Biomolecular Mass Spectrometry and Proteomics

2025

Acquisition of Fc-afucosylation of PfEMP1-specific IgG is age-dependent and associated with clinical protection against malaria

Lopez-Perez, M., Seidu, Z., Larsen, M. D., Wang, W., Nouta, J., Wuhrer, M., Vidarsson, G., Ofori, M. F. & Hviid, L., 2 Jan 2025, In: Nature Communications. 16, 1, 237.

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Affinity-based covalent sialyltransferase probes enabled by ligand-directed chemistry

Ong, J. Y., Alvarado-Melendez, E. I., Maliepaard, J. C. L., Reiding, K. R. & Wennekes, T., 21 Feb 2025, In: Chemical Science. 16, 7, p. 3336-3344 9 p.

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Bisecting N-Acetylglucosamine of the N-Glycan of Immunoglobulin G Does Not Affect Binding to Fc Gamma Receptors

Bosman, G. P., Stoof, I. D., Bastiaansen, H. P., Quarles van Ufford, L., Dobruchowska, J. M., Langenbach, J. W. H., Boruah, B. M., Moremen, K. W., Bentlage, A. E. H., Lissenberg-Thunnissen, S. N., Vidarsson, G. & Boons, G. J., 21 Mar 2025, In: ACS Chemical Biology. 20, 3, p. 680-689 10 p.

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Blocking MIF secretion enhances CAR T-cell efficacy against neuroblastoma

Strijker, J. G. M., Pascual-Pasto, G., Grothusen, G. P., Kalmeijer, Y. J., Kalaitsidou, E., Zhao, C., McIntyre, B., Matlaga, S., Visser, L. L., Barisa, M., Himsworth, C., Shah, R., Muller, H., Schild, L. G., Hains, P. G., Zhong, Q., Reddel, R. R., Robinson, P. J., Catena, X. & Soengas, M. S. & 7 others, Margaritis, T., Dekker, F. J., Anderson, J., Molenaar, J. J., Bosse, K. R., Wu, W. & Wienke, J., 11 Mar 2025, In: European Journal of Cancer. 218, 115263.

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Cardiomyocyte SORBS2 expression increases in heart failure and regulates integrin interactions and extracellular matrix composition

Timmer, L. T., den Hertog, E., Versteeg, D., Post, H., Verdonschot, J. A. J., Monshouwer-Kloots, J., Kyriakopoulou, E., Perini, I., Koopmans, T., van der Kraak, P., Zentilin, L., Heymans, S. R. B., Vink, A., Giacca, M., Heck, A. J. R. & van Rooij, E., 17 Feb 2025, (E-pub ahead of print) In: Cardiovascular Research. 16 p., cvaf021.

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Characterization of intact mRNA-based therapeutics by charge detection mass spectrometry and mass photometry

Deslignière, E., Barnes, L. F., Powers, T. W., Friese, O. V. & Heck, A. J. R., 12 Jun 2025, In: Molecular Therapy Methods and Clinical Development. 33, 2, 9 p., 101454.

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Engineering of anticancer human immunoglobulin A equipped with albumin for enhanced plasma half-life

Mester, S., Chan, C., Lustig, M., Foss, S., Jansen, J. H. M., Herigstad, M. L., Evers, M., Nilsen, J., Reiding, K. R., Damen, J. M. A., Burger, R., Grevys, A., Dalhus, B., Valerius, T., Sandlie, I., Leusen, J. H. W. & Andersen, J. T., 28 Feb 2025, In: PNAS Nexus. 4, 2, 16 p., pgaf042.

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In-depth plasma N-glycoproteome profiling using narrow-window data-independent acquisition on the Orbitrap Astral mass spectrometer

Jager, S., Zeller, M., Pashkova, A., Schulte, D., Damoc, E., Reiding, K. R., Makarov, A. A. & Heck, A. J. R., 13 Mar 2025, In: Nature Communications. 16, 1, 2497.

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Individual patient and donor seroprofiles in convalescent plasma treatment of COVID-19 in REMAP-CAP clinical trial

Nurmi, V., Mayne, R., Knight, C., Almonacid-Mendoza, H. L., Secret, S., Estcourt, L., Hepojoki, J., Šuštić, T., Lamikanra, A. A., Tsang, H. P., Menon, D. K., Shankar-Hari, M., van der Schoot, C. E., Vidarsson, G., Roberts, D. J., Simmonds, P., Hedman, K. & Harvala, H., Feb 2025, In: Journal Of Infection. 90, 2, 106412.

