native Mass Spectrometry-Based Structural Biology. Journal of the American Society for Mass Spectrometry, 28(1), 1-4. https://doi.org/10.1007/s13361-016-1540-8
Alpízar, A., Marino, F., Ramos-Fernández, A., Lombardía, M., Jeko, A., Pazos, F., Paradela, A., Santiago, C., Heck, A. J. R., & Marcilla, M. (2017). A molecular basis for the presentation of phosphorylated peptides by HLA-B antigens. Molecular and Cellular Proteomics, 16(2), 181-193. https://doi.org/10.1074/mcp.M116.063800
Leney, A. C., & Heck, A. J. R. (2017). Native Mass Spectrometry: What is in the Name? Journal of the American Society for Mass Spectrometry, 28(1), 5-13. https://doi.org/10.1007/s13361-016-1545-3
van Heesbeen, R. G. H. P., Raaijmakers, J. A., Tanenbaum, M. E., Halim, V. A., Lelieveld, D., Lieftink, C., Heck, A. J. R., Egan, D. A., & Medema, R. H. (2017). Aurora A, MCAK, and Kif18b promote Eg5-independent spindle formation. Chromosoma, 126(4), 473-486. https://doi.org/10.1007/s00412-016-0607-4
Other output
Heck, A. J. R. (2017). Probing protein assemblies and interactions by hybrid mass spectrometry approaches. FASEB Journal, 31(1), 259.3. http://www.fasebj.org/doi/abs/10.1096/fasebj.31.1_supplement.259.3
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
Sankaran, S., Stojanovic, I., Barendregt, A., Heck, A. J. R., Schasfoort, R. B. M., & Jonkheijm, P. (2016). Scaffolding of Cystine-Stabilized Miniproteins. ChemistrySelect, 1(5), 1039-1046. https://doi.org/10.1002/slct.201600323
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
Liepe, J., Marino, F., Sidney, J., Jeko, A., Bunting, D. E., Sette, A., Kloetzel, P. M., Stumpf, M. P. H., Heck, A. J. R., & Mishto, M. (2016). A large fraction of HLA class I ligands are proteasome-generated spliced peptides. Science, 354(6310), 354-358. https://doi.org/10.1126/science.aaf4384
Kaplan, M., Narasimhan, S., de Heus, C., Mance, D., van Doorn, S., Houben, K., Popov-Celeketic, D., Damman, R., Katrukha, E. A., Jain, P., Geerts, W. J. C., Heck, A. J. R., Folkers, G. E., Kapitein, L. C., Lemeer, S., van Bergen En Henegouwen, P. M. P., & Baldus, M. (2016). EGFR Dynamics Change during Activation in Native Membranes as Revealed by NMR. Cell, 167(5), 1241-1251.e11. https://doi.org/10.1016/j.cell.2016.10.038
Pronker, M. F., Lemstra, S., Snijder, J., Heck, A. J. R., Thies - Weesie, D., Pasterkamp, R. J., & Janssen, B. J. C. (2016). Structural basis of myelin-associated glycoprotein adhesion and signalling. Nature Communications, 7, 1-13. Article 13584. https://doi.org/10.1038/ncomms13584
Lössl, P., van de Waterbeemd, M., & Heck, A. J. (2016). The diverse and expanding role of mass spectrometry in structural and molecular biology. EMBO Journal, Article e201694818. https://doi.org/10.15252/embj.201694818
Yang, Y., Liu, F., Franc, V., Halim, L. A., Schellekens, H., & Heck, A. J. R. (2016). Hybrid mass spectrometry approaches in glycoprotein analysis and their usage in scoring biosimilarity. Nature Communications [E], 7, 13397. https://doi.org/10.1038/ncomms13397
Chiang, D. Y., Heck, A. J. R., Dobrev, D., & Wehrens, X. H. T. (2016). Regulating the regulator: Insights into the cardiac protein phosphatase 1 interactome. Journal of Molecular and Cellular Cardiology, 101, 165-172. https://doi.org/10.1016/j.yjmcc.2016.09.009
Portegijs, V., Fielmich, L-E., Galli, M., Schmidt, R., Munoz Peralta, J., van Mourik, T., Akhmanova, A., Heck, A. J. R., Boxem, M., & van den Heuvel, S. (2016). Multisite Phosphorylation of NuMA-Related LIN-5 Controls Mitotic Spindle Positioning in C. elegans. PLoS Genetics, 12(10), 1-32. Article e1006291. https://doi.org/10.1371/journal.pgen.1006291
Lössl, P., Brunner, A. M., Liu, F., Leney, A. C., Yamashita, M., Scheltema, R. A., & Heck, A. J. R. (2016). Deciphering the Interplay among Multisite Phosphorylation, Interaction Dynamics, and Conformational Transitions in a Tripartite Protein System. ACS Central Science, 2(7), 445-455. https://doi.org/10.1021/acscentsci.6b00053
Tamara, S., Dyachenko, A., Fort, K. L., Makarov, A. A., Scheltema, R. A., & Heck, A. J. R. (2016). Symmetry of Charge Partitioning in Collisional and UV Photon-Induced Dissociation of Protein Assemblies. Journal of the American Chemical Society, 138(34), 10860-10868. https://doi.org/10.1021/jacs.6b05147
Marino, F., Mommen, G. P. M., Jeko, A., Meiring, H. D., van Gaans-van den Brink, J. A. M., Scheltema, R. A., van Els, C. A. C. M., & Heck, A. J. R. (2016). Arginine (Di)methylated Human Leukocyte Antigen Class I Peptides Are Favorably Presented by HLA-B*07. Journal of Proteome Research, 16(1), 34-44. https://doi.org/10.1021/acs.jproteome.6b00528
Liu, Q., Liu, F., Yu, K. L., Tas, R., Grigoriev, I., Remmelzwaal, S., Marques, A., Kapitein, L. C., Heck, A. J. R., & Akhmanova, A. (2016). MICAL3 flavoprotein monooxygenase forms a complex with centralspindlin and regulates cytokinesis. Journal of Biological Chemistry. https://doi.org/10.1074/jbc.M116.748186
Waaijers, S., Muñoz, J., Berends, C., Ramalho, J. J., Goerdayal, S. S., Low, T. Y., Zoumaro-Djayoon, A. D., Hoffmann, M., Koorman, T., Tas, R. P., Harterink, M., Seelk, S., Kerver - Stumpfova, J., Hoogenraad, C. C., Bossinger, O., Tursun, B., van den Heuvel, S., Heck, A. J. R., & Boxem, M. (2016). A tissue-specific protein purification approach in Caenorhabditis elegans identifies novel interaction partners of DLG-1/Discs large. BMC Biology, 14, Article 66. https://doi.org/10.1186/s12915-016-0286-x
https://dspace.library.uu.nl/bitstream/handle/1874/341483/protein.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/341483/protein.pdf?sequence=1
Barasa, B. A., van Oirschot, B. A., Bianchi, P., van Solinge, W. W., Heck, A. J. R., van Wijk, R., & Slijper, M. (2016). Proteomics reveals reduced expression of transketolase in pyrimidine 5'-nucleotidase deficient patients. Proteomics - Clinical Applications, 10(8), 859-869. https://doi.org/10.1002/prca.201500130
Snijder, J., Kononova, O., Barbu, I. M., Uetrecht, C., Rurup, W. F., Koay, M. S. T., Burnley, R. J., Cornelissen, J. J. L. M., Roos, W. H., Barsegov, V., Wuite, G. J. L., & Heck, A. J. R. (2016). Assembly and Mechanical Properties of the Cargo-Free and Cargo-Loaded Bacterial Nanocompartment Encapsulin. Biomacromolecules. https://doi.org/10.1021/acs.biomac.6b00469
Wang, G., de Jong, R. N., van den Bremer, E. T. J., Beurskens, F. J., Labrijn, A. F., Ugurlar, D., Gros, P., Schuurman, J., Parren, P. W. H. I., & Heck, A. J. R. (2016). Molecular Basis of Assembly and Activation of Complement Component C1 in Complex with Immunoglobulin G1 and Antigen. Molecular Cell, 63, 135-145. https://doi.org/10.1016/j.molcel.2016.05.016
Lebesgue, N., da Costa, G., Ribeiro, R. M., Ribeiro-Silva, C., Martins, G. G., Matranga, V., Scholten, A., Cordeiro, C., Heck, A. J. R., & Santos, R. (2016). Proteomic dataset of the sea urchin Paracentrotus lividus adhesive organs and secreted adhesive. Data in Brief, 7, 1497-505. https://doi.org/10.1016/j.dib.2016.04.002
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
Burgers, P. P., Bruystens, J., Burnley, R. J., Nikolaev, V. O., Keshwani, M., Wu, J., Janssen, B. J. C., Taylor, S. S., Heck, A. J. R., & Scholten, A. (2016). Structure of smAKAP and its regulation by PKA-mediated phosphorylation. The FEBS journal, 283(11), 2132-2148. https://doi.org/10.1111/febs.13726
Giansanti, P., Tsiatsiani, L., Low, T. Y., & Heck, A. J. R. (2016). Six alternative proteases for mass spectrometry-based proteomics beyond trypsin. Nature Protocols, 11(5), 993-1006. https://doi.org/10.1038/nprot.2016.057
Soni, S., Raaijmakers, A. J. A., Raaijmakers, L. M., Damen, J. M. A., van Stuijvenberg, L., Vos, M. A., Heck, A. J. R., van Veen, T. A. B., & Scholten, A. (2016). A Proteomics Approach to Identify New Putative Cardiac Intercalated Disk Proteins. PLoS One, 11(5), Article e0152231. https://doi.org/10.1371/journal.pone.0152231
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
Anvarian, Z., Nojima, H., van Kappel, E. C., Madl, T., Spit, M., Viertler, M., Jordens, I., Low, T. Y., van Scherpenzeel, R. C., Kuper, I., Richter, K., Heck, A. J. R., Boelens, R., Vincent, J-P., Rüdiger, S. G. D., & Maurice, M. M. (2016). Axin cancer mutants form nanoaggregates to rewire the Wnt signaling network. Nature Structural and Molecular Biology, 23, 324-332. https://doi.org/10.1038/nsmb.3191
Lebesgue, N., da Costa, G., Ribeiro, R. M., Ribeiro-Silva, C., Martins, G. G., Matranga, V., Scholten, A., Cordeiro, C., Heck, A. J. R., & Santos, R. (2016). Deciphering the molecular mechanisms underlying sea urchin reversible adhesion: A quantitative proteomics approach. Journal of Proteomics, 138, 61-71. https://doi.org/10.1016/j.jprot.2016.02.026
van de Waterbeemd, M., Snijder, J., Tsvetkova, I. B., Dragnea, B. G., Cornelissen, J. J., & Heck, A. J. R. (2016). Examining the Heterogeneous Genome Content of Multipartite Viruses BMV and CCMV by Native Mass Spectrometry. Journal of the American Society for Mass Spectrometry, 27(6), 1000-1009. https://doi.org/10.1007/s13361-016-1348-6
Schuller, J. M., Beck, F., Lössl, P., Heck, A. J. R., & Förster, F. (2016). Nucleotide-dependent conformational changes of the AAA+ ATPase p97 revisited. FEBS Letters, 590(5), 595-604. https://doi.org/10.1002/1873-3468.12091
Mommen, G. P. M., Marino, F., Meiring, H. D., Poelen, M. C. M., van Gaans-van den Brink, J. A. M., Mohammed, S., Heck, A. J. R., & van Els, C. A. C. M. (2016). Sampling from the proteome to the HLA-DR ligandome proceeds via high specificity. Molecular & Cellular Proteomics. https://doi.org/10.1074/mcp.M115.055780
Fort, K. L., Dyachenko, A., Potel, C. M., Corradini, E., Marino, F., Barendregt, A., Makarov, A. A., Scheltema, R. A., & Heck, A. J. R. (2016). Implementation of UV-photodissociation on a benchtop Q Exactive mass spectrometer and its application to phospho-proteomics. Analytical Chemistry, 88(4), 2303-2310. https://doi.org/10.1021/acs.analchem.5b04162
de Jong, R. N., Beurskens, F. J., Verploegen, S., Strumane, K., van Kampen, M. D., Voorhorst, M., Horstman, W., Engelberts, P. J., Oostindie, S. C., Wang, G., Heck, A. J. R., Schuurman, J., & Parren, P. W. H. I. (2016). A Novel Platform for the Potentiation of Therapeutic Antibodies Based on Antigen-Dependent Formation of IgG Hexamers at the Cell Surface. PloS Biology [E], 14(1), e1002344. https://doi.org/10.1371/journal.pbio.1002344
2015
Scholarly publications
Bern, M., Marino, F., Mommen, G. P. M., Leney, A. C., Bonvin, A. M. J. J., van Els, C. A. C. M., Becker, C., & Heck, A. J. R. (2015). Glycosylation on peptides presented by HLA class I molecules. Glycobiology, 25(11), 1248-1249.
Heck, A. J. R. (2015). Nico M. M. Nibbering (1938-2014). Angewandte Chemie - International Edition, 54(7), 2004. https://doi.org/10.1002/anie.201411258
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
Liu, F., & Heck, A. J. R. (2015). Interrogating the architecture of protein assemblies and protein interaction networks by cross-linking mass spectrometry. Current Opinion in Structural Biology, 35, 100-108. https://doi.org/10.1016/j.sbi.2015.10.006
Peng, M., Aye, T. T., Snel, B., Van Breukelen, B., Scholten, A., & Heck, A. J. R. (2015). Spatial Organization in Protein Kinase A Signaling Emerged at the Base of Animal Evolution. Journal of Proteome Research, 14(7), 2976-2987. https://doi.org/10.1021/acs.jproteome.5b00370
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
Low, T. Y., & Heck, A. J. (2015). Reconciling proteomics with next generation sequencing. Current Opinion in Chemical Biology, 30, 14-20. https://doi.org/10.1016/j.cbpa.2015.10.023
Tsiatsiani, L., & Heck, A. J. R. (2015). Proteomics beyond trypsin. The FEBS journal, 282(14), 2612-2626. https://doi.org/10.1111/febs.13287
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
McNulty, R., Lokareddy, R. K., Roy, A., Yang, Y., Lander, G. C., Heck, A. J. R., Johnson, J. E., & Cingolani, G. (2015). Architecture of the Complex Formed by Large and Small Terminase Subunits from Bacteriophage P22. Journal of Molecular Biology, 427(20), 3285-3299. https://doi.org/10.1016/j.jmb.2015.08.013
Snijder, J., Van De Waterbeemd, M., Glover, M. S., Shi, L., Clemmer, D. E., & Heck, A. J. R. (2015). Conformational landscape and pathway of disulfide bond reduction of human alpha defensin. Protein Science, 24(8), 1264-1271. https://doi.org/10.1002/pro.2694
Liu, F., Rijkers, D. T. S., Post, H., & Heck, A. J. R. (2015). Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry. Nature Methods, 1179-1184. https://doi.org/10.1038/nmeth.3603
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
Zeqiraj, E., Tian, L., Piggott, C. A., Pillon, M. C., Duffy, N. M., Ceccarelli, D. F., Keszei, A. F. A., Lorenzen, K., Kurinov, I., Orlicky, S., Gish, G. D., Heck, A. J. R., Guarné, A., Greenberg, R. A., & Sicheri, F. (2015). Higher-Order Assembly of BRCC36-KIAA0157 Is Required for DUB Activity and Biological Function. Molecular Cell, 59(6), 970-983. https://doi.org/10.1016/j.molcel.2015.07.028
Benevento, M., Tonge, P. D., Puri, M. C., Nagy, A., Heck, A. J. R., & Munoz Peralta, J. (2015). Fluctuations in histone H4 isoforms during cellular reprogramming monitored by middle-down proteomics. Proteomics, 15(18), 3219-3231. https://doi.org/10.1002/pmic.201500031
Corradini, E., Klaasse, G., Leurs, U., Heck, A. J. R., Martin, N. I., & Scholten, A. (2015). Charting the interactome of PDE3A in human cells using an IBMX based chemical proteomics approach. Molecular BioSystems, 11(10), 2786-2797. https://doi.org/10.1039/c5mb00142k
Evaristo, G. P. C., Pinkse, M. W. H., Chen, T., Wang, L., Mohammed, S., Heck, A. J. R., Mathes, I., Lottspeich, F., Shaw, C., Albar, J. P., & Verhaert, P. D. E. M. (2015). De novo sequencing of two novel peptides homologous to calcitonin-like peptides, from skin secretion of the Chinese Frog, Odorrana schmackeri. EuPA Open Proteomics, 8, 157-166. https://doi.org/10.1016/j.euprot.2015.07.008
Weiss, V. U., Bereszcazk, J. Z., Havlik, M., Kallinger, P., Gösler, I., Kumar, M., Blaas, D., Marchetti-Deschmann, M., Heck, A. J. R., Szymanski, W. W., & Allmaier, G. (2015). Analysis of a Common Cold Virus and Its Subviral Particles by Gas-Phase Electrophoretic Mobility Molecular Analysis and Native Mass Spectrometry. Analytical Chemistry, 87(17), 8709-8717. https://doi.org/10.1021/acs.analchem.5b01450
Dondelinger, Y., Jouan-Lanhouet, S., Divert, T., Theatre, E., Bertin, J., Gough, P. J., Giansanti, P., Heck, A. J. R., Dejardin, E., Vandenabeele, P., & Bertrand, M. J. M. (2015). NF-κB-Independent Role of IKKα/IKKβ in Preventing RIPK1 Kinase-Dependent Apoptotic and Necroptotic Cell Death during TNF Signaling. Molecular Cell. https://doi.org/10.1016/j.molcel.2015.07.032
Glas, M., Bart Van Den Berg Van Saparoea, H., McLaughlin, S. H., Roseboom, W., Liu, F., Koningstein, G. M., Fish, A., Den Blaauwen, T., Heck, A. J. R., De Jong, L., Bitter, W., De Esch, I. J. P., & Luirink, J. (2015). The soluble periplasmic domains of Escherichia coli cell division proteins FtsQ/FtsB/FtsL form a trimeric complex with submicromolar affinity. Journal of Biological Chemistry, 290(35), 21498-21509. https://doi.org/10.1074/jbc.M115.654756
Magliozzi, R., Peng, M., Mohammed, S., Guardavaccaro, D., Heck, A. J. R., & Low, T. Y. (2015). Datasets from an interaction proteomics screen for substrates of the SCFβTrCP ubiquitin ligase. Data in Brief, 4, 229-234. https://doi.org/10.1016/j.dib.2015.05.003
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
Gautier, V., Boumeester, A. J., Lössl, P., & Heck, A. J. R. (2015). Lysine conjugation properties in human IgGs studied by integrating high-resolution native mass spectrometry and bottom-up proteomics. Proteomics, 15(16), 2756-2765. https://doi.org/10.1002/pmic.201400462
Martinez-Rucobo, F. W., Kohler, R., van de Waterbeemd, M., Heck, A. J. R., Hemann, M., Herzog, F., Stark, H., & Cramer, P. (2015). Molecular Basis of Transcription-Coupled Pre-mRNA Capping. Molecular Cell, 58(6), 1079-1089. https://doi.org/10.1016/j.molcel.2015.04.004
Welling, M., Chen, H. H., Munoz Peralta, J., Musheev, M. U., Kester, L., Junker, J. P., Mischerikow, N., Arbab, M., Kuijk, E., Silberstein, L., Kharchenko, P. V., Geens, M., Niehrs, C., Van De Velde, H., Van Oudenaarden, A., Heck, A. J. R., & Geijsen, N. (2015). DAZL regulates Tet1 translation in murine embryonic stem cells. EMBO Reports, 16(7), 791-802. https://doi.org/10.15252/embr.201540538
Dyachenko, A., Wang, G., Belov, M., Makarov, A., De Jong, R. N., Van Den Bremer, E. T. J., Parren, P. W. H. I., & Heck, A. J. R. (2015). Tandem Native Mass-Spectrometry on Antibody-Drug Conjugates and Submillion da Antibody-Antigen Protein Assemblies on an Orbitrap EMR Equipped with a High-Mass Quadrupole Mass Selector. Analytical Chemistry, 87(12), 6095-6102. https://doi.org/10.1021/acs.analchem.5b00788
Zhao, Q., Ding, Y., Deng, Z., Lee, O. Y., Gao, P., Chen, P., Rose, R. J., Zhao, H., Zhang, Z., Tao, X. P., Heck, A. J. R., Kao, R., & Yang, D. (2015). Natural products triptolide, celastrol, and withaferin A inhibit the chaperone activity of peroxiredoxin i. Chemical Science, 6(7), 4124-4130. https://doi.org/10.1039/c5sc00633c
Marino, F., Bern, M., Mommen, G. P. M., Leney, A. C., van Gaans-van den Brink, J. A. M., Bonvin, A. M. J. J., Becker, C., van Els, C. A. C. M., & Heck, A. J. R. (2015). Extended O-GlcNAc on HLA Class-I-Bound Peptides. Journal of the American Chemical Society, 10922–10925. https://doi.org/10.1021/jacs.5b06586
Heck, A. J. R. (2015). Gaining weight in structural biology: Applications of mass spectrometry in protein science. Protein Science, 24(8), 1173-1175. https://doi.org/10.1002/pro.2725
Giansanti, P., Aye, T. T., van den Toorn, H., Peng, M., van Breukelen, B., & Heck, A. J. R. (2015). An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas. Cell Reports [E], 11(11), 1834-1843. https://doi.org/10.1016/j.celrep.2015.05.029
Shakiba, N., White, C. A., Lipsitz, Y. Y., Yachie-Kinoshita, A., Tonge, P. D., Hussein, S. M. I., Puri, M. C., Elbaz, J., Morrissey-Scoot, J., Li, M., Munoz Peralta, J., Benevento, M., Rogers, I. M., Hanna, J. H., Heck, A. J. R., Wollscheid, B., Nagy, A., & Zandstra, P. W. (2015). CD24 tracks divergent pluripotent states in mouse and human cells. Nature Communications [E], 6, Article 7329. https://doi.org/10.1038/ncomms8329
Hussein, S. M. I., Puri, M. C., Tonge, P. D., Benevento, M., Corso, A. J., Clancy, J. L., Mosbergen, R., Li, M., Lee, D-S., Cloonan, N., Wood, D. L. A., Munoz, J., Middleton, R., Korn, O., Patel, H. R., White, C. A., Shin, J-Y., Gauthier, M. E., Cao, K-A. L., ... Nagy, A. (2015). Corrigendum: Genome-wide characterization of the routes to pluripotency. Nature, 523(7562). https://doi.org/10.1038/nature14606
Selvan, N., Mariappa, D., Van Den Toorn, H. W. P., Heck, A. J. R., Ferenbach, A. T., & Van Aalten, D. M. F. (2015). The early metazoan Trichoplax adhaerens possesses a functional O-GlcNAc system. Journal of Biological Chemistry, 290(19), 11969-11982. https://doi.org/10.1074/jbc.M114.628750
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
Corradini, E., Heck, A. J. R., & Scholten, A. (2015). Separation of PKA and PKG signaling nodes by chemical proteomics. Methods in Molecular Biology, 1294, 191-201. https://doi.org/10.1007/978-1-4939-2537-7_15
Binai, N. A., Marino, F., Soendergaard, P., Bache, N., Mohammed, S., & Heck, A. J. R. (2015). Rapid analyses of proteomes and interactomes using an integrated solid-phase extraction-liquid chromatography-MS/ms system. Journal of Proteome Research, 14(2), 977-985. https://doi.org/10.1021/pr501011z
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
Corradini, E., Burgers, P. P., Plank, M., Heck, A. J. R., & Scholten, A. (2015). Huntingtin-Associated Protein 1 (HAP1) is a cGMP-dependent Kinase Anchoring Protein (GKAP) specific for the cGMP-dependent protein kinase Iβ isoform. Journal of Biological Chemistry, 290(12), 7887-7896. https://doi.org/10.1074/jbc.M114.622613
The, I., Ruijtenberg, S., Bouchet, B. P., Cristobal Gonzalez de Durana, A., Prinsen, M. B. W., van Mourik, T., Koreth, J., Xu, H., Heck, A. J. R., Akhmanova, A., Cuppen, E., Boxem, M., Munoz Murillo, A., & van den Heuvel, S. (2015). Rb and FZR1/Cdh1 determine CDK4/6-cyclin D requirement in C. elegans and human cancer cells. Nature Communications [E], 6, 5906. https://doi.org/10.1038/ncomms6906
Burgers, P. P., van der Heyden, M. A. G., Kok, B., Heck, A. J. R., & Scholten, A. (2015). A systematic evaluation of protein kinase a-a-kinase anchoring protein interaction motifs. Biochemistry, 54(1), 11-21. https://doi.org/10.1021/bi500721a
2014
Scholarly publications
Overman, J. P., Preisinger, C., Prummel, K., Bonetti, M., Giansanti, P., Heck, A., & Den Hertog, J. (2014). Phosphoproteomics-mediated identification of Fer kinase as a target of mutant Shp2 in Noonan and LEOPARD syndrome. PLoS One, 9(9), Article e106682. https://doi.org/10.1371/journal.pone.0106682
Low, T. Y., Peng, M., Magliozzi, R., Mohammed, S., Guardavaccaro, D., & Heck, A. J. R. (2014). A systems-wide screen identifies substrates of the SCFβTrCP ubiquitin ligase. Science Signaling, 7(356), Article rs8. https://doi.org/10.1126/scisignal.2005882
Luque, D., De La Escosura, A., Snijder, J., Brasch, M., Burnley, R. J., Koay, M. S. T., Carrascosa, J. L., Wuite, G. J. L., Roos, W. H., Heck, A. J. R., Cornelissen, J. J. L. M., Torres, T., & Castón, J. R. (2014). Self-assembly and characterization of small and monodisperse dye nanospheres in a protein cage. Chemical Science, 5(2), 575-581. https://doi.org/10.1039/c3sc52276h
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
Bereszczak, J. Z., Havlik, M., Weiss, V. U., Marchetti-Deschmann, M., van Duijn, E., Watts, N. R., Wingfield, P. T., Allmaier, G., Steven, A. C., & Heck, A. J. R. (2014). Sizing up large protein complexes by electrospray ionisation-based electrophoretic mobility and native mass spectrometry: morphology selective binding of Fabs to hepatitis B virus capsids. Analytical and Bioanalytical Chemistry, 406(5), 1437-46. https://doi.org/10.1007/s00216-013-7548-z
Veesler, D., Khayat, R., Krishnamurthy, S., Snijder, J., Huang, R. K., Heck, A. J. R., Anand, G. S., & Johnson, J. E. (2014). Architecture of a dsDNA viral capsid in complex with its maturation protease. Structure, 22(2), 230-7. https://doi.org/10.1016/j.str.2013.11.007
Thompson, N. J., Merdanovic, M., Ehrmann, M., van Duijn, E., & Heck, A. J. R. (2014). Substrate occupancy at the onset of oligomeric transitions of DegP. Structure, 22(2), 281-90. https://doi.org/10.1016/j.str.2013.11.010
Yates, J. R., Mohammed, S., & Heck, A. J. R. (2014). Phosphoproteomics. Analytical Chemistry, 86(3), 1313. https://doi.org/10.1021/ac404019p
Snijder, J., Burnley, R. J., Wiegard, A., Melquiond, A. S. J., Bonvin, A. M. J. J., Axmann, I. M., & Heck, A. J. R. (2014). Insight into cyanobacterial circadian timing from structural details of the KaiB-KaiC interaction. Proceedings of the National Academy of Sciences of the United States of America, 111(4), 1379-84. https://doi.org/10.1073/pnas.1314326111
D'Annibale, S., Kim, J., Magliozzi, R., Low, T. Y., Mohammed, S., Heck, A. J. R., & Guardavaccaro, D. (2014). Proteasome-dependent degradation of transcription factor activating enhancer-binding protein 4 (TFAP4) controls mitotic division. Journal of Biological Chemistry, 289(11), 7730-7. https://doi.org/10.1074/jbc.M114.549535
Rurup, W. F., Snijder, J., Koay, M. S. T., Heck, A. J. R., & Cornelissen, J. J. L. M. (2014). Self-sorting of foreign proteins in a bacterial nanocompartment. Journal of the American Chemical Society, 136(10), 3828-32. https://doi.org/10.1021/ja410891c
Benevento, M., Di Palma, S., Snijder, J., Moyer, C. L., Reddy, V. S., Nemerow, G. R., & Heck, A. J. R. (2014). Adenovirus composition, proteolysis, and disassembly studied by in-depth qualitative and quantitative proteomics. Journal of Biological Chemistry, 289(16), 11421-30. https://doi.org/10.1074/jbc.M113.537498
Snijder, J., Benevento, M., Moyer, C. L., Reddy, V., Nemerow, G. R., & Heck, A. J. R. (2014). The cleaved N-terminus of pVI binds peripentonal hexons in mature adenovirus. Journal of Molecular Biology, 426(9), 1971-9. https://doi.org/10.1016/j.jmb.2014.02.022
Mommen, G. P. M., Frese, C. K., Meiring, H. D., van Gaans-van den Brink, J., de Jong, A. P. J. M., van Els, C. A. C. M., & Heck, A. J. R. (2014). Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD). Proceedings of the National Academy of Sciences of the United States of America, 111(12), 4507-12. https://doi.org/10.1073/pnas.1321458111
Diebolder, C. A., Beurskens, F. J., De Jong, R. N., Koning, R. I., Strumane, K., Lindorfer, M. A., Voorhorst, M., Ugurlar, D., Rosati, S., Heck, A. J. R., Van De Winkel, J. G. J., Wilson, I. A., Koster, A. J., Taylor, R. P., Saphire, E. O., Burton, D. R., Schuurman, J., Gros, P., & Parren, P. W. H. I. (2014). Complement is activated by IgG hexamers assembled at the cell surface. Science, 343(6176), 1260-1263. https://doi.org/10.1126/science.1248943
Rosati, S., Yang, Y., Barendregt, A., & Heck, A. J. R. (2014). Detailed mass analysis of structural heterogeneity in monoclonal antibodies using native mass spectrometry. Nature Protocols, 9(4), 967-76. https://doi.org/10.1038/nprot.2014.057
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
Lössl, P., Snijder, J., & Heck, A. J. R. (2014). Boundaries of mass resolution in native mass spectrometry. Journal of the American Society for Mass Spectrometry, 25(6), 906-17. https://doi.org/10.1007/s13361-014-0874-3
Bereszczak, J. Z., Watts, N. R., Wingfield, P. T., Steven, A. C., & Heck, A. J. R. (2014). Assessment of differences in the conformational flexibility of hepatitis B virus core-antigen and e-antigen by hydrogen deuterium exchange-mass spectrometry. Protein Science, 23(7), 884-96. https://doi.org/10.1002/pro.2470
Walzer, M., Pernas, L. E., Nasso, S., Bittremieux, W., Nahnsen, S., Kelchtermans, P., Pichler, P., van den Toorn, H. W. P., Staes, A., Vandenbussche, J., Mazanek, M., Taus, T., Scheltema, R. A., Kelstrup, C. D., Gatto, L., van Breukelen, B., Aiche, S., Valkenborg, D., Laukens, K., ... Martens, L. (2014). qcML: an exchange format for quality control metrics from mass spectrometry experiments. Molecular & Cellular Proteomics, 13(8), 1905-13. https://doi.org/10.1074/mcp.M113.035907
van Holten, T. C., Bleijerveld, O. B., Wijten, P., de Groot, P. G., Heck, A. J. R., Barendrecht, A. D., Merkx, T. H., Scholten, A., & Roest, M. (2014). Quantitative proteomics analysis reveals similar release profiles following specific PAR-1 or PAR-4 stimulation of platelets. Cardiovascular Research, 103(1), 140-146. https://doi.org/10.1093/cvr/cvu113
Snijder, J., van de Waterbeemd, M., Damoc, E., Denisov, E., Grinfeld, D., Bennett, A., Agbandje-McKenna, M., Makarov, A., & Heck, A. J. R. (2014). Defining the stoichiometry and cargo load of viral and bacterial nanoparticles by Orbitrap mass spectrometry. Journal of the American Chemical Society, 136(20), 7295-9. https://doi.org/10.1021/ja502616y
Giansanti, P., Preisinger, C., Huber, K. V. M., Gridling, M., Superti-Furga, G., Bennett, K. L., & Heck, A. J. R. (2014). Evaluating the promiscuous nature of tyrosine kinase inhibitors assessed in A431 epidermoid carcinoma cells by both chemical- and phosphoproteomics. ACS Chemical Biology, 9(7), 1490-1498. https://doi.org/10.1021/cb500116c
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
Paardekooper Overman, J., Yi, J-S., Bonetti, M., Soulsby, M., Preisinger, C., Stokes, M. P., Hui, L., Silva, J. C., Overvoorde, J., Giansanti, P., Heck, A. J. R., Kontaridis, M. I., den Hertog, J., & Bennett, A. M. (2014). PZR coordinates Shp2 Noonan and LEOPARD syndrome signaling in zebrafish and mice. Molecular and Cellular Biology, 34(15), 2874-2889. https://doi.org/10.1128/MCB.00135-14
Kelstrup, C. D., Frese, C., Heck, A. J. R., Olsen, J. V., & Nielsen, M. L. (2014). Analytical utility of mass spectral binning in proteomic experiments by SPectral Immonium Ion Detection (SPIID). Molecular & Cellular Proteomics, 13(8), 1914-24. https://doi.org/10.1074/mcp.O113.035915
Corradini, E., Vallur, R., Raaijmakers, L. M., Feil, S., Feil, R., Heck, A. J. R., & Scholten, A. (2014). Alterations in the cerebellar (Phospho)proteome of a cyclic guanosine monophosphate (cGMP)-dependent protein kinase knockout mouse. Molecular & Cellular Proteomics, 13(8), 2004-2016. https://doi.org/10.1074/mcp.M113.035154
Kleppe, R., Rosati, S., Jorge-Finnigan, A., Alvira, S., Ghorbani, S., Haavik, J., Valpuesta, J. M., Heck, A. J. R., & Martinez, A. (2014). Phosphorylation dependence and stoichiometry of the complex formed by tyrosine hydroxylase and 14-3-3γ. Molecular & Cellular Proteomics, 13(8), 2017-30. https://doi.org/10.1074/mcp.M113.035709
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
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
Liu, F., van Breukelen, B., & Heck, A. J. R. (2014). Facilitating protein disulfide mapping by a combination of pepsin digestion, electron transfer higher energy dissociation (EThcD), and a dedicated search algorithm SlinkS. Molecular & Cellular Proteomics, 13(10), 2776-86. https://doi.org/10.1074/mcp.O114.039057
Binai, N. A., Bisschops, M. M. M., van Breukelen, B., Mohammed, S., Loeff, L., Pronk, J. T., Heck, A. J. R., Daran-Lapujade, P., & Slijper, M. (2014). Proteome adaptation of Saccharomyces cerevisiae to severe calorie restriction in Retentostat cultures. Journal of Proteome Research, 13(8), 3542-3553. https://doi.org/10.1021/pr5003388
Snijder, J., & Heck, A. J. R. (2014). Analytical approaches for size and mass analysis of large protein assemblies. Annual review of analytical chemistry (Palo Alto, Calif.), 7, 43-64. https://doi.org/10.1146/annurev-anchem-071213-020015
van de Waterbeemd, M., Lössl, P., Gautier, V., Marino, F., Yamashita, M., Conti, E., Scholten, A., & Heck, A. J. R. (2014). Simultaneous assessment of kinetic, site-specific, and structural aspects of enzymatic protein phosphorylation. Angewandte Chemie-International Edition, 53(36), 9660-4. https://doi.org/10.1002/anie.201404637
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
Matheron, L., van den Toorn, H., Heck, A. J. R., & Mohammed, S. (2014). Characterization of biases in phosphopeptide enrichment by Ti(4+)-immobilized metal affinity chromatography and TiO2 using a massive synthetic library and human cell digests. Analytical Chemistry, 86(16), 8312-20. https://doi.org/10.1021/ac501803z
Muñoz, J., & Heck, A. J. R. (2014). From the human genome to the human proteome. Angewandte Chemie-International Edition, 53(41), 10864-6. https://doi.org/10.1002/anie.201406545
Magliozzi, R., Kim, J., Low, T. Y., Heck, A. J. R., & Guardavaccaro, D. (2014). Degradation of Tiam1 by casein kinase 1 and the SCFβTrCP ubiquitin ligase controls the duration of mTOR-S6K signaling. Journal of Biological Chemistry, 289(40), 27400-9. https://doi.org/10.1074/jbc.M114.575571
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
Kim, J., D'Annibale, S., Magliozzi, R., Low, T. Y., Jansen, P., Shaltiel, I. A., Mohammed, S., Heck, A. J. R., Medema, R. H., & Guardavaccaro, D. (2014). USP17- and SCFβTrCP--regulated degradation of DEC1 controls the DNA damage response. Molecular and Cellular Biology, 34(22), 4177-85. https://doi.org/10.1128/MCB.00530-14
Marino, F., Cristobal, A., Binai, N. A., Bache, N., Heck, A. J. R., & Mohammed, S. (2014). Characterization and usage of the EASY-spray technology as part of an online 2D SCX-RP ultra-high pressure system. Analyst, 139(24), 6520-8. https://doi.org/10.1039/c4an01568a
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
Chen, H-H., Welling, M., Bloch, D. B., Muñoz, J., Mientjes, E., Chen, X., Tramp, C., Wu, J., Yabuuchi, A., Chou, Y-F., Buecker, C., Krainer, A., Willemsen, R., Heck, A. J., & Geijsen, N. (2014). DAZL limits pluripotency, differentiation, and apoptosis in developing primordial germ cells. Stem Cell Reports [E], 3(5), 892-904. https://doi.org/10.1016/j.stemcr.2014.09.003
Staals, R. H. J., Zhu, Y., Taylor, D. W., Kornfeld, J. E., Sharma, K., Barendregt, A., Koehorst, J. J., Vlot, M., Neupane, N., Varossieau, K., Sakamoto, K., Suzuki, T., Dohmae, N., Yokoyama, S., Schaap, P. J., Urlaub, H., Heck, A. J. R., Nogales, E., Doudna, J. A., ... van der Oost, J. (2014). RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus. Molecular Cell, 56(4), 518-30. https://doi.org/10.1016/j.molcel.2014.10.005
Clancy, J. L., Patel, H. R., Hussein, S. M. I., Tonge, P. D., Cloonan, N., Corso, A. J., Li, M., Lee, D-S., Shin, J-Y., Wong, J. J. L., Bailey, C. G., Benevento, M., Munoz, J., Chuah, A., Wood, D., Rasko, J. E. J., Heck, A. J. R., Grimmond, S. M., Rogers, I. M., ... Preiss, T. (2014). Small RNA changes en route to distinct cellular states of induced pluripotency. Nature Communications [E], 5, Article 5522. https://doi.org/10.1038/ncomms6522
Benevento, M., Tonge, P. D., Puri, M. C., Hussein, S. M. I., Cloonan, N., Wood, D. L., Grimmond, S. M., Nagy, A., Munoz, J., & Heck, A. J. R. (2014). Proteome adaptation in cell reprogramming proceeds via distinct transcriptional networks. Nature Communications [E], 5, Article 5613. https://doi.org/10.1038/ncomms6613
Hussein, S. M. I., Puri, M. C., Tonge, P. D., Benevento, M., Corso, A. J., Clancy, J. L., Mosbergen, R., Li, M., Lee, D-S., Cloonan, N., Wood, D. L. A., Munoz, J., Middleton, R., Korn, O., Patel, H. R., White, C. A., Shin, J-Y., Gauthier, M. E., Lê Cao, K-A., ... Nagy, A. (2014). Genome-wide characterization of the routes to pluripotency. Nature, 516(7530), 198-206. https://doi.org/10.1038/nature14046
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
Peng, M., Scholten, A., Heck, A. J. R., & van Breukelen, B. (2014). Identification of Enriched PTM Crosstalk Motifs from Large-Scale Experimental Data Sets. Journal of Proteome Research, 13(1), 249-259. https://doi.org/10.1021/pr4005579
2013
Scholarly publications
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
Heck, A. J. R. (2013). Peptidyl-Lys Metalloendopeptidase. In Handbook of Proteolytic Enzymes (Vol. 1, pp. 1266-1270). Elsevier Ltd. https://doi.org/10.1016/B978-0-12-382219-2.00285-4
Rosati, S., Thompson, N. J., & Heck, A. J. R. (2013). Tackling the increasing complexity of therapeutic monoclonal antibodies with mass spectrometry. TrAC - Trends in Analytical Chemistry, 48, 72-80. https://doi.org/10.1016/j.trac.2013.02.013
Smith, L. M., Kelleher, N. L., & Heck, A. J. R. (2013). Proteoform: a single term describing protein complexity. Nature Methods, 10(3), 186-7. https://doi.org/10.1038/nmeth.2369
Thompson, N. J., Hendriks, L. J. A., de Kruif, J., Throsby, M., & Heck, A. J. R. (2013). Complex mixtures of antibodies generated from a single production qualitatively and quantitatively evaluated by native Orbitrap mass spectrometry. mAbs, 6(1), 197-203. https://doi.org/10.4161/mabs.27126
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
Halim, V. A., Alvarez Fernandez, M., Xu, Y. J., Aprelia, M., van den Toorn, H. W. P., Heck, A. J. R., Mohammed, S., & Medema, R. H. (2013). Comparative Phosphoproteomic Analysis of Checkpoint Recovery Identifies New Regulators of the DNA Damage Response. Science Signaling [E], 6(272), 1-10. Article rs9. https://doi.org/10.1126/scisignal.2003664
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
Berends, C. W. H., Muñoz, J., Portegijs, V. C., Schmidt, R., Grigoriev, I. S., Boxem, M., Akhmanova, A. S., Heck, A. J. R., & van den Heuvel, S. (2013). F-actin asymmetry and the endoplasmic reticulum-associated TCC-1 protein contribute to stereotypic spindle movements in the Caenorhabditis elegans embryo. Molecular Biology of the Cell, 24(14), 2201-2215. https://doi.org/10.1091/mbc.E13-02-0076
Mellacheruvu, D., Wright, Z., Couzens, A. L., Low, T. Y., Halim, V. A., Heck, A. J. R., Mohammed, S., & Nesvizhskii, A. (2013). The CRAPome: a contaminant repository for affinity purification–mass spectrometry data. Nature Methods, 10, 730-736. https://doi.org/10.1038/nmeth.2557
Bleijerveld, O. B., van Holten, T. C., Preisinger, C., van der Smagt, J. J., Farndale, R. W., Kleefstra, T., Willemsen, M. H., Urbanus, R. T., de Groot, P. G., Heck, A. J. R., Roest, M., & Scholten, A. (2013). Targeted phosphotyrosine profiling of glycoprotein VI signaling implicates oligophrenin-1 in platelet filopodia formation. Arteriosclerosis, Thrombosis and Vascular Biology, 33(7), 1538-1543. https://doi.org/10.1161/ATVBAHA.112.300916
Rose, R. J., Damoc, E., Denisov, E., & Heck, A. J. R. (2013). High-sensitivity Orbitrap mass analysis of intact macromolecular assemblies. Nature Methods, 9(11), 1084-1086. https://doi.org/10.1038/nmeth.2208
Wijten, P., van Holten, T. C., Woo, L. L., Bleijerveld, O. B., Roest, M., Heck, A. J. R., & Scholten, A. (2013). High precision platelet releasate definition by quantitative reversed protein profiling--Brief report. Arteriosclerosis, Thrombosis and Vascular Biology, 33, 1635-1638. https://doi.org/10.1161/ATVBAHA.113.301147
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
Chin, P. T. K., van der Linden, M., van Harten, E. J., Barendregt, A., Rood, M. T. M., Koster, A. J., van Leeuwen, F. W. B., de Mello Donega, C., Heck, A. J. R., & Meijerink, A. (2013). Enhanced luminescence of Ag nanoclusters via surface modification. Nanotechnology, 24(7), Article 075703. https://doi.org/10.1088/0957-4484/24/7/075703
Srivastava, S. K., Ruigrok, V. J. B., Thompson, N. J., Trilling, A. K., Heck, A. J. R., van Rijn, C., Beekwilder, M. J., & Jongsma, M. A. (2013). 16 kDa heat shock protein from heat-inactivated Mycobacterium tuberculosis is a homodimer - suitability for diagnostic applications with specific llama VHH monoclonals. PLoS One, 8(5), Article e64040. https://doi.org/10.1371/journal.pone.0064040
Zhang, H., Zhou, H., Berke, L., Heck, A. J. R., Mohammed, S., Scheres, B. J. G., & Menke, F. L. H. (2013). Quantitative phosphoproteomics after auxin-stimulated lateral root induction identifies an SNX1 protein phosphorylation site required for growth. Molecular & Cellular Proteomics, 12, 1158-1169. https://doi.org/10.1074/mcp.M112.021220
Giansanti, P., Stokes, M. P., Silva, J. C., Scholten, A., & Heck, A. J. R. (2013). Interrogating cAMP-dependent kinase signaling in jurkat T cells via a protein kinase A targeted immune-precipitation phosphoproteomics approach. Molecular & Cellular Proteomics, 12(11), 3350-3359. https://doi.org/10.1074/mcp.O113.028456
Marx, H., Lemeer, S., Schliep, J. E., Matheron, L. I., Mohammed, S., Cox, J., Mann, M., Heck, A. J. R., & Kuster, B. (2013). A large synthetic peptide and phosphopeptide reference library for mass spectrometry–based proteomics. Nature Biotechnology, 31, 557-564. https://doi.org/10.1038/nbt.2585
Magliozzi, R., Low, T. Y., Weijts, B. G. M. W., Cheng, T., Spanjaard, E., Mohammed, S., van Veen, A., Ovaa, H., de Rooij, J., Zwartkruis, G. J. T., Bos, J. L., de Bruin, A., & Heck, A. J. R. (2013). Control of Epithelial Cell Migration and Invasion by the IKKβ- and CK1α-Mediated Degradation of RAPGEF2. Developmental Cell, 27, 574-585. https://doi.org/10.1016/j.devcel.2013.10.023
Thompson, N. J., Rosati, S., & Heck, A. J. R. (2013). Performing native mass spectrometry analysis on therapeutic antibodies. Methods, 65(1), 11-17. https://doi.org/10.1016/j.ymeth.2013.05.003
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
Scholten, A., & Heck, A. J. R. (2013). Determining Protein Concentrations of the Human Ventricular Proteome. Methods in Molecular Biology, 1005, 11-24. https://doi.org/10.1007/978-1-62703-386-2_2
Ekkebus, R., van Kasteren, S. I., Kulathu, Y., Scholten, A., Berlin, I., Geurink, P. P., de Jong, A., Goerdayal, S. S., Neefjes, J., Heck, A. J. R., Komander, D., & Ovaa, H. (2013). On Terminal Alkynes That Can React with Active-Site Cysteine Nucleophiles in Proteases. Journal of the American Chemical Society, 135(8), 2867-2870. https://doi.org/10.1021/ja309802n
Rosati, S., van den Bremer, E. T. J., Schuurman, J., Parren, P. W. H. I., Kamerling, J. P., & Heck, A. J. R. (2013). In-depth qualitative and quantitative analysis of composite glycosylation profiles and other micro-heterogeneity on intact monoclonal antibodies by high-resolution native mass spectrometry using a modified Orbitrap. mAbs, 5(6), 917-924. https://doi.org/10.4161/mabs.26282
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
Low, T. Y., van Heesch, S. A. A. C., van den Toorn, H. W. P., Giansanti, P., Cristobal, A., Toonen, P., Schafer, S., Hübner, N., van Breukelen, B., Mohammed, S., Cuppen, E. P. J. G., & Heck, A. J. R. (2013). Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis. Cell Reports [E], 5(5), 1469-1478. https://doi.org/10.1016/j.celrep.2013.10.041
Zhou, H., Ye, M., Dong, J., Corradini, E., Cristobal, A., Heck, A. J. R., zou, H., & Mohammed, S. (2013). Robust phosphoproteome enrichment using monodisperse microsphere-based immobilized titanium (IV) ion affinity chromatography. Nature Protocols, 8, 461-480. https://doi.org/10.1038/nprot.2013.010
Hennrich, M. L., Marino, F., Groenewold, V., Kops, G. J. P. L., Mohammed, S., & Heck, A. J. R. (2013). Universal quantitative kinase assay based on diagonal SCX chromatography and stable isotope dimethyl labeling provides high-definition kinase consensus motifs for PKA and human Mps1. Journal of Proteome Research, 12, 2214-2224. https://doi.org/10.1021/pr400074f
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
Zhou, H., Di Palma, S., Preisinger, C., Peng, M., Polat, A. N., Heck, A. J. R., & Mohammed, S. (2013). Toward a comprehensive characterization of a human cancer cell phosphoproteome. Journal of Proteome Research, 12, 260-271. https://doi.org/10.1021/pr300630k
Thompson, N. J., Rosati, S., Rose, R. J., & Heck, A. J. R. (2013). The impact of mass spectrometry on the study of intact antibodies: from post-translational modifications to structural analysis. Chemical Communications, 49(6), 538-548. https://doi.org/10.1039/c2cc36755f
Bereszczak, J. Z., Rose, R. J., van Duijn, E., Watts, N. R., Wingfield, P. T., Steven, A. C., & Heck, A. J. R. (2013). Epitope-distal Effects Accompany the Binding of Two Distinct Antibodies to Hepatitis B Virus Capsids. Journal of the American Chemical Society, 135, 6504-6512. https://doi.org/10.1021/ja402023x
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
Rose, R. J., van Berkel, P. H. C., van den Bremer, E. T. J., Labrijn, A. F., Vink, T., Schuurman, J., Heck, A. J. R., & Parren, P. W. H. I. (2013). Mutation of Y407 in the CH3 domain dramatically alters glycosylation and structure of human IgG. mAbs, 5(2), 219-228. https://doi.org/10.4161/mabs.23532
Esposito, G., Garvey, M., Alverdi, V., Pettirossi, F., Corazza, A., Fogolari, F., Polano, M., Mangione, P. P., Giorgetti, S., Stoppini, M., Rekas, A., Bellotti, V., Heck, A. J. R., & Carver, J. A. (2013). Monitoring the interaction between β2-microglobulin and the molecular chaperone αB-crystallin by NMR and mass spectrometry: αB-crystallin dissociates β2-microglobulin oligomers. Journal of Biological Chemistry, 288(24), 17844-17858. https://doi.org/10.1074/jbc.M112.448639
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
Yang, Y., Barendregt, A., Kamerling, J. P., & Heck, A. J. R. (2013). Analyzing Protein Micro-Heterogeneity in Chicken Ovalbumin by High-Resolution Native Mass Spectrometry Exposes Qualitatively and Semi-Quantitatively 59 Proteoforms. Analytical Chemistry, 85, 12037-12045. https://doi.org/10.1021/ac403057y
Mommen, G. P. M., Meiring, H. D., Heck, A. J. R., & de Jong, A. P. J. M. (2013). Mixed-Bed Ion Exchange Chromatography Employing a Salt-Free pH Gradient for Improved Sensitivity and Compatibility in MudPIT. Analytical Chemistry, 85, 6608-6616. https://doi.org/10.1021/ac400995e
Scholten, A., Preisinger, C., Corradini, E., Bourgonje, V. J. A., Hennrich, M. L., van Veen, T. A. B., Swaminathan, P. D., Joiner, M. L., Vos, M. A., Anderson, M. E., & Heck, A. J. R. (2013). Phosphoproteomics study based on in vivo inhibition reveals sites of calmodulin-dependent protein kinase II regulation in the heart. Journal of the American Heart Association, 2(4), e000318. Article e000318. https://doi.org/10.1161/?JAHA.113.000318
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
Staals, R. H. J., Agari, Y., Maki-Yonekura, S., Zhu, Y., Taylor, D. W., van Duijn, E., Barendregt, A., Vlot, M. C., Koehorst, J. J., Sakamoto, K., Masuda, A., Dohmae, N., Schaap, P. J., Doudna, J. A., Heck, A. J. R., Yonekura, K., van der Oost, J., & Shinkai, A. (2013). Structure and Activity of the RNA-Targeting Type III-B CRISPR-Cas Complex of Thermus thermophilus. Molecular Cell, 52(1), 135-145. https://doi.org/10.1016/j.molcel.2013.09.013
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
Snijder, J., Rose, R. J., Veesler, D., Johnson, J. A., & Heck, A. J. R. (2013). Studying 18 MDa Virus Assemblies with Native Mass Spectrometry. Angewandte Chemie-International Edition, 52(14), 4020-4023. https://doi.org/10.1002/anie.201210197
Di Palma, S., Zoumaro-Djayoon, A. D., Peng, M., Post, H., Preisinger, C., Munoz, J., & Heck, A. J. R. (2013). Finding the same needles in the haystack? A comparison of phosphotyrosine peptides enriched by immuno-affinity precipitation and metal-based affinity chromatography. Journal of Proteomics, 91, 331-337. https://doi.org/10.1016/j.jprot.2013.07.024
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
Tseng, Y. H., Uetrecht, C., Yang, S. C., Barendregt, A., Heck, A. J. R., & Peng, W. P. (2013). Game-Theory-Based Search Engine to Automate the Mass Assignment in Complex Native Electrospray Mass Spectra. Analytical Chemistry, 85, 11275-11283. https://doi.org/10.1021/ac401940e
Snijder, J., Uetrecht, C., Rose, R. J., Sanchez-Eugenia, R., Marti, G. A., Agirre, J., Guérin, D. M. A., Wuite, G. J. L., Heck, A. J. R., & Roos, W. H. (2013). Probing the biophysical interplay between a viral genome and its capsid. Nature Chemistry, 5, 502-509. https://doi.org/10.1038/nchem.1627
Other output
Serra-Marques, A., Liu, Q., Post, H., Grigoriev, I. S., Gordon, D. E., Peden, A. A., Altelaar, M., Heck, A. J. R., & Akhmanova, A. S. (2013). Characterization of the fusion machinery fot Rab6-secretory vesicles.. Poster session presented at Gordon Research Conference - Molecular Membrane Biology, Andover NH, USA.
Waaijers, S., Zoumaro-Djayoon, A. D., Goerdayal, S. S., Munoz, J., Heck, A. J. R., & Boxem, M. (2013). Tissue-specific purification of protein complexes in C. elegans. Poster session presented at 19th International C. elegans meeting, Los Angeles, UCLA.
2012
Scholarly publications
Rosati, S., Rose, R. J., Thompson, N. J., Van Duijn, E., Damoc, E., Denisov, E., Makarov, A., & Heck, A. J. R. (2012). Exploring an orbitrap analyzer for the characterization of intact antibodies by native mass spectrometry. Angewandte Chemie - International Edition, 51(52), 12992-12996. https://doi.org/10.1002/anie.201206745
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.
Smith, A. B., Lopez-Villarejo, J., Diago-Navarro, E., Mitchenall, L. A., Barendregt, A., Heck, A. J. R., Lemonnier, M., Maxwell, A., & Diaz-Orejas, R. (2012). A common origin for the bacterial toxin-antitoxin systems parD and ccd, suggested by analyses of toxin/target and toxin/antitoxin interactions. PLoS One, 7(9), 46499. https://doi.org/10.1371/journal.pone.0046499
Munoz-Peralta, J., Stange, D. J., Schepers, A. G., van de Wetering, M., Itzkovitz, S., Volckmann, R., Kung, K. S., Koster, J., Radulescu, S., Myant, K., Versteeg, R., Sansom, O. J., Barker, N., van Oudenaarden, A., Mohammed, S., Heck, A. J. R., & Clevers, H. C. (2012). The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers. EMBO Journal, 31(14), 3079-3091. https://doi.org/10.1038/emboj
Kovanich, D., Aye, T. T., Heck, A. J. R., & Scholten, A. (2012). Probing the specificity of protein-protein interactions by quantitative chemical proteomics. In Chemical Proteomics (pp. 167-181) https://doi.org/10.1007/978-1-61779-364-6_12.
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
Preisinger, C., Schwarz, J. P., Bleijerveld, O. B., Corradini, E., Muller, P. J., Anderson, K. I., Kolch, W., Scholten, A., & Heck, A. J. R. (2012). Imatinib-dependent tyrosine phosphorylation profiling of Bcr-Abl-positive chronic myeloid leukemia cells. Leukemia, 27, 743-746. https://doi.org/10.1038/leu.2012.243
Moreno-Cordoba, I., Diago-Navarro, E., Barendregt, A., Heck, A. J. R., Alfonso, C., Diaz-Orejas, R., Nieto, C., & Espinosa, M. (2012). The toxin-antitoxin proteins relBE2Spn of Streptococcus pneumoniae: characterization and association to their DNA target. Proteins: Structure function and bioinformatics, 80(7), 1834-1846. https://doi.org/10.1002/prot.24081
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
Low, T. Y., Magliozzi, R., & Heck, A. J. R. (2012). Unraveling the ubiquitin-regulated signaling networks by mass spectrometry-based proteomics. Proteomics, 13(3-4), 526-537. https://doi.org/10.1002/pmic.201200244
Choukrallah, M. A., Kobi, D., Martianov, I., Pijnappel, W. W. M., Mischerikow, N., Ye, T., Heck, A. J. R., Timmers, H. T. M., & Davidson, I. (2012). Interconversion between active and inactive TATA-binding protein transcription complexes in the mouse genome. Nucleic Acids Research, 40(4), 1446-1459. https://doi.org/10.1093/nar/gkr802
Kukrer, B., Barbu, I. M., Copps, J., Hogan, P., Taylor, S. S., van Duijn, E., & Heck, A. J. R. (2012). Conformational isomers of calcineurin follow distinct dissociation pathways. Journal of the American Society for Mass Spectrometry, 23, 1534-1543. https://doi.org/10.1007/s13361-012-0441-8
Munoz, J., Low, T. Y., Kok, Y. J., Chin, A., Frese, C., Ding, V., Choo, A., & Heck, A. J. R. (2012). The quantitative proteomes of human induced pluripotent stem cells and embryonic stem cells. Molecular Systems Biology [E], 7(550). https://doi.org/10.1038/msb.2011.84
Cote, R. G., Griss, J., Dianes, J. A., Wang, R., Wright, J. C., van den Toorn, H. W. P., van Breukelen, B., Heck, A. J. R., Hulstaert, N., Martens, L., Reisinger, F., Csordas, A., Ovelleiro, D., Perez-Rivevol, Y., Barsnes, H., Hermjakob, H., & Vizcaino, J. A. (2012). The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium. Molecular & Cellular Proteomics, 12, 1682-1689. https://doi.org/10.1074/mcp.O112.021543
Mithoe, S. C., Boersema, P. J., Berke, L., Snel, B., Heck, A. J. R., & Menke, F. L. H. (2012). Targeted quantitative phosphoproteomics approach for the detection of phospho-tyrosine signaling in plants. Journal of Proteome Research, 11, 438-448. https://doi.org/10.1021/pr200893k
Cristobal, A., Hennrich, M. L., Giansanti, P., Goerdayal, S. S., Heck, A. J. R., & Mohammed, S. (2012). In-house construction of a UHPLC system enabling the identification of over 4000 protein groups in a single analysis. Analyst, 137, 3541-3548. https://doi.org/10.1039/c2an35445d
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
Aye, T. T., Low, T. Y., Bjorlykke, Y., Barsnes, H., Heck, A. J. R., & Berven, F. S. (2012). Use of stable isotope dimethyl labeling coupled to selected reaction monitoring to enhance throughput by multiplexing relative quantitation of targeted proteins. Analytical Chemistry, 84, 4999-5006. https://doi.org/10.1021/ac300596r
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
Li, V. S. W., Boersema, P. J., Low, T. Y., Gerlach, J. P., Mohammed, S., Heck, A. J. R., Maurice, M. M., & Clevers, H. C. (2012). Wnt Signaling through Inhibition of β-Catenin Degradation in an Intact Axin1 Complex. Cell, 149, 1245-1256. http://www.ncbi.nlm.nih.gov/pubmed/22682247
van Noort, V., Seebacher, J., Bader, S., Mohammed, S., Vonkova, I., Betts, M. J., Kuhner, S., Kumar, R., Maier, T., O'Flaherty, M. C., Rybin, V., Schmeisky, A., Yus, E., Stulke, J., Serrano, L., Russell, R. B., Heck, A. J. R., Bork, P., & Gavin, A-C. (2012). Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Molecular Systems Biology [E], 8(571). https://doi.org/10.1038/msb.2012.4
Bereszczak, J. Z., Barbu, I. M., Tan, M., Xia, M., Jiang, X., van Duijn, E., & Heck, A. J. R. (2012). Structure, stability and dynamics of norovirus P domain derived protein complexes studied by native mass spectrometry. Journal of Structural Biology, 177, 273-282. https://doi.org/10.1016/j.jsb.2012.01.005
Bensimon, A., Heck, A. J. R., & Aebersold, R. (2012). Mass spectrometry-based proteomics and network biology. Annual Review of Biochemistry, 81, 379-405. https://doi.org/10.1146/annurev-biochem-072909-100424
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
Di Palma, S., Mohammed, S., & Heck, A. J. R. (2012). ZIC-cHILIC as a fractionation method for sensitive and powerful shotgun proteomics. Nature Protocols, 7(11), 2041-2055. https://doi.org/10.1038/nprot.2012.124
Burgers, P. P., Ma, Y., Margarucci, L., Mackey, M., van der Heyden, M. A. G., Ellisman, M., Scholten, A., Taylor, S. S., & Heck, A. J. R. (2012). A Small Novel A-Kinase Anchoring Protein (AKAP) That Localizes Specifically Protein Kinase A-Regulatory Subunit I (PKA-RI) to the Plasma Membrane. Journal of Biological Chemistry, 287(52), 43789-43797. http://www.ncbi.nlm.nih.gov/pubmed/23115245
Rosati, S., Thompson, N. J., Barendregt, A., Hendriks, L. J. A., Bakker, A. B. H., De Kruif, J., Throsby, M., van Duijn, E., & Heck, A. J. R. (2012). Qualitative and semiquantitative analysis of composite mixtures of antibodies by native mass spectrometry. Analytical Chemistry, 84, 7227-7232. https://doi.org/10.1021/ac301611d
Zoumaro-Djayoon, A. D., Heck, A. J. R., & Munoz, J. (2012). Targeted analysis of tyrosine phosphorylation by immuno-affinity enrichment of tyrosine phosphorylated peptides prior to mass spectrometric analysis. Methods, 56(2), 268-274.
Kruiswijk, F., Yuniati, L., Low, T. Y., Lim, R., Bolder, R., Mohammed, S., Proud, C. G., Heck, A. J. R., & Pagano, M. (2012). Coupled activation and degradation of eEF2K regulates protein synthesis in response to genotoxic stress. Science Signaling [E], 5(227), 1-12. https://doi.org/10.1126/scisignal.2002718
Peng, M., Ms. Taouatas, N., Cappadona, S., van Breukelen, B., Mohammed, S., Scholten, A., & Heck, A. J. R. (2012). Protease bias in absolute protein quantitation. Nature Methods, 9(6), 524-525. https://doi.org/10.1038/nmeth.2031
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.
Lindhoud, S., van den Berg, W. A. M., van den Heuvel, R. H. H., Heck, A. J. R., van Mierlo, C. P. M., & van Berkel, W. J. H. (2012). Cofactor binding protects flavodoxin against oxidative stress. PLoS One, 7(7). https://doi.org/10.1371/journal.pone.0041363
Mommen, G. P. M., van de Waterbeemd, B., Meiring, H. D., Kersten, G., Heck, A. J. R., & de Jong, A. P. J. M. (2012). Unbiased selective isolation of protein N-terminal peptides from complex proteome samples using phospho tagging (PTAG) and TiO(2)-based depletion. Molecular & Cellular Proteomics, 9, 832-842. https://doi.org/10.1074/mcp.O112.018283
Hennrich, M. L., van den Toorn, H. W. P., Groenewold, V., Heck, A. J. R., & Mohammed, S. (2012). Ultra acidic strong cation exchange enabling the efficient enrichment of basic phosphopeptides. Analytical Chemistry, 84, 1804-1808. https://doi.org/10.1021/ac203303t
Aye, T. T., Soni, S., van Veen, T. A. B., van der Heyden, M. A. G., Cappadona, S., Varro, A., de Weger, R. A., de Jonge, N., Vos, M. A., Heck, A. J. R., & Scholten, A. (2012). Reorganized PKA-AKAP associations in the failing human heart. Journal of Molecular and Cellular Cardiology, 52(2), 511-518. https://doi.org/10.1016/j.yjmcc.2011.06.003
Di Palma, S., Hennrich, M. L., Heck, A. J. R., & Mohammed, S. (2012). Recent advances in peptide separation by multidimensional liquid chromatography for proteome analysis. Journal of Proteomics, 75, 3791-3813. https://doi.org/10.1016/j.jprot.2012.04.033
Nenci, S., Piano, V., Rosati, S., Aliverti, A., Pandini, V., Fraaije, M. W., Heck, A. J. R., Edmondson, D. E., & Mattevi, A. (2012). Precursor of ether phospholipids is synthesized by a flavoenzyme through covalent catalysis. Proceedings of the National Academy of Sciences of the United States of America, 109(46), 18791-18796. https://doi.org/10.1073/pnas.1215128109
Cappadona, S., Baker, P. R., Cutillas, P., Heck, A. J. R., & van Breukelen, B. (2012). Current challenges in software solutions for mass spectrometry-based quantitative proteomics. Amino Acids, 43, 1087-1108. https://doi.org/10.1007/s00726-012-1289-8.
van Duijn, E., Barbu, I. M., Barendregt, A., Jore, M. M., Wiedenheft, B., Lundgren, M., Westra, E. R., Brouns, S. J. J., Doudna, J. A., van der Oost, J., & Heck, A. J. R. (2012). Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced shot-palindromic-repeats (CRISPR)-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa. Molecular & Cellular Proteomics, 11, 1430-1441. https://doi.org/10.1074/mcp.M112.020263
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.
Glatter, T., Ludwig, C., Ahrne, E., Aebersold, R., Heck, A. J. R., & Schmidt, A. (2012). Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion. Journal of Proteome Research, 11, 5145-5156. https://doi.org/10.1021/pr300273g
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
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., Maarten Altelaar, A. F., 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 Ninth Symposium Kluyver Centre for Genomics of Industrial Fermentation, Noordwijkerhout.
Krijgsheld, P., Maarten Altelaar, A. F., 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. Poster session presented at Ninth Symposium Kluyver Centre for Genomics of Industrial Fermentation, Noordwijkerhout.
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
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
Abrahams, J-P., Apweiler, R., Balling, R., Bertero, M. G., Bujnicki, J. M., Chayen, N. E., Chène, P., Corthals, G. L., Dyląg, T., Förster, F., Heck, A. J. R., Henderson, P. J. F., Herwig, R., Jehenson, P., Kokalj, S. J., Laue, E., Legrain, P., Martens, L., Migliorini, C., ... Taussig, M. J. (2011). "4D Biology for health and disease" workshop report. Biotechnology Journal, 28(4), 291-3. https://doi.org/10.1016/j.nbt.2010.10.003
Dewalick, S., Bexkens, M. L., van Balkom, B. W. M., Wu, Y-P., Smit, C. H., Hokke, C. H., de Groot, P. G., Heck, A. J. R., Tielens, A. G. M., & van Hellemond, J. J. (2011). The proteome of the insoluble Schistosoma mansoni eggshell skeleton. International Journal for Parasitology, 41(5), 523-32. https://doi.org/10.1016/j.ijpara.2010.12.005
Galli, M., Munoz, J., Portegijs, V. C., Boxem, M., Grill, S. W., Heck, A. J. R., & van den Heuvel, S. J. L. (2011). aPKC phosphorylates NuMa-related LIN-5 to position the mitotic spindle during asymmetric division. Nature Cell Biology, 13(9), 1132-1138. https://doi.org/10.1038/ncb2315
Labrijn, A. F., Rispens, T., Meesters, J., Rose, R. J., den Bleker, T. H., Loverix, S., van den Bremer, E. T. J., Neijssen, J., Vink, T., Lasters, I., Aalberse, R. C., Heck, A. J. R., van de Winkel, J. G. J., Schuurman, J., & Parren, P. W. H. I. (2011). Species-specific determinants in the IgG CH3 domain enable Fab-arm exchange by affecting the noncovalent CH3-CH3 interaction strength. Journal of Immunology, 187(6), 3238-3246. https://doi.org/10.4049/jimmunol.1003336
de Lau, W., Low, T. Y., Kujala, P., Peters, P. J., Schasfoort, R. B. M., Mohri, Y., Nishimori, K., Mohammed, S., Heck, A. J. R., & Clevers, H. C. (2011). Lgr5 homologues associate with Wnt receptors and mediate R-spondin signalling. Nature, 476(7360), 293-297. https://doi.org/10.1038/nature10337
Uetrecht, C., Barbu, I. M., Shoemaker, G. K., van Duijn, E., & Heck, A. J. R. (2011). Interrogating viral capsid assembly with ion mobility-mass spectrometry. Nature Chemistry, 3(2), 126-132.
Helbig, A. O., Daran-Lapujade, P., van Maris, A. J., de Hulster, E. A., de Ridder, D., Pronk, J. T., Heck, A. J. R., & Slijper, M. (2011). The diversity of protein turnover and abundance under nitrogen-limited steady-state conditions in Saccharomyces cerevisiae. Molecular BioSystems, 7(12), 3313-3326.
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.
Tseng, Y. H., Uetrecht, C., Heck, A. J. R., & Peng, W. P. (2011). Interpreting the charge state assignment in electrospray mass spectra of bioparticles. Analytical Chemistry, 83(6), 1960-1968.
Brasch, M., de la Escosura, A., Ma, Y., Uetrecht, C., Heck, A. J. R., Torres, T., & Cornelissen, J. J. L. M. (2011). Encapsulation of phthalocyanine supramolecular stacks into virus-like particles. Journal of the American Chemical Society, 133(18), 6878-6881.
Blattner, C., Jennebach, S., Herzog, F., Mayer, A., Cheung, A. C., Witte, G., Lorenzen, K., Hopfner, K. P., Heck, A. J. R., Aebersold, R., & Cramer, P. (2011). Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth. Genes and Development, 25(19), 2093-2105. https://doi.org/10.1101/glad.17663311
Jore, M. M., Lundgren, M., van Duijn, E., Bultema, J. B., Waghmare, S. P., Wiedenheft, B., Pul, U., Wurm, R., Wagner, R., Beijer, M. R., Barendregt, A., Zhou, K., Snijders, A. P. L., Dickman, M. J., Doudna, J. A., Boekema, E. J., Heck, A. J. R., van der Oost, J., & Brouns, S. J. J. (2011). Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nature Structural and Molecular Biology, 18(5), 529-536.
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
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
Garcia-Alles, L. F., Collmann, A., Versluis, C., Lindner, B., Guiard, J., Maveyraud, L., Huc, E., Im, J. S., Sansano, S., Brando, T., Julien, S., Prandi, J., Gilleron, M., Porcelli, S. A., de la Salle, H., Heck, A. J. R., Mori, L., Puzo, G., Mourey, L., & de Libero, G. (2011). Structural reorganization of the antigen-binding groove of human CD1b for presentation of mycobacterial sulfoglycolipids. Proceedings of the National Academy of Sciences of the United States of America, 108(43), 17755-17760.
Scholten, A., Mohammed, S., Low, T. Y., Zanivan, S., van Veen, A. A. B., Delanghe, B., & Heck, A. J. R. (2011). In-depth quantitative cardiac proteomics combining electron transfer dissociation and the metalloendopeptidase Lys-N with the SILAC mouse. Molecular & Cellular Proteomics, 10(10), O111.008474. http://www.ncbi.nlm.nih.gov/pubmed/21705516
Karagoz, E., dos santos Duarte, A., Ippel, H., Uetrecht, C., Sinnige, T., Van Rosmalen, M., Hausmann, J., Heck, A. J. R., Boelens, R., & Rüdiger, S. G. D. (2011). N-terminal domain of human Hsp90 triggers binding to the cochaperone p23. Proceedings of the National Academy of Sciences of the United States of America, 108(2), 580-585. https://doi.org/10.1073/pnas.1011867108
Uetrecht, C., & Heck, A. J. R. (2011). Modern biomolecular mass spectrometry and its role in studying virus structure, dynamics, and assembly. Angewandte Chemie-International Edition, 50, 8248-8262. https://doi.org/10.1002/anie.201008120
Vogels, M. W., van Balkom, B. W. M., Kaloyanova, D. V., Batenburg, J. J., Heck, A. J. R., Helms, J. B., Rottier, P. J. M., & de Haan, C. A. M. (2011). Identification of host factors involved in coronavirus replication by quantitative proteomics analysis. Proteomics, 11(1), 64-80. https://doi.org/10.1002/pmic.201000309
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
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.
Vogels, M. W., van Balkom, B. W. M., Heck, A. J. R., de Haan, C. A. M., Rottier, P. J. M., Batenburg, J. J., Kaloyanova, D. V., & Helms, J. B. (2011). Quantitative proteomic identification of host factors involved in the Salmonella syphimuruim infectin cycle. Proteomics, 11, 4477-4491. https://doi.org/10.1002/pmic.201100224
Di Palma, S., Boersema, P. J., Heck, A. J. R., & Mohammed, S. (2011). Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC and ZIC-cHILIC) provide high resolution separation and increase sensitivity in proteome analysis. Analytical Chemistry, 83(9), 3440-3447.
Margarucci, L., Roest, M., Preisinger, C., Bleijerveld, O. B., van Holten, T. C., Heck, A. J. R., & Scholten, A. (2011). Collagen stimulation of platelets induces a rapid spatial response of cAMP and cGMP signaling scaffolds. Molecular BioSystems, 7, 2311-2319. http://www.ncbi.nlm.nih.gov/pubmed/21597619
Baclayon, M., Shoemaker, G. K., Uetrecht, C., Crawford, S. E., Estes, M. K., Prasad, B. V. V., Heck, A. J. R., Wuite, G. J. L., & Roos, W. H. (2011). Prestress strengthens the shell of norwalk virus nanoparticles. Nano Letters, 9(11), 4865-4869.
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.
Zhou, H., Low, T. Y., Hennrich, M. L., van den Toorn, H. W. P., Schwend, T. A., zou, H., Mohammed, S., & Heck, A. J. R. (2011). Enhancing the identification of phosphopeptides from putative basophilic kinase substrates using Ti (IV) based IMAC enrichment. Molecular & Cellular Proteomics, 10(10).
Mohammed, S., & Heck, A. J. R. (2011). Strong cation exchange (SCX) based analytical mehtods for the targeted analysis of protein post-translational modifications. Current Opinion in Biotechnology, 22, 9-16.
Rose, R. J., Labrijn, A. F., van den Bremer, E. T. J., Loverix, S., Lasters, I., van Berkel, P. H. C., van de Winkel, J. G. J., Schuurman, J., Parren, P. W. H. I., & Heck, A. J. R. (2011). Quantitative analysis of the interaction strength and dynamics of human IgG4 half molecules by native mass spectrometry. Structure, 19(9), 1274-1282.
Wiedenheft, B., van Duijn, E., Bultema, J. B., Waghmare, S. P., Zhou, K., Barendregt, A., Westphal, W., Heck, A. J. R., Boekema, E. J., Dickman, M. J., & Doudna, J. A. (2011). RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions. Proceedings of the National Academy of Sciences of the United States of America, 108(25), 10092-10097.
Boekhorst, J., Boersema, P. J., Tops, B. B. J., van Breukelen, B., Heck, A. J. R., & Snel, B. (2011). Evaluating experimental bias and completeness in comparative phosphoproteomics analysis. PLoS One, 6(8), 23276.
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
Garcia-Alles, L. F., Giacometti, G., Versluis, C., Maveyraud, L., de Paepe, D., Guiard, J., Tranier, S., Gilleron, M., Prandi, J., Hanau, D., Heck, A. J. R., Mori, L., de Libero, G., Puzo, G., Mourey, L., & de la Salle, H. (2011). Crystal structure of human CD1e reveals a groove suited for lipid-exchange processess. Proceedings of the National Academy of Sciences of the United States of America, 108(32), 13230-13235.
Di Palma, S., Stange, D., van de Wetering, M., Clevers, H. C., Heck, A. J. R., & Mohammed, S. (2011). Highly sensitive proteome analysis of FACS-sorted adult colon stem cells. Journal of Proteome Research, 10(8), 3814-3819.
Zoumaro-Djayoon, A. D., Ding, V., Foong, L. Y., Choo, A., Heck, A. J. R., & Munoz, J. (2011). Investigating the role of FGF-2 in stem cell maintenance by global phosphoproteomics profiling. Proteomics, 11(20), 3962-3971. https://doi.org/10.1002/pmic.201100048
Cappadona, S., Munoz, J., Spee, W. P. E., Low, T. Y., Mohammed, S., van Breukelen, B., & Heck, A. J. R. (2011). Deconvolution of overlapping isotopic clusters improves quantification of stable isotope-labeled peptides. Journal of Proteomics, 74(10), 2204-2209.
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.
Hennrich, M. L., Groenewold, V., Kops, G. J. P. L., Heck, A. J. R., & Mohammed, S. (2011). Improving depth in phosphoproteomics by using a strong cation exchange-weak anion exchange-reversed phase multidimensional separation approach. Analytical Chemistry, 83(18), 7137-7143.
Ding, V. M., Boersema, P. J., Foong, L. Y., Preisinger, C., Koh, G., Natarajan, S., Lee, D. Y., Boekhorst, J., Snel, B., Lemeer, S. M., Heck, A. J. R., & Choo, A. (2011). Tyrosine phosphorylation profiling in FGF-2 stimulated human embryonic stem cells. PLoS One, 6(3), 17538.
Monti, M. C., Cohen, S. X., Fish, A., Winterwerp, H. H., Barendregt, A., Friedhoff, P., Perrakis, A., Heck, A. J. R., Sixma, T. K., van den Heuvel, R. H. H., & Lebbink, J. H. (2011). Native mass spectrometry provides direct evidence for DNA mismatch-induced regulation of asymmetric nucleotide binding in mismatch repair protein MutS. Nucleic Acids Research, 39(18), 8052-8064.
Mischerikow, N., & Heck, A. J. R. (2011). Targeted large-scale analysis of protein acetylation. Proteomics, 11(4), 571-589. https://doi.org/10.1002/pmic.201000397
Professional publications
Ms. Taouatas, N., Mohammed, S., & Heck, A. J. R. (2011). Exploring new proteome space: combining Lys-N proteolytic digestion and strong cation exchange (SCX) separation in peptide-centric MS-driven proteomics. In Gel free proteomics: Methods in Molecular Biology (pp. 157-167). (753). Springer. https://doi.org/10.1007/978-1-61779-148-2_11
Pinkse, M. W. H., Lemeer, S. M., & Heck, A. J. R. (2011). A protocol on the use of titanium dioxide chromatography for phosphoproteomics. In Gel free proteomics; Methods in Molecular Biology (pp. 215-228). (753). Springer. https://doi.org/10.1007/978-1-61779-148-2_14
Munoz, J., & Heck, A. J. R. (2011). Quantitative proteome and phosphoproteome analysis of human pluripotent stem cells. In Human pluripotent stem cells; methods in molecular biology (pp. 297-312). (767; No. 4). Springer. https://doi.org/10.1007/978-1-61779-201-4_22
Other output
Krijgsheld, P., Altelaar, M., Post, H., Ringrose, J. H., Heck, A. J. R., & Wösten, H. A. B. (2011). Secretome analysis of concentric zones of Aspergillus niger colonies. Abstract from 26th Fungal Genetics Conference Asilomar 2011, Asilomar, USA.
2010
Scholarly publications
Helbig, A. O., Rosati, S., Pijnappel, W. W. M. P., van Breukelen, B., Timmers, H. T. M., Mohammed, S., Slijper, M., & Heck, A. J. R. (2010). Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels. BMC Genomics, 11(1). https://doi.org/10.1186/1471-2164-11-685
Van Breukelen, B., Georgiou, A., Drugan, M. M., Taouatas, N., Mohammed, S., & Heck, A. J. R. (2010). LysNDeNovo: An algorithm enabling de novo sequencing of Lys-N generated peptides fragmented by electron transfer dissociation. Proteomics, 10(6), 1196-1201. https://doi.org/10.1002/pmic.200900405
Kovanich, D., van der Heyden, M. A. G., Aye, T. T., van Veen, A. A. B., Heck, A. J. R., & Scholten, A. (2010). Sphingosine kinase interacting protein is an A-kinase anchoring protein specific for type I cAMP-dependent protein kinase. ChemBioChem, 11(7), 963-971.
Hoogenraad, C. C., Popa, I. L., Futai, K., Martinez Sanchez, E., Wulf, P. S., van Vlijmen, T., Dortland, B., Oorschot, V. M. J., Govers, R., Monti, M., Heck, A. J. R., Sheng, M., Klumperman, J., Rehmann, H., Jaarsma, D., Kapitein, L. C., & van der Sluijs, P. (2010). Neuron specific Rab4 effector GRASP-1 coordinates membrane specialization and maturation of recycling endosomes. PloS Biology [E], 8(1), e1000283. http://www.ncbi.nlm.nih.gov/pubmed/20098723
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).
Helbig, A. O., Heck, A. J. R., & Slijper, M. (2010). Exploring the membrane proteome--challenges and analytical strategies. Journal of Proteomics, 73, 868-878.
Ng, S. S., Boersema, P. J., Mohammed, S., Heck, A. J. R., & Clevers, H. C. (2010). MAP3K1 functionally interacts with Axin1 in the canonical Wnt signalling pathway. Biological Chemistry, 391(2-3), 171-180. http://www.ncbi.nlm.nih.gov/pubmed/20128690
Shoemaker, G. K., van Duijn, E., Crawford, S. E., Uetrecht, C., Baclayon, M., Roos, W. H., Wuite, G. J. L., Estes, M. K., Prasad, B. V. V., & Heck, A. J. R. (2010). Norwalk virus assembly and stability monitored by mass spectrometry. Molecular & Cellular Proteomics, 9, 1742-1751.
Gouw, J. W., Krijgsveld, J., & Heck, A. J. R. (2010). Quantitative proteomics by metabolic labeling of model organisms. Molecular & Cellular Proteomics, 9, 11-24.
Schaaij-Visser, B. M., Bremmer, J. F., Braakhuis, B. J. M., Heck, A. J. R., Slijper, M., van der Waal, I., & Brakenhoff, R. H. (2010). Evaluation of cornulin, keratin 4, keratin 13 expression and grade of dysplasia for predicting malignant progression of oral leukoplakia. Oral Oncology, 46, 123-127.
Alvarez Fernandez, M., Halim, V. A. H., Krenning, L., Aprelia, M., Mohammed, S., Heck, A. J. R., & Medema, R. H. (2010). Recovery from a DNA-damage-induced G2 arrest requires Cdk-dependent activation of FoxM1. EMBO Reports, 11, 452-458.
Wu, H., Sun, L., Blombach, F., Brouns, S. J. J., Snijders, A. P. L., Lorenzen, K., van den Heuvel, R. H. H., Heck, A. J. R., Fu, S., Li, X., Zhang, X. C., & van der Oost, J. (2010). Structure of the ribosome associating GTPase HflX. Proteins: Structure function and bioinformatics, 15(78), 705-713.
Frederiks, F., Welsem, T., Oudgenoeg, G., Heck, A. J. R., Janzen, C. J., & van Leeuwen, F. (2010). Heterologous expression reveals distinct enzymatic activities of two DOT1 histone methyltransferase of Trypanosoma brucei. Journal of Cell Science, 123, 4019-4023.
Mahmoudi, T., Ms. Taouatas, N., Mohammed, S., Heck, A. J. R., & Clevers, H. C. (2010). The Leukemia-Associated Mllt10/Af10-Dot1l Are Tcf4//β-Catenin Coactivators essential for intestinal homeostasis. PloS Biology [E], 8(11), e1000539. http://www.ncbi.nlm.nih.gov/pubmed/21103407
van Gestel, R. A., van Solinge, W. W., van den Toorn, H. W. P., Rijksen, G., Heck, A. J. R., van Wijk, R., & Slijper, M. (2010). Quantitative erythrocyte membrane proteome analysis with Blue-native/SDS PAGE. Journal of Proteomics, 73, 456-465.
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.
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.
Alpert, A. J., Petritis, K., Kangas, L., Smith, R. D., Mechtler, K., Mitulovic, G., Mohammed, S., & Heck, A. J. R. (2010). Peptide orientation affects selectivity in ion-exchange chromatography. Analytical Chemistry, 82(12), 5253-5259.
van Hoof, D., Dormeyer, W., Braam, S. R., Passier, R., Monshouwer-Kloots, J., Heck, A. J. R., Krijgsveld, J., & Mummery, C. L. (2010). Identification of Cell Surface Proteins for Antibody-Based Selection of Human Embryonic Stem Cell-Derived Cardiomyocytes. Journal of Proteome Research, 9(3), 1610-1618. http://www.ncbi.nlm.nih.gov/pubmed/20088484
van Gestel, R. A., Rijken, P. J., Surinova, S., O'Flaherty, M., Heck, A. J. R., Killian, J. A., de Kroon, A. I. P. M., & Slijper, M. (2010). The influence of the acyl chain composition of cardiolipin on the stability of mitochondrial complexes; An unexpected effect of cardiolipin in α-ketoglutarate dehydrogenase and prohibitin complexes. Journal of Proteomics, 73(4), 806-814. https://doi.org/10.1016/j.jprot.2009.11.009
Lau, N. C., Mulder, K. W., Brenkman, A. B., Mohammed, S., van den Broek, N. J. F., Heck, A. J. R., & Timmers, H. T. M. (2010). Phosphorylation of Not4p Functions Parallel to BUR2 to Regulate Resistance to Cellular Stresses in Saccharomyces cerevisiae. PLoS One, 5(4), e9864. http://www.ncbi.nlm.nih.gov/pubmed
Tops, B. B. J., Gauci, S., Heck, A. J. R., & Krijgsveld, J. (2010). Worms from venus and mars: proteomics profiling of sexual differences in Caenorhabditis elegans using in vivo 15N isotope labeling. Journal of Proteome Research, 9, 341-351.
Wit, N. C. J., Heck, A. J. R., & Thornton, S. (2010). The effect of oxytocin and an oxytocin antagonist on the human myometrial proteome. Reproductive Sciences, 17, 40-46.
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.
Mortensen, P., Gouw, J. W., Olsen, J. V., Ong, S-E., Rigbolt, K. T. G., Bunkenborg, J., Cox, J., Foster, L. J., Heck, A. J. R., Blagoev, B., Andersen, J. S., & Mann, M. (2010). MSQuant, an open source platform for mass spectrometry-based quantitative proteomics. Journal of Proteome Research, 9, 393-403.
Buschow, S. I., van Balkom, B. W. M., Aalberts, M., Heck, A. J. R., Wauben, M. H. M., & Stoorvogel, W. (2010). MHC class II-associated proteins in B-cells exosomes and potential functional implications for exosome biogenesis. Immunology and Cell Biology, 88(8), 851-856.
Oberprieler, N. G., Lemeer, S. M., kalland, M. E., Torgersen, K. M., Heck, A. J. R., & Tasken, K. (2010). High-resolution mapping of prostaglandin E2-dependent signaling networks identifies a constitutively active PKA signaling node in CD8+CD45RO+ T cells. Blood, 116(13), 2253-2265. http://www.ncbi.nlm.nih.gov/pubmed/20558615
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.
Koschubs, T., Lorenzen, K., Baumli, S., Sandstrom, S., Heck, A. J. R., & Cramer, P. (2010). Preparation and topology of the Mediator middle module. Nucleic Acids Research, 38(10), 3186-3195.
Aye, T. T., Scholten, A., Ms. Taouatas, N., Varro, A., van Veen, T. A. B., Vos, M. A., & Heck, A. J. R. (2010). Proteome-wide protein concentrations in the human heart. Molecular BioSystems, 6(10), 1917-1927.
Uetrecht, C., Watts, N. R., Stahl, S. J., Wingfield, P. T., Steven, A. C., & Heck, A. J. R. (2010). Subunit exchange rates in Hepatitis B virus capsids are geometry- and temperature-dependent. Physical Chemistry Chemical Physics, 12, 13368-13371.
Schaaij-Visser, B. M., Brakenhoff, R. H., Leemans, C. R., Heck, A. J. R., & Slijper, M. (2010). Protein biomarker discovery for head and neck cancer. Journal of Proteomics, 73, 1790-1803.
Girardi, E., Wang, J., Mac, T. T., Versluis, C., Bhowruth, V., Besra, G., Heck, A. J. R., van Rhijn, I., & Zajonc, D. M. (2010). Crystal structure of bovine CD1b3 with endogenously bound ligands. Journal of Immunology, 185, 376-386. https://doi.org/10.4049/jimmunol.1000042
Roos, W. H., Gibbons, M. M., Arkhipov, A., Uetrecht, C., Watts, N. R., Wingfield, P. T., Steven, A. C., Heck, A. J. R., Schulten, K., Klug, W. S., & Wuite, G. J. L. (2010). Squeezing protein shells: how continuum elastic models, molecular dynamics simulations, and experiments coalesce at the nanoscale. Biophysical Journal, 99, 1175-1181.
Kukrer, B., Filipe, V., van Duijn, E., Kasper, P. T., Vreeken, R. J., Heck, A. J. R., & Jiskoot, W. (2010). Mass spectrometric analysis of intact human monoclonal antibody aggregates fractionated by size-exclusion chromatography. Pharmaceutical Research, 27, 2197-2204.
Brettschneider, C., Rose, R. J., Hertel, S., Axmann, I. M., Heck, A. J. R., & Kollmann, M. (2010). A sequestration feedback determines dynamics and temperature entrainment of the KaiABC circadian clock. Molecular Systems Biology [E], 6.
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.
Fu, C-Y., Uetrecht, C., Kang, S., Morais, M. C., Heck, A. J. R., Walter, M. R., & Prevelige, P. E. (2010). A docking model based on mass spectrometric and biochemical data describes phage packaging motor incorporation. Molecular & Cellular Proteomics, 9, 1764-1773.
Spedale, G., Mischerikow, N., Heck, A. J. R., Timmers, H. T. M., & Pijnappel, W. W. M. (2010). Identification of Pep4p as the protease responsible for formation of the SAGA-related SLIK protein complex. Journal of Biological Chemistry, 285(30), 22793-22799. http://www.ncbi.nlm.nih.gov/pubmed/20498363
Hah, N., Kolkman, A., Ruhl, D. D., Pijnappel, W. W. M., Heck, A. J. R., Timmers, H. T. M., & Kraus, W. L. (2010). Role for BAF57 in cell cycle-dependent transcriptional regulation by the SWI/SNF chromatin remodeling complex. Cancer Research, 70, 4402-4411. http://www.ncbi.nlm.nih.gov/pubmed/20460533
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.
Barbu, I. M., Smith, D. F., van Breukelen, B., van der Burgt, Y. E. M., Duursma, M. C., Heck, A. J. R., Heeren, R. M. A., & Krijgsveld, J. (2010). On-the-fly targeted selection of labeled peptides in liquid chromatography/mass spectrometry based quantitative proteomics. Rapid Communications in Mass Spectrometry, 24, 239-241.
Geiger, S. R., Lorenzen, K., Schreieck, A., Hanecker, P., Kostrewa, D., Heck, A. J. R., & Cramer, P. (2010). RNA polymerase I contains a TFIIF related DNA binding subcomplex. Molecular Cell, 39, 583-594.
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.
Kim, S., Mischerikow, N., Bandeira, N., Navarro Herrero, J. D., Wich, L., Mohammed, S., Heck, A. J. R., & Pevzner, P. A. (2010). The generating function of CID, ETD, and CID/ETD pairs of tandem Mass Spectra: applications to Database search. Molecular & Cellular Proteomics, 9, 2840-2852.
Uetrecht, C., Rose, R. J., van Duijn, E., Lorenzen, K., & Heck, A. J. R. (2010). Ion mobility mass spectrometry of proteins and protein assemblies. Chemical Society Reviews, 39, 1633-1655.
Christis, C., Fullaondo, A., Schildknegt, D., Mkrtchian, S., Heck, A. J. R., & Braakman, L. J. (2010). Regulated increase in folding capacity prevents unfolded protein stress in the ER. Journal of Cell Science, 123(5), 787-794. https://doi.org/10.1242/jcs.041111
https://dspace.library.uu.nl/bitstream/handle/1874/200563/Regulated-increase-in-folding-capacity_2010_Journal-of-Cell-Science.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/200563/Regulated-increase-in-folding-capacity_2010_Journal-of-Cell-Science.pdf?sequence=1
Ms. Taouatas, N., Heck, A. J. R., & Mohammed, S. (2010). Evaluation of metalloendopeptidase Lys-N protease performance under different sample handling conditions. Journal of Proteome Research, 9, 4282-4288.
Professional publications
Heck, A. J. R. (2010). At the interface of interaction proteomics and structural biology. Molecular & Cellular Proteomics, 9, 1633-1633.
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
Boersema, P., Foong, L. Y., Ding, V., Lemeer, S., Mohammed, S., Raijmakers, R., van Breukelen, B., Boekhorst, J., Choo, A. B. H., & Heck, A. J. R. (2009). Large Scale Multiplex Stable Isotope Dimethyl Labeling Applied to the Quantitative Analysis of Tyrosine Phosphorylation. Molecular & Cellular Proteomics, S47-S47. https://www.researchgate.net/publication/295938897_Large_Scale_Multiplex_Stable_Isotope_Dimethyl_Labeling_Applied_to_the_Quantitative_Analysis_of_Tyrosine_Phosphorylation
van Breukelen, B., van den Toorn, H. W. P., Drugan, M. M., & Heck, A. J. R. (2009). StatQuant: A post-quantification analysis toolbox for improving quantitative mass spectrometry. Bioinformatics, 25(11), 1472-1473. https://doi.org/10.1093/bioinformatics/btp181
Gauci, S., Veenhoff, L. M., Heck, A. J. R., & Krijgsveld, J. (2009). Orthogonal separation techniques for the characterization of the yeast nuclear proteome. Journal of Proteome Research, (8), 3451-3463.
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
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.
Boersema, P. J., Mohammed, S., & Heck, A. J. R. (2009). Phosphopeptide fragmentation and analysis by mass spectrometry. Journal of Mass Spectrometry, (44), 861-878.
Lau, N. C., Kolkman, A., van Schaik, F. M. A., Mulder, K. W., Pijnappel, W. W. M., Heck, A. J. R., & Timmers, H. T. M. (2009). Human Ccr4-Not complexes contain variable deadenylase subunits. Biochemical Journal, 422, 443-453. http://www.ncbi.nlm.nih.gov/pubmed/19558367?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=2
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.
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.
Muñoz, J., & Heck, A. J. R. (2009). Perspectives in stem cell proteomics. Genome Medicine, 1(4), Article 45. https://doi.org/10.1186/gm45
Diago-Navarro, E., Kamphuis, M. B., Boelens, R., Barendregt, A., Heck, A. J. R., van den Heuvel, R. H. H., & Diaz-Orejas, R. (2009). A mutagenic analysis of the RNase mechanism of the bacterial Kid toxin by mass spectrometry. The FEBS journal, (276), 4973-4986.
Mahmoudi, T., Ms. Taouatas, N., Mohammed, S., Heck, A. J. R., & Clevers, J. C. (2009). The kinase TNIK is an essential activator of Wnt target genes. EMBO Journal, 28(21), 3329-3340.
van Hoof, D., Munoz-Peralta, J., Braam, S. R., Pinkse, M. W. H., Linding, R., Heck, A. J. R., Mummery, C. L., & Krijgsveld, J. (2009). Phosphorylation dynamics during early differentiation of human embryonic stem cells. Cell Stem Cell, 5(2), 214-226. http://www.ncbi.nlm.nih.gov/pubmed/19664995
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.
van Duijn, E., Barendregt, A., Synowsky, S. A., Versluis, C., & Heck, A. J. R. (2009). Chaperonin complexes monitored by ion mobility mass spectrometry. Journal of the American Chemical Society, (131), 1452-1459.
Schaaij-Visser, B. M., Brakenhoff, R. H., Jansen, J. W. A., O'Flaherty, M. C., Smeets, S. J., Heck, A. J. R., & Slijper, M. (2009). Comparative proteome analysis to explore p53 pathway disruption in head and neck carcinogenesis. Journal of Proteomics, (72), 803-814.
Schaaij-Visser, B. M., Graveland, A. P., Gauci, S., Braakhuis, B. J. M., Buijze, M., Heck, A. J. R., Kuik, D. J., Bloemena, E., Leemans, C. R., Slijper, M., & Brakenhoff, R. H. (2009). Differential Proteomics Identifies Protein Biomarkers that predict local relapse of head and neck squamous cell carcinomas. Clinical Cancer Research, (15), 7666-7675.
Aye, T. T., Mohammed, S., van den Toorn, H. W. P., van Veen, T. A. B., van der Heyden, M. A. G., Scholten, A., & Heck, A. J. R. (2009). Selectivity in enrichment of cAMP-dependent protein kinase regulatory subunits type I and type II and their interactors using modified cAMP affinity resins. Molecular & Cellular Proteomics, 8(5), 1016-1028.
Rodriguez, H., Snyder, M., Uhlen, M., Andrews, P., Beavis, R., Borchers, C., Chalkley, R. J., Cho, S. Y., Cottingham, K., Dunn, M., Dylag, T., Edgar, R., Hare, P., Heck, A. J. R., Hirsch, R. F., Kennedy, K., Kolar, P., Kraus, H-J., Mallick, P., ... Apweiler, R. (2009). Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. Journal of Proteome Research, (8), 3689-3692.
Sneekes, E. J., Han, J., Elliot, M., Ausio, J., Swart, R., Heck, A. J. R., & Borchers, C. (2009). Accurate molecular weight analysis of histones using FFE and RP-HPLC on monolithic capillary columns. Journal of Separation Science, 32(16/16), 2691-2698. https://doi.org/10.1002/jssc.200800627
Helbig, A. O., de Groot, M. J. L., van Gestel, R. A., Mohammed, S., Hulster, E. A. F., van Luttik, M. A. H., Daran-Lapujade, P., Pronk, J. T., Heck, A. J. R., & Slijper, M. (2009). A three-way proteomics strategy allows differential analysis of yeast mitochondrial membrane protein complexes under anaerobic and aerobic conditions. Proteomics, (9), 4787-4798.
Leferink, N. G. H., van Duijn, E., Barendregt, A., Heck, A. J. R., & van Berkel, W. J. H. (2009). Galactonolactone dehydrogenase requires a redox-sensitive thiol for optimal production of vitamin C. Plant Physiology, (150), 596-605.
Pinkse, M. W. H., Rijkers, D. T. S., Dostmann, W. R. G., & Heck, A. J. R. (2009). Mode of action of cGMP-dependent protein kinase-specific inhibitors probed by photoaffinity cross-linking mass spectrometry. Journal of Biological Chemistry, (284), 16354-16368.
van Anken, E., Pena, F., Hafkemeijer, N., Christis, C., Romijn, E. P., Grauschopf, U., Oorschot, V. M. J., Pertel, T., Engels, S., Ora, A., Lastun, V., Glockshuber, R., Klumperman, J., Heck, A. J. R., Luban, J., & Braakman, I. (2009). Efficient IgM assembly and secretion require the plasma cell induced endoplasmic reticulum protein pERp1. Proceedings of the National Academy of Sciences of the United States of America, 106(40), 17019-17024.
Hennrich, M. L., Boersema, P. J., van den Toorn, H. W. P., Mischerikow, N., Heck, A. J. R., & Mohammed, S. (2009). Effect of chemical modifications on peptide fragmentation behavior upon electron transfer induced dissociation. Analytical Chemistry, 81(18), 7814-7822.
Dadvar, P., O'Flaherty, M. C., Scholten, A., Rumpel, K., & Heck, A. J. R. (2009). A chemical proteomics based enrichment technique targeting the interactome of the PDE5 inhibitor PF-4540124. Molecular BioSystems, (5), 472-482.
Lemeer, S. M., & Heck, A. J. R. (2009). The phosphoproteomics data explosion. Current Opinion in Chemical Biology, (13), 414-420.
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.
Bantscheff, M., Scholten, A., & Heck, A. J. R. (2009). Revealing promiscuous drug-target interactions by chemical proteomics. Drug Discovery Today. Technologies, (14), 1021-1029.
de Vries, E., Bakker, N., Krijgsveld, J., Knox, D. P., Heck, A. J. R., & Yatsuda, A. P. (2009). An AC-5 cathepsin B-like protease purified from Haemonchus contortus excretory secretory products shows protective antigen potential for lambs. Veterinary Research, 40, 41.
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.
Gauci, S., Helbig, A. O., Slijper, M., Krijgsveld, J., Heck, A. J. R., & Mohammed, S. (2009). Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach. Analytical Chemistry, (81), 4493-4501.
Munoz-Peralta, J., & Heck, A. J. R. (2009). Snapshots of kinase activities. Nature Biotechnology, (27), 912-913.
Gouw, J. W., Pinkse, M. W. H., Vos, H. R., Moshkin, Y. M., Verrijzer, C. P., Heck, A. J. R., & Krijgsveld, J. (2009). In vivo stable isotope labeling of fruit flies reveals post-transcriptional regulation in the maternal-to-zygotic transition. Molecular & Cellular Proteomics, 8(7), 1566-1578.
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
Boekhorst, J., van Breukelen, B., Heck, A. J. R., & Snel, B. (2008). Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes. Genome Biology, 9, R144.1-R144.9.
Uetrecht, C., Versluis, C., Watts, N. R., Roos, W. H., Wuite, G. J. L., Wingfield, P. T., Steven, A. C., & Heck, A. J. R. (2008). High Resolution Mass Spectrometry of Viral Assemblies: Molecular Compositions and Stability of Dimorphic Hepatitis B Virus Capsids. Proceedings of the National Academy of Sciences of the United States of America, 105(27), 9216-9229.
Gauci, S., van Breukelen, B., Lemeer, S. M., Krijgsveld, J., & Heck, A. J. R. (2008). A versatile peptide pI calculator for phosphorylated and N-terminal acetylated peptides experimentally tested using peptide isoelectric focusing. Proteomics, 8(23-24), 4898-4906.
Moonen, M. J. H., Synowsky, S. A., van den Berg, W. A. M., Westphal, A. H., Heck, A. J. R., van den Heuvel, R. H. H., Fraaije, M. W., & van Berkel, W. J. H. (2008). Hydroquinone Dioxygenase from Pseudomonas fluorescens ACB: A Novel Member of the Family of Non-Heme Iron(II)-Dependent Dioxygenases. Journal of Bacteriology, 190(15), 5199-5209.
Heck, A. J. R. (2008). Native mass spectrometry: a bridge between interactomics and structural biology. Nature Methods, 5(11), 927-933.
Lemeer, S. M., Jopling, J. C., Gouw, J. W., Mohammed, S., Heck, A. J. R., & Slijper, M. (2008). Comparative phosphoproteomics of zebrafish Fyn/Yes morpholino knockdown embryos. Molecular & Cellular Proteomics, 7, 2176-2187.
Dormeyer, W., van Hoof, D., Mummery, C. L., Krijgsveld, J., & Heck, A. J. R. (2008). A practical guide for the identification of membrane and plasma membrane proteins in human embryonic stem cells and human embryonal carcinoma cells. Proteomics, 8, 4036-4053. http://www.ncbi.nlm.nih.gov/sites/entrez/18763709
Whetton, A. D., Williamson, A. J. K., Krijgsveld, J., Lee, B. H., Lemischka, I., Oh, S., Pera, M., Mummery, C. L., & Heck, A. J. R. (2008). The time is right; Proteome Biology of Stem Cells. Cell Stem Cell, 2(3), 215-217.
Jin, X., Mazon, H. F. M., van den Heuvel, R. H. H., Heck, A. J. R., Janssen, D. B., & Fraaije, M. W. (2008). Covalent flavinylation of vanillyl-alcohol oxidase is an autocatalytic process. The FEBS journal, 275, 5191-5200.
Ms. Taouatas, N., Drugan, M. M., Mohammed, S., & Heck, A. J. R. (2008). Straightforward ladder sequencing of peptides using a Lys-N metalloendopeptidase. Nature Methods, 5(5), 405-407.
Geels, R. B. J., Calmat, S., Heck, A. J. R., van der Vies, S. M., & Heeren, R. M. A. (2008). Thermal activation of the co-chaperonins GroES and gp31 probed by mass spectrometry. Rapid Communications in Mass Spectrometry, 22, 3633-3641.
Boersema, P. J., Aye, T. T., van Veen, T. A. B., Heck, A. J. R., & Mohammed, S. (2008). Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates. Proteomics, 8, 4624-4632.
Synowsky, S. A., & Heck, A. J. R. (2008). The yeast Ski complex is a hetero-tetramer. Protein Science, 17, 119-125.
Hellemond, E. W., Mazon, H. F. M., Heck, A. J. R., van den Heuvel, R. H. H., Heuts, D. P. H. M., Janssen, D. B., & Fraaije, M. W. (2008). ADP competes with FAD binding in putrescine oxidase. Journal of Biological Chemistry, 283(42), 28259-28264.
Lorenzen, K., Olia, A. S., Uetrecht, C., Cingolani, G., & Heck, A. J. R. (2008). Determination of stoichiometry and conformational changes in the first step of the P22 tail assembly. Journal of Molecular Biology, 379, 385-396.
Dormeyer, W., van Hoof, D., Braam, S. R., Heck, A. J. R., Mummery, C. L., & Krijgsveld, J. (2008). Plasma membrane proteomics of human embryonic stem cells and human embryonal carcinoma cells. Journal of Proteome Research, 7, 2936-2951.
Mohammed, S., Kraiczek, K., Pinkse, M. W. H., Lemeer, S. M., Benschop, J. J., & Heck, A. J. R. (2008). Chip based enrichment and nanoLC MS/MS analysis of phosphopeptides from whole lysates. Journal of Proteome Research, 7, 1565-1571.
Pinkse, M. W. H., Mohammed, S., Gouw, J. W., van Breukelen, B., Vos, H. R., & Heck, A. J. R. (2008). Highly Robust, Automated, and Sensitive Online TiO2-Based Phosphoproteomics Applied To Study Endogenous Phosphorylation in Drosophila melanogaster. Journal of Proteome Research, 7, 687-697.
https://dspace.library.uu.nl/bitstream/handle/1874/26426/39_highly_Pinkse.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26426/39_highly_Pinkse.pdf?sequence=1
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.
Zhang, Z., Zheng, Y., Mazon, H. F. M., Milgrom, E., Kitagawa, N., Kish-Trier, E., Heck, A. J. R., Kane, P. M., & Wilkens, S. (2008). Structure of the Yeast Vacuolar ATPase. Journal of Biological Chemistry, 283(51), 35983-35995.
Mohammed, S., Lorenzen, K., Kerkhoven, R., van Breukelen, B., Vannini, A., Cramer, P., & Heck, A. J. R. (2008). ) Multiplexed proteomics mapping of yeast RNA polymerase II and III allows near-complete sequence coverage and reveals several novel phosphorylation sites. Analytical Chemistry, 80(10), 3584-3592.
Gouw, J. W., Tops, B. B. J., Mortensen, P., Heck, A. J. R., & Krijgsveld, J. (2008). ) Optimizing identification and quantitation of 15N-labeled proteins in comparative proteomics. Analytical Chemistry, 80(20), 7796-7803.
Boersema, P. J., Mohammed, S., & Heck, A. J. R. (2008). Hydrophilic Interaction liquid chromatography (HILIC) in proteomics. Analytical and Bioanalytical Chemistry, 391, 151-159.
Scholten, A., Aye, T. T., & Heck, A. J. R. (2008). A Multi-Angular Mass Spectrometric View at Cyclic Nucleotide Dependent Protein Kinases. Mass Spectrometry Reviews, 27, 331-353.
van Vlijmen, T., Vleugel, M. M., Evers, M., Mohammed, S., Wulf, P. S., Heck, A. J. R., Hoogenraad, C. C., & van der Sluijs, P. (2008). A unique residue in rab3c determines the interaction with novel binding protein Zwint-1. The FEBS journal, 582, 2838-2842.
Carol-Visser, N. F. C., & Heck, A. J. R. (2008). Surface plasmon resonance – mass spectrometry in proteomics. Expert Review Proteomics, 5(3), 425-433.
Heck, A. J. R., Mummery, C. L., Whetton, A., Oh, S., Lee, B., Pera, M., Lemischka, I., & Krijgsveld, J. (2008). Proteome biology of stem cells. Molecular & Cellular Proteomics, 7(1), 204-205.
https://dspace.library.uu.nl/bitstream/handle/1874/26500/41.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26500/41.pdf?sequence=1
Alverdi, V., Mazon, H. F. M., Versluis, C., Hemrika, W., Esposito, G., van den Heuvel, R. H. H., Scholten, A., & Heck, A. J. R. (2008). cGMP-binding prepares PKG for substrate binding by disclosing the C-terminal domain. Journal of Molecular Biology, 375, 1380-1393.
https://dspace.library.uu.nl/bitstream/handle/1874/32609/1.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/32609/1.pdf?sequence=1
Kitagawa, N., Mazon, H. F. M., & Heck, A. J. R. (2008). Stoichiometry of the peripheral stalk subunits E and G of Yeast V1-ATPase determined by mass spectrometry. Journal of Biological Chemistry, 283(6), 3329-3337.
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
van Hoof, D., Braam, S. R., Dormeyer, W., Heck, A. J. R., Krijgsveld, J., & Mummery, C. L. (2008). Feeder-free monolayer cultures of human embryonic stem cells express an epithelial plasma membrane protein profile. Stem Cells, 26, 2777-2781.
Ringrose, J. H., van Solinge, W. W., Mohammed, S., O'Flaherty, M. C., van Wijk, H. A., Heck, A. J. R., & Slijper, M. (2008). Highly efficient depletion strategy for the two most abundant erythrocyte soluble proteins improves proteome coverage dramatically. Journal of Proteome Research, 7, 3060-3063.
Stelzer, W., Poschner, B. C., Stalz, H., Heck, A. J. R., & Langosch, D. (2008). Sequence-specific conformational flexibility of SNARE transmembrane helices probed by hydrogen/deuterium exchange. Biophysical Journal, 95(3), 1326-1335.
Rojas, R., van Vlijmen, T., Mardones, G. A., Prabhu, Y., Rojas, A. L., Mohammed, S., Heck, A. J. R., Raposo, G., van der Sluijs, P., & Bonifacino, J. S. (2008). Regulation of retromer recruitment to endosomes by sequential action of Rab5 and Rab7. Journal of Cell Biology, 183(3), 513-526.
Mousson, F., Kolkman, A., Pijnappel, W. W. M., Timmers, H. T. M., & Heck, A. J. R. (2008). Quantitative proteomics reveals regulation of dynamic components within TATA-binding protein (TBP) transcription complexes. Molecular & Cellular Proteomics, 7.5, 845-852.
Laoukili, J., Alvarez, M., Meijer, L. A. T., Stahl, M., Mohammed, S., Kleij, L., Heck, A. J. R., & Medema, R. H. (2008). Activation of FoxM1 during G2 requires CyclinA/Cdk-dependent relief of auto-repression by the FoxM1 N-terminal domain. Molecular and Cellular Biology, 28(9), 3076-3087.
Lemeer, S. M., Pinkse, M. W. H., Mohammed, S., van Breukelen, B., den Hertog, J., Slijper, M., & Heck, A. J. R. (2008). Online automated in vivo zebrafish phosphoproteomics: From large-scale analysis down to a single embryo. Journal of Proteome Research, 7(4), 1555-1564.
Krijgsveld, J., Whetton, A. D., Lee, B., Lemischka, I., Oh, S., Mummery, C. L., & Heck, A. J. R. (2008). Proteome Biology of Stem Cells: A New Joint HUPO and ISSCR Initiative. Molecular & Cellular Proteomics, 7.1, 204-205.
Sneekes, E. J., Damen, J. M. A., Swart, R., & Heck, A. J. R. (2008). Isoform separation of a multi-acetylated protein using capillary polystyrene-divinylbenzene monolithic columns. Journal of Chromatography A, 1194, 199-204.
Uetrecht, C., Versluis, C., Watts, N. R., Wingfield, P. T., Steven, A. C., & Heck, A. J. R. (2008). Stability and Shape of Hepatitis B Virus Capsids in vacuo. Angewandte Chemie-International Edition, 47(33), 6247-6251. https://doi.org/10.1002/anie.200802410
Professional publications
Gavin, A-C., Aebersold, R., & Heck, A. J. R. (2008). ) Meeting Report on the 7th World Congress of the Human Proteome Organization (HUPO) in Amsterdam: Proteome Biology. Molecular & Cellular Proteomics, 7.11, 2288-2291.
2007
Scholarly publications
Geels, R. B. J., van der Vies, S. M., Heck, A. J. R., & Heeren, R. M. A. (2007). Comparative gas-phase activation of two similar non-covalent heptameric protein complexes: gp31 and GroES. International Journal of Mass Spectrometry, 265(2-3), 159-168. https://doi.org/10.1016/j.ijms.2007.02.008
Benschop, J. J., Mohammed, S., O'Flaherty, M., Heck, A. J. R., Slijper, M., & Menke, F. L. H. (2007). Quantitative phosphoproteomics of early elicitor signaling in Arabidopsis. Molecular and Cellular Proteomics, 6(7), 1198-1214. https://doi.org/10.1074/mcp.M600429-MCP200
Mihalca, R., van der Burgt, Y. E. M., Heck, A. J. R., & Heeren, R. M. A. (2007). Disulfide bond cleavages observed in SORI-CID of three nonapeptides complexed with divalent transition-metal cations. Journal of Mass Spectrometry, 42(4), 450-458. https://doi.org/10.1002/jms.1175
Kool, J., Reubsaet, J. L. E., Wesseldijk, F., Maravilha, R. T., Pinkse, M. W. H., D'Santos, C. S., van Hilten, J. J., Zijlstra, F. J., & Heck, A. J. R. (2007). Suction blister fluid as potential body fluid for biomarker proteins. Proteomics, 7, 3638-3650.
https://dspace.library.uu.nl/bitstream/handle/1874/26404/18_suction_kool.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26404/18_suction_kool.pdf?sequence=1
Scholten, A., Fuss, H., Heck, A. J. R., & Dostmann, W. R. G. (2007). The hinge region operates as a stability switch in cGMP-dependent protein kinase I. The FEBS journal, 274, 2274-2286.
https://dspace.library.uu.nl/bitstream/handle/1874/26419/26_hinge_scholten.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26419/26_hinge_scholten.pdf?sequence=1
Lorenzen, K., Versluis, C., van Duijn, E., van den Heuvel, R. H. H., & Heck, A. J. R. (2007). Optimizing macromolecular tandem mass spectrometry of large non covalent complexes using heavy collision gases. International Journal of Mass Spectrometry, 268, 198-206.
https://dspace.library.uu.nl/bitstream/handle/1874/26367/31_optimizing_lorenzen.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26367/31_optimizing_lorenzen.pdf?sequence=1
Stanley, W. A., Versluis, C., Schultz, C., Heck, A. J. R., & Wilmanns, M. (2007). Investigation of the ligand spectrum of human sterol carrier protein 2 using a direct mass spectrometry assay. Archives of Biochemistry and Biophysics, 461, 50-58.
https://dspace.library.uu.nl/bitstream/handle/1874/26401/12_investigation_versluis.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26401/12_investigation_versluis.pdf?sequence=1
Kamphuis, M. B., Monti, M. C., van den Heuvel, R. H. H., Santos-Sierra, S., Folkers, G. E., Lemonnier, M., Diaz-Orejas, R., Heck, A. J. R., & Boelens, R. (2007). Interactions between the toxin kid of the bacterial parD system and the antitoxins Kis and MazE. Proteins: Structure function and bioinformatics, 67, 219-231.
https://dspace.library.uu.nl/bitstream/handle/1874/26116/524.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26116/524.pdf?sequence=1
Lemeer, S. M., Jopling, J. C., Ruijtenbeek, R., Slijper, M., Heck, A. J. R., & den Hertog, J. (2007). Protein-tyrosine kinase activity profiling in knock down zebrafish embryos. PLoS One, 7, e581.
https://dspace.library.uu.nl/bitstream/handle/1874/26414/22_proteintyrosine_lemeer.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26414/22_proteintyrosine_lemeer.pdf?sequence=1
Mihalca, R., van der Burgt, Y. E. M., Heck, A. J. R., & Heeren, R. M. A. (2007). Disulfide bond cleavages observed in SORI-CIS of three nonapeptides complexed with divalent transition-metal cations. Journal of Mass Spectrometry, 42, 450-458.
https://dspace.library.uu.nl/bitstream/handle/1874/26382/11_disulfide_mihalca.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26382/11_disulfide_mihalca.pdf?sequence=1
Monti, M. C., Hernandez-Arriaga, A. M., Kamphuis, M. B., Lopez-Villarejo, J., Heck, A. J. R., Boelens, R., Diaz-Orejas, R., & van den Heuvel, R. H. H. (2007). Interactions of Kid-Kis toxin-antitoxin complexes with the parD operator-promotor region of plasmid R1 are piloted by the Kis antitoxin and tuned by the stoichiometry of Kid-Kis oligomers. Nucleic Acids Research, 35(5), 1737-1749.
https://dspace.library.uu.nl/bitstream/handle/1874/26117/523.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26117/523.pdf?sequence=1
Scholten, A., van Veen, A. A. B., Vos, M. A., & Heck, A. J. R. (2007). Diversity of cAMP-dependent protein kinase isoforms and their anchoring proteins in mouse ventricular tissue. Journal of Proteome Research, 6(5), 1705-1717.
https://dspace.library.uu.nl/bitstream/handle/1874/26186/25_diversity_scholten.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26186/25_diversity_scholten.pdf?sequence=1
Brunner, E., Ahrens, C. H., Mohanty, S., Baetschmann, H., Loevenich, S., Potthast, F., Deutsch, E. W., Panse, C., de Lichtenberg, U., Rinner, O., Lee, H., Pedrioli, P. G. A., Malmstrom, J., Koehler, K., Schrimpf, S., Krijgsveld, J., Kregenow, F., Heck, A. J. R., Hafen, E., ... Aebersold, R. (2007). A high quality catalog of the Drosophila melanogaster proteome. Nature Biotechnology, 25(5), 576-583.
https://dspace.library.uu.nl/bitstream/handle/1874/26364/24_highquality_brunner.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26364/24_highquality_brunner.pdf?sequence=1
Carol-Visser, N. F. C., Scholten, A., van den Heuvel, R. H. H., & Heck, A. J. R. (2007). Surface-Plasmon-Resonance-Bases Chemical Proteomics: Efficient Specific Extraction and Semiquantitative Identification of Cyclic Nucleotide-Binding Proteins from Cellular Lysates by Using a Combination of Surface Plasmon Resonance, Sequential Elution and Liquid Chromatography-Tandem Mass Spectrometry. ChemBioChem, 8, 298-305.
https://dspace.library.uu.nl/bitstream/handle/1874/26378/2_surface_Natasja.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26378/2_surface_Natasja.pdf?sequence=1
Mazon, H. F. M., Gabor, K., Leys, D., Heck, A. J. R., & van der Oost, J. (2007). Transcriptional activation by CprK1 is regulated by protein structural changes induced by effector binding and redox state. Journal of Biological Chemistry, 282(15), 11281-11290.
https://dspace.library.uu.nl/bitstream/handle/1874/26365/29_transcriptional_mazon.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26365/29_transcriptional_mazon.pdf?sequence=1
de Groot, M. J. L., Daran-Lapujade, P., van Breukelen, B., Knijnenburg, T. A., Hulster, E. A. F., Reinders, M. J. T., Pronk, J. T., Heck, A. J. R., & Slijper, M. (2007). Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes. Microbiology, 153, 3864-3878.
https://dspace.library.uu.nl/bitstream/handle/1874/26402/14_quantitative_degroot.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26402/14_quantitative_degroot.pdf?sequence=1
Taylor, C. F., Paton, N. W., Lilley, K. S., Binz, P-A., Julian, R. K., Jones, A. R., Zhu, W., Apweiler, R., Aebersold, R., Deutsch, E. W., Dunn, M. J., Heck, A. J. R., Leitner, A., Macht, M., Mann, M., Martens, L., Neubert, T. A., Patterson, S. D., Ping, P., ... Hermjakob, H. (2007). The minimum information about a proteomics experiment (MIAPE). Nature Biotechnology, 25(8), 887-893.
https://dspace.library.uu.nl/bitstream/handle/1874/26362/21_minimum_Lilley.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26362/21_minimum_Lilley.pdf?sequence=1
Poliakov, A., van Duijn, E., Lander, G., Fu, C., Johnson, J. E., Prevelige, P. E., & Heck, A. J. R. (2007). Macromolecular mass spectrometry and electron microscopy as complementary tools for investigation of the hereogeneity of bacteriophage portal assemblies. Journal of Structural Biology, 157, 371-383.
https://dspace.library.uu.nl/bitstream/handle/1874/26330/3_Macromolecular_Poliakov.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26330/3_Macromolecular_Poliakov.pdf?sequence=1
van Hoof, D., Pinkse, M. W. H., Ward-van Oostwaard, D., Mummery, C. L., Heck, A. J. R., & Krijgsveld, J. (2007). An experimental correction for arginine-to-proline conversion artifacts in SILAC-based quantitative proteomics. Nature Methods, 4(9), 677-678.
https://dspace.library.uu.nl/bitstream/handle/1874/26334/19_experimental_hoof.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26334/19_experimental_hoof.pdf?sequence=1
Boersema, P. J., Divecha, N., Heck, A. J. R., & Mohammed, S. (2007). Evaluation and Optimization of ZIC-HILIC-RP as an alternative MudPIT Strategy. Journal of Proteome Research, 6, 937-946.
https://dspace.library.uu.nl/bitstream/handle/1874/26377/1_Evaluation_boersema.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26377/1_Evaluation_boersema.pdf?sequence=1
Benschop, J. J., Mohammed, S., O'Flaherty, M. C., Heck, A. J. R., Slijper, M., & Menke, F. L. H. (2007). Quantitative phospho-proteomics of early elicitor signalling in Arabidopsis. Molecular & Cellular Proteomics, Feb 21 (E).
https://dspace.library.uu.nl/bitstream/handle/1874/26427/28_quantitative_benschop.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26427/28_quantitative_benschop.pdf?sequence=1
Lorenzen, K., Vannini, A., Cramer, P., & Heck, A. J. R. (2007). Structural biology of RNA polymerase III: mass spectrometry elucidates subcomplex architecture. Structure, 15, 1237-1245.
https://dspace.library.uu.nl/bitstream/handle/1874/26332/15_structural_lorenzen.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26332/15_structural_lorenzen.pdf?sequence=1
Orchard, S., Heck, A. J. R., Uhlen, M., & Ping, P. (2007). Publication committee Meeting HUPO 5th Annual World congress. Proteomics, 7, 1009-1011.
https://dspace.library.uu.nl/bitstream/handle/1874/26421/27_HUPO_heck.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26421/27_HUPO_heck.pdf?sequence=1
van Duijn, E., Heck, A. J. R., & van der Vies, S. M. (2007). Inter-ring communication allows the GroEL chaperonin complex to distinguish between different substrates. Protein Science, 16, 956-965.
https://dspace.library.uu.nl/bitstream/handle/1874/26416/23_interring_duijn.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26416/23_interring_duijn.pdf?sequence=1
Daran-Lapujade, P., Rossell, S., van Gulik, W. M., van Luttik, M. A. H., de Groot, M. J. L., Slijper, M., Heck, A. J. R., Daran, J-M., de Winde, J. H., Westerhoff, H. V., Pronk, J. T., & Bakker, B. M. (2007). The fluxes through glycolytic enzymes in S. cerevisiae are predominantly regulated at posttranscriptional levels. Proceedings of the National Academy of Sciences of the United States of America, 104(40), 15753-15758.
https://dspace.library.uu.nl/bitstream/handle/1874/26403/17_fluxes_daran.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26403/17_fluxes_daran.pdf?sequence=1
Dormeyer, W., Mohammed, S., van Breukelen, B., Krijgsveld, J., & Heck, A. J. R. (2007). Targeted Analysis of Protein Termini. Journal of Proteome Research.
https://dspace.library.uu.nl/bitstream/handle/1874/26333/16_targeted_dormeyer.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26333/16_targeted_dormeyer.pdf?sequence=1
Lemeer, S. M., Ruijtenbeek, R., Pinkse, M. W. H., Jopling, J. C., Heck, A. J. R., den Hertog, J., & Slijper, M. (2007). Endogenous phosphotyrosine signaling in zebrafish embryos. Molecular & Cellular Proteomics.
https://dspace.library.uu.nl/bitstream/handle/1874/26410/20_endogenous_lemeer.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/26410/20_endogenous_lemeer.pdf?sequence=1
2006
Scholarly publications
Jones, D. R., Bultsma, Y., Keune, W. J., Halstead, J. R., Elouarrat, D., Mohammed, S., Heck, A. J., D'Santos, CS. S., & Divecha, N. (2006). Nuclear PtdIns5P as a Transducer of Stress Signaling: An In Vivo Role for PIP4Kbeta. Molecular Cell, 23(5), 685-695. https://doi.org/10.1016/j.molcel.2006.07.014
Halstead, J. R., van Rheenen, J., Snel, MH. H. J., Meeuws, S., Mohammed, S., D'Santos, C. S., Heck, AJ. J., Jalink, K., & Divecha, N. (2006). A Role for PtdIns(4,5)P2 and PIP5Kα in Regulating Stress-Induced Apoptosis. Current Biology, 16(18), 1850-1856. https://doi.org/10.1016/j.cub.2006.07.066
Eman, M. R., Regan-Klapisz, E., Pinkse, M. W. H., Koop, I. M., Haverkamp, J., Heck, A. J. R., Verkleij, A. J., & Post, J. A. (2006). Protein expression dynamics during replicative senescence of endothelial cells studied by 2-D differences in-gel electrophoresis. Electrophoresis, 27(8), 1669-1682. https://doi.org/10.1002/elps.200500746
Jones, D. R., Bultsma, Y., Keune, W-J., Halstead, J. R., Elouarrat, D., Mohammed, S., Heck, A. J. R., De Santos, C. S., & Divecha, N. (2006). Nuclear Ptdlns5P as a transducer of stress signaling: an in vivo role for PIP4Kbeta. Molecular Cell, 23, 685-695.
Siebert, H-C., Born, K., André, S., Frank, M., Kaltner, H., von der Lieth, C-W., Heck, A. J. R., Jiménez-Barbero, J., Kopitz, J., & Gabius, H-J. (2006). Carbohydrate Chain of Ganglioside GM1 as a Ligand: Identification of the Binding Strategies of Three 15 mer Peptides and Their Divergence from the Binding Modes of Growth-Regulatory Galectin-1 and Cholera Toxin. Chemistry-A European Journal, 12, 388-402.
Halstead, J. R., Van Rheenen, J., Snel, M. H. J., Meeuws, S., Mohammed, S., De Santos, C. S., Heck, A. J. R., Jalink, K., & Divecha, N. (2006). A role for Ptdlns(4,5)P2 and PIP5Kα in regulating stress-induced apoptosis. Current Biology, 16, 1850-1856.
Mihalca, R., van der Burgt, Y. E. M., McDonnell, L. A., Duursma, M., Cerjak, I., Heck, A. J. R., & Heeren, R. M. A. (2006). Combined infrared multiphoton dissociation and electron-capture dissociation using co-linear and overlapping beams in Fourier transform ion cyclotron resonance mass spectrometry. Rapid Communications in Mass Spectrometry, 20, 1838-1844.
https://dspace.library.uu.nl/bitstream/handle/1874/19757/12_combined.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/19757/12_combined.pdf?sequence=1
Synowsky, S. A., van den Heuvel, R. H. H., Mohammed, S., Pijnappel, P. W., & Heck, A. J. R. (2006). Probing genuine strong interactions and post-translational modifications in the heterogeneous yeast exosome protein complex. Molecular & Cellular Proteomics, 5, 1581-1592.
Eman, M. R., Regan-Klapisz, E. E., Pinkse, M. W. H., Koop, I. M., Haverkamp, J., Heck, A. J. R., Verkleij, A. J., & Post, J. A. (2006). Protein expression dynamics during replicative senescence of endothelial cells studied by 2-D difference in-gel electrophoresis. Electrophoresis, 27, 1669-1682.
Krijgsveld, J., Gauci, S., Dormeyer, W., & Heck, A. J. R. (2006). In-Gel isoelectric focusing of peptides as a tool for improved protein identification. Journal of Proteome Research, 5, 1721-1730.
https://dspace.library.uu.nl/bitstream/handle/1874/19987/7_inGel.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/19987/7_inGel.pdf?sequence=1
van Duijn, E., & Heck, A. J. R. (2006). Mass spectrometric analysis of intact macromolecular chaperone complexes. Drug Discovery Today. Technologies, 3, 21-27.
Poot, A. J., Ruijter, E., Nuijens, T., Dirksen, E. H. C., Heck, A. J. R., Slijper, M., Rijkers, D. T. S., & Liskamp, R. M. J. (2006). Selective enrichment of Ser-/Thr-phosphorylated peptides in the presence of Ser-/Thr-glycosylated peptides. Proteomics, 6, 6394-6399.
Boumann, H. A., Gubbens, J., Koorengevel, M. C., Oh, C-S., Martin, C. E., Heck, A. J. R., Patton-Vogt, J., Henry, S. A., de Kruijff, B., & de Kroon, A. I. P. M. (2006). Depletion of phosphatidylcholine in yeast induces shortening and increased saturation of the lipid acyl chains: evidence for regulation of intrinsic membrane curvature in a eukaryote. Molecular Biology of the Cell, 17, 1006-1017.
https://dspace.library.uu.nl/bitstream/handle/1874/19761/Boumann-Depletion%2520of%2520phosphatidylcholine.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/19761/Boumann-Depletion%2520of%2520phosphatidylcholine.pdf?sequence=1
Wijte, D., de Jong, A. L., Mol, M. A. E., Van Baar, B. L. M., & Heck, A. J. R. (2006). ProteomeIQ Blue, a potent post-stain for the visualization and subsequent Mass Spectrometry based identification of fluorescent stained proteins on 2D-gels. Journal of Proteome Research, 5, 2033-2038.
Kolkman, A., Daran-Lapujade, P., Fullaondo, A., Olsthoorn, M. M. A., Pronk, J. T., Slijper, M., & Heck, A. J. R. (2006). Proteome analysis of yeast response to various nutrient limitations. Molecular Systems Biology [E].
van Hoof, D., Krijgsveld, J., Hosman - Mummery, C. L., & Heck, A. J. R. (2006). Embryonic Stem Cell Proteomics; seeking human and mouse embryonic stem cell-specific proteins. BioForum Europe, 10, 42-43.
van den Heuvel, R. H. H., van Duijn, E., Mazon, H. F. M., Synowsky, S. A., Lorenzen, K., Versluis, C., Brouns, S. J. J., Langridge, D., Van der Oost, J., Hoyes, J., & Heck, A. J. R. (2006). Improving the performance of a Quadrupole Time-of-Flight instrument for Macromolecular Mass Spectrometry. Analytical Chemistry, 78, 7473-7483.
https://dspace.library.uu.nl/bitstream/handle/1874/19285/16_improving.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/19285/16_improving.pdf?sequence=1
Yatsuda, A. P., Bakker, N., Krijgsveld, J., Knox, D. P., Heck, A. J. R., & de Vries, E. (2006). Identification of secreted cysteine proteases from the parasitic nematode Haemonchus contortus detected by biotinylated inhibitors. Infection and Immunity, 74, 1989-1993.
https://dspace.library.uu.nl/bitstream/handle/1874/19780/yatsuda%2520et%2520al%2520%282006%29.pdf?sequence=2
https://dspace.library.uu.nl/bitstream/handle/1874/19780/yatsuda%2520et%2520al%2520%282006%29.pdf?sequence=2
van Breukelen, B., Barendregt, A., Heck, A. J. R., & van den Heuvel, R. H. H. (2006). Resolving stoichiometries and oligomeric states of glutamate synthase protein complexes with curve fitting and simulation of electrospray mass spectra. Rapid Communications in Mass Spectrometry, 20, 2490-2496.
Garcia-Alles, L. F., Versluis, C., Maveyraud, L., Vallina, A. T., Sansano, S., Bello, N. F., Gober, H-J., Guillet, V., De la Salle, H., Puzo, G., Mori, L., Heck, A. J. R., De Libero, G., & Mourey, L. (2006). Endogenous phosphatidylcholine and an long spacer ligand stabilize the lipid-binding groove of CD1b. EMBO Journal, 25, 3684-3692.
https://dspace.library.uu.nl/bitstream/handle/1874/19781/22_endgenous.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/19781/22_endgenous.pdf?sequence=1
van Duijn, E., Simmons, D. A., van den Heuvel, R. H. H., Bakkes, P. J., van Heerikhuizen, H., Heeren, R. M. A., Robinson, C. V., van der Vies, S. M., & Heck, A. J. R. (2006). Tandem Mass Spectrometry of intact GroEL-substrate complexes reveals substrate-specific conformational changes in the trans Ring. Journal of the American Chemical Society, 128, 4694-4702.
Meiring, H. D., Soethout, E. C., Poelen, M. C. M., Mooibroek, D., Hoogerbrugge, R., Timmermans, H., Boog, C. J., Heck, A. J. R., de Jong, A. P. J. M., & van Els, C. A. C. M. (2006). Stable Isotope Tagging of Epitopes. Molecular & Cellular Proteomics, 5, 902-913.
Dirksen, E. H. C., Pinkse, M. W. H., Rijkers, D. T. S., Cloos, J., Liskamp, R. M. J., Slijper, M., & Heck, A. J. R. (2006). Investigating the dynamic nature of the interactions between nuclear proteins and histones upon DNA damage using an immobilized peptide chemical proteomics approach. Journal of Proteome Research, 5, 2380-2388.
Gavin, A-C., & Heck, A. J. R. (2006). Expanding the frontiers in proteomics. Drug Discovery Today. Technologies, 3, 315-316.
Scholten, A., Poh, M. K., van Veen, A. A. B., van Breukelen, B., Vos, M. A., & Heck, A. J. R. (2006). Analysis of the cGMP/cAMP interactome using a chemical proteomics approach in mammalian heart tissue validates sphingosine kinase type 1-interacting protein as a genuine and highly abundant AKAP. Journal of Proteome Research, 5(6), 1435-1447.
van Hoof, D., Passier, R., Ward-van Oostwaard, D., Pinkse, M. W. H., Heck, A. J. R., Hosman - Mummery, C. L., & Krijgsveld, J. (2006). A quest for human and mouse embryonic stem cell-specific proteins. Molecular & Cellular Proteomics, 5, 1261-1273.
Geels, R. B. J., van der Vies, S. M., Heck, A. J. R., & Heeren, R. M. A. (2006). Electron capture dissociation as structural probe for noncovalent gas-phase protein assemblies. Analytical Chemistry, 20, 7191-7196.
https://dspace.library.uu.nl/bitstream/handle/1874/19758/19_electron.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/19758/19_electron.pdf?sequence=1
Scholten, A., Carol-Visser, N. F. C., van den Heuvel, R. H. H., & Heck, A. J. R. (2006). Analysis of protein-protein interaction surfaces usinga combination of efficient lysine acetylation and nanoLC-MALDI-MS/MS applied to the E9:Im9 bacteriotoxin-immunity protein complex. Journal of the American Society for Mass Spectrometry, 17, 983-994.
van Hoof, D., Mummery, C. L., Heck, A. J. R., & Krijgsveld, J. (2006). Embryonic stem cell proteomics. Expert Review of Proteomics, 3(4), 427-437.
https://dspace.library.uu.nl/bitstream/handle/1874/19286/ExpRevProteomics%282006%29427.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/19286/ExpRevProteomics%282006%29427.pdf?sequence=1
Pinkse, M. W. H., & Heck, A. J. R. (2006). Essential enrichment strategies in phosphoproteomics. Drug Discovery Today. Technologies, 3, 331-337.
Kleinnijenhuis, A. J., Mihalca, R., Heeren, R. M. A., & Heck, A. J. R. (2006). Atypical behavior in the electron capture induced dissociation of biologically relevant transition metal ion complexes of the peptide hormone oxytocin. International Journal of Mass Spectrometry, 253, 217-224.
Dirksen, E. H. C., Cloos, J., Braakhuis, B. J. M., Brakenhoff, R. H., Heck, A. J. R., & Slijper, M. (2006). Human Lymphoblastoid proteome analysis reveals a role for the inhibitor of acetyltransferases complex in DNA double-strand break response. Cancer Research, 3, 1473-1480.
2005
Scholarly publications
van Balkom, B. W. M., van Gestel, R. A., Brouwers, J. F. H. M., Krijgsveld, J., Tielens, A. G. M., Heck, A. J. R., & van Hellemond, J. J. (2005). Mass spectrometric analysis of the Schistosoma mansoni tegumental sub-proteome. Journal of Proteome Research, 4(3), 958-966. https://doi.org/10.1021/pr050036w
Kleinnijenhuis, A. J., Heck, A. J. R., Duursma, M. C., & Heeren, R. M. A. (2005). Does Double Electron Capture Lead to the Formation of Biradicals? An ECD-SORI-CID Study on Lacticin 481. Journal of the American Society for Mass Spectrometry, 2261-2270.
van der Veken, P., Dirksen, E. H. C., Ruijter, E., Elgersma, R. C., Heck, A. J. R., Rijkers, D. T. S., Slijper, M., & Liskamp, R. M. J. (2005). Development of a Novel Chemical Probe for the Selective Enrichment of Phosphorylated Serine- and Threonine-Containing Peptides. ChemBioChem, 6, 2271-2280.
Kranenburg, O., Gent, Y. Y. J., Romijn, E. P., Voest, E. E., Heck, A. J. R., & Gebbink, M. F. B. G. (2005). Amyloid-beta-stimulated plasminogen activation by tissue-type plasminogen activator results in processing of neuroendocrine factors. Neuroscience, 131, 877-886.
Kolkman, A., Olsthoorn, M. M. A., Heeremans, C. E. M., Heck, A. J. R., & Slijper, M. (2005). Comparative Proteome Analysis of Saccharomyces cerevisiae grown in chemostat cultures limited for glucose or ethanol. Molecular & Cellular Proteomics, 4, 1-11.
https://dspace.library.uu.nl/bitstream/handle/1874/11660/kolkman_05_comparative_proteome.pdf?sequence=2
https://dspace.library.uu.nl/bitstream/handle/1874/11660/kolkman_05_comparative_proteome.pdf?sequence=2
Catalina Caballero, M. I., Fischer, M. J. E., Dekker, F. J., Liskamp, R. M. J., & Heck, A. J. R. (2005). Binding of a diphosphorylated-ITAM peptide to spleen tyrosine kinase (Syk) induces distal conformational changes: a hydrogen exchange mass spectrometry study. Journal of the American Society for Mass Spectrometry, 16, 1039-1051.
Kruithof, C. A., Casado Lacabra, M. A., Guillena, G., Egmond, M. R., van der Kerk-van Hoof, A. C., Heck, A. J. R., Klein Gebbink, R. J. M., & van Koten, G. (2005). Lipase Active-Site-Directed Anchoring of Organometallics:Metallopincer/Protein Hybrids. Chemistry-A European Journal, 11, 6869-6877.
Romijn, E. P., Christis, C., Wieffer, M., Gouw, J. W., Fullaondo, A., van der Sluijs, P., Braakman, L. J., & Heck, A. J. R. (2005). Expression Clustering Reveals Detailed Co-expression Patterns of Functionally Related Proteins during B Cell Differentiation. Molecular & Cellular Proteomics, 4, 1297-1310.
van der Knaap, J. A., Prasphanth Kumar, B. R., Moshkin, Y. M., Langenberg, K., Krijgsveld, J., Heck, A. J. R., Karch, F., & Verrijzer, C. P. (2005). GMP Synthetase Stimulates Histone H2B Deubiquitylation by the Epigenetic Silencer USP7. Molecular Cell, 17, 695-707.
Römpp, A., Mihalca, R., Taban, I., Heck, A. J. R., Kleinnijenhuis, A. J., McDonnell, L. A., Mize, T. H., & Heeren, R. M. A. (2005). Examples of FTICR-MS developments: from ion physics to remote acces biochemical mass spectrometry. European Journal of Mass Spectrometry, 11, 443-456.
van den Bremer, E. T. J., Keeble, A. H., Kleanthous, C., & Heck, A. J. R. (2005). Metal induced selectivity in phosphate ion binding in E9 Dnase. Chemical Communications, 9, 1137-1139.
van den Heuvel, R. H. H., Gato, S., Versluis, C., Gerbaux, P., Kleanthous, C., & Heck, A. J. R. (2005). Real-time monitoring of enzymatic DNA hydrolysis by electrospray ionization mass spectrometry. Nucleic Acids Research, 33(10).
de Mol, N. J., Catalina Caballero, M. I., Dekker, F. J., Fischer, M. J. E., Heck, A. J. R., & Liskamp, R. M. J. (2005). Protein flexibility and ligand rigidity: a thermodynamic and kinetic study of ITAM based ligand binding to Syk tandem SH2. ChemBioChem, 6, 2261-2270.
https://dspace.library.uu.nl/bitstream/handle/1874/14968/mol_05_proteinflexibilityandligandrigidity.pdf?sequence=2
https://dspace.library.uu.nl/bitstream/handle/1874/14968/mol_05_proteinflexibilityandligandrigidity.pdf?sequence=2
van Duijn, E., Bakkes, P. J., Heeren, R. M. A., van den Heuvel, R. H. H., van Heerikhuizen, H., van der Vies, S. M., & Heck, A. J. R. (2005). Monitoring macromolecular complexes involved in the chaperonin-assisted protein folding cycle by mass spectrometry. Nature Methods, 2(5), 371-376.
Andre, S., Kaltner, H., Lensch, M., Russwurm, R., Siebert, H-C., Fallsehr, C., Tajkhorshid, E., Heck, A. J. R., Von Knebel Doeberitz, M., Gabius, H-J., & Kopitz, J. (2005). Determination of structural and functional overlap/divergence of five proto-type galectins by analysis of the growth-regulatory interaction with ganglioside GM in silico and in vitro on human neuroblastoma cells. International Journal of Cancer, 114, 46-57.
Brandon, E. F. A., van Ooijen, R. D., Sparidans, R. W., Lazaro, L. L., Heck, A. J. R., Beijnen, J. H., & Schellens, J. H. M. (2005). Structure elucidation of aplidine metabolites formed in vitro by human liver microsomes using triple quadrupole mass spectrometry. Journal of Mass Spectrometry, 40(6), 821-831.
Kolkman, A., Slijper, M., & Heck, A. J. R. (2005). Development and application of proteomics technologies in Saccharomyces cerevisiae. Trends in Biotechnology, 23(12), 598-604.
https://dspace.library.uu.nl/bitstream/handle/1874/11659/kolkman_05_development_and_application.pdf?sequence=2
https://dspace.library.uu.nl/bitstream/handle/1874/11659/kolkman_05_development_and_application.pdf?sequence=2
Catalina Caballero, M. I., van den Heuvel, R. H. H., van Duijn, E., & Heck, A. J. R. (2005). Decharging of Globular Proteins and Protein Complexes in Electrospray. Chemistry-A European Journal, 11, 960-968.
Kolkman, A., Dirksen, E. H. C., Slijper, M., & Heck, A. J. R. (2005). Double Standards in Quantitative Proteomics. Molecular & Cellular Proteomics, 4, 255-266.
https://dspace.library.uu.nl/bitstream/handle/1874/11661/kolkman_05_double_standards_in_quantitative_proteomics.pdf?sequence=2
https://dspace.library.uu.nl/bitstream/handle/1874/11661/kolkman_05_double_standards_in_quantitative_proteomics.pdf?sequence=2
Groen, A. J., Lemeer, S. M., van der Wijk, T., Overvoorde, J., Heck, A. J. R., Ostman, A., Barford, D., Slijper, M., & den Hertog, J. (2005). Differential Oxidation of Protein-tyrosine Phosphatases. Journal of Biological Chemistry, 280(11), 10298-10304.
Neeft, M. A., Wieffer, M., de Jong, A. S., Negroiu, G., Metz, C. H. G., van Loon, A., Griffith, J. M., Krijgsveld, J., Wulffraat, N. M., Koch, H., Heck, A. J. R., Brose, N., Kleijmeer, M. J., & van der Sluijs, P. (2005). Munc13-4 is an effector of rab27a and controls secretion of lysosomes in hematopoietic cells. Molecular Biology of the Cell, 16(2), 731-741.
van den Heuvel, R. H. H., Tahallah, N., Kamerbeek, N. M., Fraaije, M. W., van Berkel, W. J. H., Janssen, D. B., & Heck, A. J. R. (2005). Coenzyme Binding during Catalysis Is Beneficial for the Stability of 4-Hydroxyacetophenone Monooxygenase. Journal of Biological Chemistry, 280(37), 32115-32121.
Rodriguez, P., Bonte, E., Krijgsveld, J., Kolodziej, K. E., Guyot, B., Heck, A. J. R., Vyas, P., de Boer, E., Grosveld, F., & Strouboulis, J. (2005). GATA-1 forms distinct activating and repressive complexes in erythroid cells. EMBO Journal, 24(13), 2354-2366.
Professional publications
van den Bremer, E. T. J., & Heck, A. J. R. (2005). Mass Spectrometry: Protein Conformational Analysis and Molecular Recognition. In W. Jiskoot, & D.J.A. Crommelin (Eds.), Methods for Structural Analysis of Protein Pharmaceuticals AAPS Press.
Romijn, E. P., & Heck, A. J. R. (2005). Mass Spectrometry: Proteomics. In W. Jiskoot, & D.J.A. Crommelin (Eds.), Methods for Structural Analysis of Protein Pharmaceuticals AAPS Press.
2004
Scholarly publications
Bosch, B. J., Martina, B. E. E., Van Der Zee, R., Lepault, J., Haijema, B. J., Versluis, C., Heck, A. J. R., De Groot, R., Osterhaus, A. D. M. E., & Rottier, P. J. M. (2004). Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides. Proceedings of the National Academy of Sciences of the United States of America, 101(22), 8455-8460. https://doi.org/10.1073/pnas.0400576101
van den Bremer, E. T. J., Keeble, A. H., Visser, A. J. W. G., Hoek, A., Kleanthous, C., Heck, A. J. R., & Jiskoot, W. (2004). Ligand-induced changes in the conformational dynamics of a bacterial cytotoxic endonuclease. Biochemistry, 43, 4347-4355.
Catalina Caballero, M. I., de Mol, N. J., Fischer, M. J. E., & Heck, A. J. R. (2004). Probing factors affecting the gas phase stabilities of noncovalent complexes formed by peptides bound to the Grb2 SH2 domain protein. Physical Chemistry Chemical Physics, 6, 2572-2579.
van den Heuvel, R. H. H., Westphal, A. H., Heck, A. J. R., Walsh, M. A., Rovida, S., van Berkel, W. J. H., & Mattevi, A. (2004). Structural Studies on Flavin Reductase PheA2 Reveal Binding of NAD in an Unusual Folded Conformation and Support Novel Mechanism of Action. Journal of Biological Chemistry, 279, 12860-12867.
Boumann, H. A., de Kruijff, B., Heck, A. J. R., & de Kroon, A. I. P. M. (2004). The selective utilization of substrates in vivo by the phosphatidylethanolamine and phosphatidylcholine biosynthetic enzymes Ept1p and Cpt1p in yeast. FEBS Letters, 569, 173-177.
https://dspace.library.uu.nl/bitstream/handle/1874/14460/Boumann-The%2520selective%2520utilization.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/14460/Boumann-The%2520selective%2520utilization.pdf?sequence=1
Krijgsveld, J., & Heck, A. J. R. (2004). Quantitative proteomics by metabolic labeling with stable isotopes. DDT: TARGETS Elsevier, 3, 11-15.
de Mol, N. J., Catalina Caballero, M. I., Fischer, M. J. E., Broutin, I., Maier, C. S., & Heck, A. J. R. (2004). Changes in structural dynamics of the Grb2 adaptor protein upon binding of phosphotyrosine ligand to its SH2 domain. Biochimica et Biophysica Acta-Proteins Proteomics, 1700(1), 53-64.
https://dspace.library.uu.nl/bitstream/handle/1874/14965/mol_04_changesinstructuraldynamics.pdf?sequence=2
https://dspace.library.uu.nl/bitstream/handle/1874/14965/mol_04_changesinstructuraldynamics.pdf?sequence=2
Heck, A. J. R., & Jorgensen, T. J. D. (2004). Vancomycin in vacuo. International Journal of Mass Spectrometry, 236, 11-23.
Beumer, J. H., Rosing, H., Hillebrand, MJ., Nan-Offeringa, LG., Foley, K., Yule, SM., Heck, A. J. R., Schellens, J. H. M., & Beijnen, J. H. (2004). Quantitative determination of the novel anticancer drug E7070 (indisulam) and its metabolite (1,4-benzenedisulphonamide) in human plasma, urine and faeces by high-performance liquid chromatography coupled with electrospray ionization tandem mass spectrometry. Rapid Communications in Mass Spectrometry, 18(23), 2839-48.
Boumann, H. A., Chin, P. T. K., Heck, A. J. R., de Kruijff, B., & de Kroon, A. I. P. M. (2004). The yeast phospholipid N-methyltransferases catalyzing the synthesis of phosphatidylcholine preferentially convert di-C16:1 substrates both in vivo and in vitro. Journal of Biological Chemistry, 279, 40314-40319.
https://dspace.library.uu.nl/bitstream/handle/1874/14609/Boumann-The%2520yeast%2520phospholipid.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/14609/Boumann-The%2520yeast%2520phospholipid.pdf?sequence=1
van den Bremer, E. T. J., Keeble, A. H., Jiskoot, W., Spelbrink, R. E. J., Maier, C. S., Hoek, A., Visser, A. J. W. G., James, R., Moore, G. R., Kleanthous, C., & Heck, A. J. R. (2004). Distinct conformational stability and functional activity of four highly homologous endonuclease colicins. Protein Science, 13, 1391-1401.
Mihalca, R., Kleinnijenhuis, A. J., McDonnell, L. A., Heck, A. J. R., & Heeren, R. M. A. (2004). Electron Capture Dissociation at Low Temperatures Reveals Selective Dissociations. Journal of the American Society for Mass Spectrometry, 15, 1869-1873.
Heck, A. J. R., & Krijgsveld, J. (2004). Mass spectrometry-based quantitative proteomics. Expert Review Proteomics, 1(3), 317-326.
Mohrmann, L., Langenberg, K., Krijgsveld, J., Kal, A. J., Heck, A. J. R., & Verrijzer, C. P. (2004). Differential Targeting of Two Distinct SWI/SNF-Related Drosophila Chromatin-Remodeling Complexes. Molecular and Cellular Biology, 3077-3088.
Pinkse, M. W. H., & Heck, A. J. R. (2004). Probing Noncovalent Protein-Ligand Interactions of the cGMP-Dependent Protein Kinase Using Electrospray Ionization Time of Flight Mass Spectrometrie. Journal of the American Society for Mass Spectrometry, 15, 1392-1399.
Ridder, A. N. J. A., Spelbrink, R. E. J., Demmers, J. A. A., Rijkers, D. T. S., Liskamp, R. M. J., Brunner, J., Heck, A. J. R., de Kruijff, B., & Killian, J. A. (2004). Photo-crosslinking analysis of preferential interactions between a transmembrane peptide and matching lipids. Biochemistry, 43, 4482-4489.
https://dspace.library.uu.nl/bitstream/handle/1874/14449/Ridder-Photo-crosslinking%2520analysis.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/14449/Ridder-Photo-crosslinking%2520analysis.pdf?sequence=1
Pinkse, M. W. H., Uitto, P. M., Hilhorst, M. J., Ooms, B., & Heck, A. J. R. (2004). Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. Analytical Chemistry, 76, 3935-3943.
Kol, M. A., Kuster, D. W. D., Boumann, H. A., de Cock, J. J. P. A., Heck, A. J. R., de Kruijff, B., & de Kroon, A. I. P. M. (2004). Uptake and remodeling of exogenous phosphatidylethanolamine in E. coli. Biochimica et Biophysica Acta, 1636, 205-212.
https://dspace.library.uu.nl/bitstream/handle/1874/14638/Kol-Uptake%2520and%2520remodeling.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/14638/Kol-Uptake%2520and%2520remodeling.pdf?sequence=1
Heck, A. J. R., & van den Heuvel, R. H. H. (2004). Investigation of intact protein complexes by Mass Spectrometry. Mass Spectrometry Reviews, 23, 368-389.
van den Heuvel, R. H. H., & Heck, A. J. R. (2004). Mass spectrometry as a novel tool in protein structural biology. Spectroscopy Europe, 16(2), 6-13.
van den Heuvel, R. H. H., & Heck, A. J. R. (2004). Native protein mass spectrometry: from intact oligomers to functional machineries. Current Opinion in Chemical Biology, (8), 519-526.
Iovan Avram, D., Romijn, E. P., Pap, E. H. W., Heck, A. J. R., & Wirtz, K. W. A. (2004). Identification of proteins in activated human neutrophils susceptible to tyrosyl radical attack. A proteomic study using a tyrosylating fluorophore. Proteomics, 4, 2397-2407.
https://dspace.library.uu.nl/bitstream/handle/1874/14663/5.Avram%25202004%2520pp%25202397-407.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/14663/5.Avram%25202004%2520pp%25202397-407.pdf?sequence=1
Professional publications
Iovan Avram, D., Romijn, E. P., Heck, A. J. R., & Wirtz, K. W. A. (2004). Activation of human neutrophils leads to the cross-linking of tyrosyl radicals to endogenous anti-inflamatory and anti-bacterial proteins. Application of a tyrosylating fluorophore. In NATO Science Series, Series I, Life and Behavioural Sciences, vol. 358 (pp. 32-39). (1. Life and behavioural Sciences; No. 358). IOS Press.
2003
Scholarly publications
Yatsuda, A. P., Krijgsveld, J., Cornelissen, A. W. C. A., Heck, A. J. R., & de Vries, E. (2003). Comprehensive analysis of the secreted proteins of the parasite Haemonchus contortus reveals extensive sequence variation and differential immune recognition. Journal of Biological Chemistry, 278(19), 16941-16951.
de Boer, E., Rodriguez, P., Bonte, E., Krijgsveld, J., Katsantoni, E., Heck, A. J. R., Grosveld, F., & Strouboulis, J. (2003). Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice. Proceedings of the National Academy of Sciences of the United States of America, 100(13), 7480-7485.
Krijgsveld, J., Ketting, R. F., Mahmoudi, T., Johansen, J., Artal-Sanz, M., Verrijzer, C. P., & Heck, A. J. R. (2003). Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nature Biotechnology, 21(8), 927-931.
Blokland, M. H., Sterk, S. S., van Ginkel, L. A., Stephany, R. W., & Heck, A. J. R. (2003). Analysis for endogenous and recombinant porcine somatotropine in serum. Analytica Chimica Acta, 483, 201-206.
Demmers, J. A. A., van Dalen, A., de Kruijff, B., Heck, A. J. R., & Killian, J. A. (2003). Interaction of the K+ channel KcsA with membrane phospholipids as studied by ESI mass spectrometry. FEBS Letters, 541, 28-32. https://www.sciencedirect.com/science/article/pii/S0014579303002825
Boumann, H. A., Damen, J. M. A., Versluis, C., Heck, A. J. R., de Kruijff, B., & de Kroon, A. I. P. M. (2003). The two biosynthetic routes leading to posphatidylcholine in yeast produce different sets of molecular species. Evidence for lipid remodeling. Biochemistry, 42, 3054-3059.
https://dspace.library.uu.nl/bitstream/handle/1874/14364/Boumann-The%2520two%2520biosynthetic.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/14364/Boumann-The%2520two%2520biosynthetic.pdf?sequence=1
Pinkse, M. W. H., Maier, C. S., Kim, J. I., Oh, B. H., & Heck, A. J. R. (2003). Macromolecular assembly of Helicobacter pylori urease investigated by mass spectrometry. Journal of Mass Spectrometry, 38, 315--320.
Kopitz, J., André, S., Von Reitzenstein, C., Versluis, C., Kaltner, H., Pieters, R. J., Wasano, K., Kuwabara, I., Liu, F-T., Cantz, M., Heck, A. J. R., & Gabius, H-J. (2003). Homodimeric galectin-7 (p53-induced gene 1) is a negative growth regulator for human neuroblastoma cells. Oncogene, 22, 6277-6288.
de Wit, N. J. C., Vatish, M., Heck, A. J. R., & Thornton, S. (2003). The application of proteomics to fetal and maternal medicine. Fetal and Maternal Medicine Review, 14, 47-55.
Breukink, E. J., van Heusden, H. E., Bonnici, P. J., Swiezewska, E., Brunner, L., Walker, S. M., Heck, A. J. R., & de Kruijff, B. (2003). Lipid II is an intrinsic component of the pore induced by nisin in bacterial membranes. Journal of Biological Chemistry, 278, 19898-19903.
https://dspace.library.uu.nl/bitstream/handle/1874/14365/Breukink-Lipid%2520II%2520is%2520an%2520intrinsic.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/14365/Breukink-Lipid%2520II%2520is%2520an%2520intrinsic.pdf?sequence=1
Houtman, R., Krijgsveld, J., Kool, M., Romijn, E. P., Redegeld, F. A. M., Nijkamp, F. P., Heck, A. J. R., & Humphery-Smith, I. (2003). Lung proteome alterations in a mouse model for nonallergic asthma. Proteomics, 3, 2008-2018.
Catalina Caballero, M. I., Dekker, F. J., Liskamp, R. M. J., Versluis, C., Maier, C. S., & Heck, A. J. R. (2003). Structural analysis of high affinity divalent phosphopeptide hybrids of spleen tyrosine kinase. International Journal of Mass Spectrometry, 228, 879-890.
Romijn, E. P., Krijgsveld, J., & Heck, A. J. R. (2003). Recent liquid chromatographic-(tandem) mass spectrometric applications in proteomics. Journal of Chromatography A, 1000, 589-608.
van Anken, E., Romijn, E. P., Maggioni, M. C., Mezghrani, A., Sitia, R., Braakman, L. J., & Heck, A. J. R. (2003). Sequential Waves of Functionally Related Proteins Are Expressed When B Cells Prepare for Antibody Secretion. Immunity, 18, 243-253.
Kleinnijenhuis, A. J., Duursma, M. C., Breukink, E. J., Heeren, R. M. A., & Heck, A. J. R. (2003). Localization of intramolecular monosulfide bridges in lantibiotics determined with electron capture induced dissociation. Analytical Chemistry, 75, 3219-3225.
https://dspace.library.uu.nl/bitstream/handle/1874/14955/Kleinnijenhuis-Localization.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/14955/Kleinnijenhuis-Localization.pdf?sequence=1
Bonnici, P. J., Breukink, E. J., & Heck, A. J. R. (2003). Getting closer to the real bacterial cell wall target: biomolecular interactions of water-soluble lipid II with glycopeptide antibiotics. Chemistry-A European Journal, 9, 1556-1565.
https://dspace.library.uu.nl/bitstream/handle/1874/14378/Vollmerhaus-Getting%2520closer.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/14378/Vollmerhaus-Getting%2520closer.pdf?sequence=1
2002
Scholarly publications
Wills, M., Morris, D., Breukink, E., Bonnici, P. J., & Heck, A. J. R. (2002). Stereocontrolled synthesis of angularly fused tricyclic ring systems by means of 1-metalla-1,3,5-hexatrienes (M = Cr, W). Chemistry - A European Journal, 8(4), 910-916. https://doi.org/10.1002/1521-3765(20020215)8:4<910::AID-CHEM910>3.0.CO;2-T
Siebert, H-C., Lü, S-Y., Frank, M., Kramer, J., Wechselberger, R. W., Joosten, J., André, S., Rittenhouse-Olson, K., Roy, R., von der Lieth, C-W., Kaptein, R., Vliegenthart, J. F. G., Heck, A. J. R., & Gabius, H-J. (2002). Analysis of protein-carbohydrate interaction at the lower size limit of the protein part (15-mer peptide) by NMR Spectroscopy, electrospray ionization mass spectrometry and molecular modeling. Biochemistry, 41, 9707-9717.
https://dspace.library.uu.nl/bitstream/handle/1874/14252/BC_41.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/14252/BC_41.pdf?sequence=1
Heck, A. J. R., & Maier, C. S. (2002). Biomolecular mass spectrometry related to drug research. In H. van der Goot (Ed.), Proceedings of 13th Noordwijkerhout-Camerino symposium trends in drug research (pp. 81-94)
de Brouwer, A. P. M., Versluis, C., Westermann, J., Roelofsen, B., Heck, A. J. R., & Wirtz, K. W. A. (2002). Determination of the stability of the noncovalent phospholipid transfer protein-lipid complex by electrospray time-of-flight mass spectrometry. Biochemistry, 41, 8013-8018.
https://dspace.library.uu.nl/bitstream/handle/1874/14385/5.De%2520Brouwer%25202002%2520pp%25208013-18.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/14385/5.De%2520Brouwer%25202002%2520pp%25208013-18.pdf?sequence=1
Demmers, J. A. A., Rijkers, D. T. S., Haverkamp, J., Killian, J. A., & Heck, A. J. R. (2002). Factors affecting gas-phase deuterium scrambling in peptide ions and their implications for protein structure determination. Journal of the American Chemical Society, 124, 11191-11198.
https://dspace.library.uu.nl/bitstream/handle/1874/14253/Demmers-Factors%2520affecting.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/14253/Demmers-Factors%2520affecting.pdf?sequence=1
Fiammengo, R., Timmerman, P., Huskens, J., Versluis, K., Heck, A. J. R., & Reinhoudt, D. N. (2002). Non-covalent synthesis of calix[4]arene-cappes porpyrins in polar solvents via ionic interactions. Tetrahedron, 58, 757-764.
Heck, A. J. R., Maier, C. S., Tahallah, N., Bossi, R. T., Aliverti, A., Zanetti, G., Ferrari, D., Rizzi, M., & Mattevi, A. (2002). An unprecedented covalent modification of NADP+ revealed by atomic resolution structure of FprA, a Mycobacterium tuberculosis oxidoreductase. Biochemistry, 41, 8807-8818.
van den Bremer, E. T. J., Jiskoot, W., James, R., Moore, G. R., Kleanthous, C., Heck, A. J. R., & Maier, C. S. (2002). Probing metal ion binding and conformational properties of the colicin E9 endonuclease by electrospray ionization time-of-flight mass spectrometry. Protein Science, 11, 1738-1752.
Ruijtenbeek, R., Versluis, C., Heck, A. J. R., Redegeld, F. A. M., Nijkamp, F. P., & Liskamp, R. M. J. (2002). Characterization of a phosphorylated peptide and peptoid and peptoid-peptide hybrids by mass spectrometry. Journal of Mass Spectrometry, 37, 47-55.
Vollmerhaus, P. J., Tempels, F. W. A., Kettenes-van den Bosch, J. J., & Heck, A. J. R. (2002). Molecular interactions of glycopeptide antibiotics investigated by affinity capillary electrophoresis and bioaffinity electrospray ionization-mass spectrometry. Electrophoresis, 23, 868-879.
Corbellini, F., Fiammengo, R., Timmerman, P., Crego-Calama, M., Versluis, K., Heck, A. J. R., Luyten, I., & Reinhoudt, D. N. (2002). Guest encapsulation and self-assembly of molecular capsules in polar solvents via multiple ionic interactions. Journal of the American Chemical Society, 124, 6569-6575.
Tahallah, N., van den Heuvel, R. H. H., van den Berg, W. A. M., Maier, C. S., van Berkel, W. J. H., & Heck, A. J. R. (2002). Cofactor-dependent assembly of the flavoenzyme vanillyl-alcohol oxidase. Journal of Biological Chemistry, 277, 36425-36432.
Surroca, Y., Haverkamp, J., & Heck, A. J. R. (2002). Towards the understanding of molecular mechanisms in the early stages of heat-induced aggregation of beta-lactoglobulin AB. Journal of Chromatography A, 970, 275-285.
Jeric, I., Versluis, C., Horvat, S., & Heck, A. J. R. (2002). Tracing glycoprotein structures: electron ionization tandem mass spectrometric analysis of sugar-peptide adducts. Journal of Mass Spectrometry, 37, 803-811.
2001
Scholarly publications
Waterval, J. C. M., Bestebreurtje, P., Lingeman, H., Versluis, C., Heck, A. J. R., Bult, A., & Underberg, W. J. M. (2001). Robust and cost-effective capillary electrophoresis-mass spectrometry interfaces suitable for combination with on-line analyte preconcentration. Electrophoresis, 22, 2701-2708.
Farine, S., Versluis, C., Bonnici, P. J., Heck, A. J. R., L'homme, C., Puigserver, A., & Biagini, A. (2001). Application of high performance anion exchange chromtography to study invertase-catalysed hydrolysis of sucrose and formation of intermediate fructan products. Applied Microbiology and Biotechnology, 55, 55-60.
Bonnici, P. J., Damen, J. M. A., Waterval, J. C. M., & Heck, A. J. R. (2001). Formation and efficacy of vancomycin group glycopeptide antibiotic stereoisomers studied by capillary electrophoresis and bioaffinity mass spectrometry. Analytical Biochemistry, 290, 292-301.
Cadee, J. A., van Steenbergen, M. J., Versluis, C., Heck, A. J. R., Underberg, W. J. M., den Otter, W., Jiskoot, W., & Hennink, W. E. (2001). Oxidation of Recombinant Human interleukin-2 by Potassium Peroxodisulfate. Pharmaceutical Research, 18, 1461-1467.
Morris, L. A., Jaspars, M., Kettenes-van den Bosch, J. J., Versluis, C., Heck, A. J. R., Kelly, S. M., & Price, N. C. (2001). Metal binding of Lissoclinum patella metabolites. Part 1: Patellamides A, C and ulithiacyclamide. Tetrahedron, 57, 3185-3197.
Demmers, J. A. A., van Duijn, E., Haverkamp, J., Greathouse, D. V., Koeppe II, R. E., Heck, A. J. R., & Killian, J. A. (2001). Interfacial positioning and stability of transmembrane peptides in lipid bilayers studied by combining hydrogen/deuterium exchange and mass spectrometry. Journal of Biological Chemistry, 276, 34501-34508.
Versluis, C., van der Staaij, A., Stokvis, E., Heck, A. J. R., & de Craene, B. (2001). Metastable Ion Formation and Disparate Charge Separation in the Gas-Phase Dissection of Protein Assemblies studied by Orthogonal Time-of-Flight Mass Spectrometry. Journal of the American Society for Mass Spectrometry, 12, 329-336.
Morris, L. A., Milne, B. F., Jaspars, M., Kettenes-van den Bosch, J. J., Versluis, C., Heck, A. J. R., Kelly, S. M., & Price, N. C. (2001). Metal binding of Lissoclinum patella metabolites. Part 2: Lissoclinamides 9 and 10. Tetrahedron, 57, 3199-3207.
Versluis, C., & Heck, A. J. R. (2001). On the gas-phase dissociation of hemoglobin. International Journal of Mass Spectrometry, 210/211, 637-649.
Roscic, M., Versluis, C., Kleinnijenhuis, A. J., Horvat, S., & Heck, A. J. R. (2001). The early glycation products of the Maillard reaction: mass spectrometric characterization of novel imidazolidinones derived from an opioid pentapeptide and glucose. Rapid Communications in Mass Spectrometry, 15, 1022-1029.
Farine, S., Versluis, C., Bonnici, P. J., Heck, A. J. R., Peschet, J. L., Puigserver, A., & Biagini, A. (2001). Separation and identification of enzymatic sucrose hydrolysis products by high-performance anion-exchange chromatography with pulsed amperometric detection. Journal of Chromatography A, 920, 299-308.
Tahalla, N., Pinkse, M. W. H., Maier, C. S., & Heck, A. J. R. (2001). The effect of the source pressure on the abundance of ions of noncovalent protein assemblies in an electrospray ionization orthogonal time-f-flight instrument. Rapid Communications in Mass Spectrometry, 15, 596-601.
Waterval, J. C. M., Hommels, G., Bestebreurtje, P., Versluis, C., Heck, A. J. R., Bult, A., & Underberg, W. J. M. (2001). Capillary electrophoresis bioanalysis of therapeutically active peptides with UV and mass spectrometric detection after on-capillary preconcentration. Electrophoresis, 22, 2709-2716.
Heck, A. J. R., Bonnici, P. J., Breukink, E. J., Morris, D., & Wills, M. (2001). Modification and inhibition of vancomycin group antibiotics by formaldehyde and acetaldehyde. Chemistry-A European Journal, 7, 910-916.
Other output
Houtman, R., Romijn, E. P., Krijgsveld, J., Heck, A. J. R., & Redegeld, F. A. M. (2001). Identification of novel target molecule in asthma using proteomics. FASEB Journal, 15, 2701-2708.
2000
Scholarly publications
Kenny, J. A., Versluis, K., Heck, A. J. R., Walsgrove, T., & Wills, M. (2000). The detection of intermediates in the ruthenium(II) catalysed asymmetric hydrogenation of ketones using electrospray ionisation mass spectrometry. Chemical Communications, (1), 99-100. https://doi.org/10.1039/a908098h
Nuijen, B., Bouma, M., Henrar, R. E. C., Floriano, P., Jimeno, J. M., Talsma, H., Kettenes-van den Bosch, J. J., Heck, A. J. R., Bult, A., & Beijnen, J. H. (2000). Related Articles Pharmaceutical development of a parenteral lyophilized formulation of the novel antitumor agent aplidine. PDA Journal of Pharmaceutical Science and Technology, 54, 193-208.
Staroske, T., O'Brien, D. P., Jorgensen, T. J. D. J., Roepstorff, P., Williams, D. H., & Heck, A. J. R. (2000). The formation of Heterodimers by Vancomycin Group Antibiotics. Chemistry-A European Journal, 6, 504-509.
van Berkel, W. J. H., van den Heuvel, R. H. H., Versluis, C., & Heck, A. J. R. (2000). Detection of intact megaDalton protein assemblies of vanillyl-alcohol oxidase by mass spectrometry. Protein Science, 9, 435-439.
Stokvis, E., Clugston, S. L., Honek, J. F., & Heck, A. J. R. (2000). Characterization of Glyoxalase I (E.coli)-Inhibitor Interactions by Electrospray Time-of-Flight Mass Spectrometry and Enzyme Kinetic Analysis. Journal of Protein Chemistry, 19, 389-397.
Demmers, J. A. A., Haverkamp, J., Heck, A. J. R., Koeppe, R. E., & Killian, J. A. (2000). Electrospray ionazation mass spectrometry as a tool to analyze hydrogen/deuterium exchange kinetics to transmembrane peptides in lipid bilayers. Proceedings of the National Academy of Sciences of the United States of America, 97, 3189-3194.
van Dongen, W. D., & Heck, A. J. R. (2000). Binding of selected carbohydrates to apo-concanavalin A studied by electrospray ionazation mass spectrometry. Analyst, 125, 583-589.
Nuijen, B., Bouma, M., Henrar, R. E. C., Floriano, P., Jimeno, J. M., Talsma, H., Kettenes-van den Bosch, J. J., Heck, A. J. R., Bult, A., & Beijnen, J. H. (2000). Pharmaceutical development of a parenteral lyophilized formulation of the novel antitumour agent aplidine. PDA Journal of Pharmaceutical Science and Technology, 54(3), 193-208.
van Maanen, M. J., Doesburg Smits, K., Damen, J. M. A., Heck, A. J. R., & Beijnen, J. H. (2000). Stability of thioTEPA and its metabolites, TEPA, monochloroTEPA and thioTEPA-mercapturate, in plasma and urine. International Journal of Pharmaceutics, 200, 187-194.
Kenny, J. A., Versluis, C., Heck, A. J. R., Walsgrove, T., & Wills, M. (2000). The detection of intermediates in the rythenium (II) catalysed asymmetric hydrogenation of ketones using electrospray ionisation mass spectrometry. Chemical Communications, 99-100.
1999
Scholarly publications
van Maanen, M. J., Tijhof, I. M., Damen, J. M. A., Versluis, C., Kettenes-van den Bosch, J. J., Heck, A. J. R., Rodenhuis, S., & Beijnen, J. H. (1999). A search for new metabolites of N,N',N"-triethylenethiophosphoramide. Cancer Research, 59, 4720-4724.
van der Kerk-van Hoof, A. C., & Heck, A. J. R. (1999). Covalent and Non-covalent Dissociations of Gas-phase Complexes of Avoparcin and Bacterial Receptor Mimicking Precursor Peptides Studied by Collisionally Activated Decomposition Mass Spectrometry. Journal of Mass Spectrometry, 34, 813-819.
Smith, A. R. C., Heck, A. J. R., Kenny, J. A., Kettenes-van den Bosch, J. J., & Wills, M. (1999). Synthesis and electrospray mass spectrometric studies on a chiral, non-racemic, phosphoramide receptor molecule. Tetrahedron-Asymmetry, 10, 3267-3271.
Neyer, D. W., Heck, A. J. R., & Chandler, D. W. (1999). Photodissociation of N2O : J-dependent anisotropy revealed in N2 photofragment images. Chemical Physics, 110, 3411-3417.
Neyer, D. W., Heck, A. J. R., Chandler, D. W., Teule, J. M., & Janssen, M. H. M. (1999). Speed-dependent alignment and angular distributions of O 1D2 from the ultraviolet photodissociation of N20. Journal of Physical Chemistry A, 103, 10388-10397.
Heck, A. J. R. (1999). Mass spectrometry : Ion Imaging Using Mass Spectrometry. In J. C. Lindon, G. E. Tranter, & J. L. Holmes (Eds.), Encyclopedia of Spectroscopy and Spectrometry Academic Press Inc..
van der Kerk-van Hoof, A. C., & Heck, A. J. R. (1999). Interactions of - and -avoparcin with bacterial cell-wall receptor-mimicking peptides studied by electrospray ionization mass spectrometry. Journal of Antimicrobial Chemotherapy, 44, 593-599.
Lafitte, D., Heck, A. J. R., Hill, T. J., Jumel, K., Harding, S. E., & Derrick, P. J. (1999). Evidence of noncovalent dimerization of calmodulin. European Journal of Biochemistry, 261, 337-344.
Jorgensen, T. J. D. J., Staroske, T., Roepstorff, P., Williams, D. H., & Heck, A. J. R. (1999). Subtle differences in molecular recognition between modified glycopeptide antibiotics and bacterial receptor peptides identified by electrospray ionization mass spectrometry. Journal of the Chemical Society. Perkin transactions II, physical organic chemistry, 9, 1859-1863.
Silva, C. M. L., Duarte, M. F., Mira, M. L., Florincio, M. H., Versluis, C., & Heck, A. J. R. (1999). Copper and iron interactions with angiotensin - converting enzyme inhibitors. A study by FAB / MS study. Rapid Communications in Mass Spectrometry, 13, 1098-1103.
1998
Scholarly publications
Heck, A. J. R., Jørgensen, T. J. D., O'Sullivan, M., von Raumer, M., & Derrick, P. J. (1998). Gas-phase noncovalent interactions between vancomycin-group antibiotics and bacterial cell-wall precursor peptides probed by hydrogen/deuterium exchange. Journal of the American Society for Mass Spectrometry, 9(12), 1255-1266. https://doi.org/10.1016/S1044-0305(98)00110-X
Jørgensen, T. J. D., Roepstorff, P., & Heck, A. J. R. (1998). Direct Determination of Solution Binding Constants for Noncovalent Complexes between Bacterial Cell Wall Peptide Analogues and Vancomycin Group Antibiotics by Electrospray Ionization Mass Spectrometry. Analytical Chemistry, 70(20), 4427-4432. https://doi.org/10.1021/ac980563h