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Local structural flexibility drives oligomorphism in computationally designed protein assemblies

Khmelinskaia, A., Bethel, N. P., Fatehi, F., Mallik, B. B., Antanasijevic, A., Borst, A. J., Lai, S.-H., Chim, H. Y., Wang, J. Y. '., 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., 26 Feb 2025, (E-pub ahead of print) In: Nature Structural and Molecular Biology. 746.

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Multitiered Proteome Analysis Displays the Hyperpermeability of the Rheumatoid Synovial Compartment for Plasma Proteins

Stork, E. M., Nteak, S. K., van Rijswijck, D. M. H., Damen, J. M. A., Scherer, H. U., Toes, R. E. M., Bondt, A., Huizinga, T. W. J. & Heck, A. J. R., Feb 2025, In: Molecular and Cellular Proteomics. 24, 2, 14 p., 100900.

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NAC regulates metabolism and cell fate in intestinal stem cells

Ramalho, S., Alkan, F., Prekovic, S., Jastrzebski, K., Barberà, E. P., Hoekman, L., Altelaar, M., de Heus, C., Liv, N., Rodríguez-Colman, M. J., Yilmaz, M., van der Kammen, R., Fedry, J., de Gooijer, M. C., Suijkerbuijk, S. J. E., Faller, W. J. & Silva, J., 10 Jan 2025, In: Science advances. 11, 2, eadn9750.

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Profiles of 71 Human Milk Oligosaccharides and Novel Sub-Clusters of Type I Milk: Results from the Ulm SPATZ Health Study

Peng, Z., Siziba, L. P., Mank, M., Stahl, B., Gonsalves, J., Wernecke, D., Rothenbacher, D. & Genuneit, J., 14 Jan 2025, In: Nutrients. 17, 2, 280.

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Prolonged Trapping of Adeno-Associated Virus Capsids Reveals that Genome Packaging Affects Single-Ion Mass Spectrometry Measurements

Ebberink, E. H. T. M., Yin, V. C., Deslignière, E., Barendregt, A., Wörner, T. P., Fort, K. L., Makarov, A. A. & Heck, A. J. R., 2 Apr 2025, In: Journal of the American Chemical Society. 147, 13, p. 10925-10934 10 p.

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Protein-bound and free glycation compounds in human milk: A comparative study with minimally processed infant formula and pasteurized bovine milk

Arena, S., De Pascale, S., Ciaravolo, V., Monroy, M. M., Gouw, J. W., Stahl, B., Bäuerl, C., Collado, M. C., De Filippo, C., Scaloni, A. & Troise, A. D., 15 Jan 2025, In: Food Chemistry. 463, Pt 2, 14 p., 141265.

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Robust and High-Resolution All-Ion Fragmentation LC-ESI-IM-MS Analysis for In-Depth Characterization or Profiling of Up to 200 Human Milk Oligosaccharides

Gonsalves, J., Bauzá-Martinez, J., Stahl, B., Dingess, K. A. & Mank, M., 18 Mar 2025, In: Analytical Chemistry. 97, 10, p. 5563-5574 12 p.

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Spatial organization of the sperm cell glycoproteome

Ji, R., Chiozzi, R. Z., van den Toorn, H., Leung, M., Zeev-Ben-Mordehai, T., Burke, N. D., Bromfield, E. G., Reiding, K. R. & Heck, A. J. R., Jan 2025, In: Molecular and Cellular Proteomics. 24, 1, 100893.

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2024

Adipocyte p53 coordinates the response to intermittent fasting by regulating adipose tissue immune cell landscape

Reinisch, I., Michenthaler, H., Sulaj, A., Moyschewitz, E., Krstic, J., Galhuber, M., Xu, R., Riahi, Z., Wang, T., Vujic, N., Amor, M., Zenezini Chiozzi, R., Wabitsch, M., Kolb, D., Georgiadi, A., Glawitsch, L., Heitzer, E., Schulz, T. J., Schupp, M. & Sun, W. & 11 others, Dong, H., Ghosh, A., Hoffmann, A., Kratky, D., Hinte, L. C., von Meyenn, F., Heck, A. J. R., Blüher, M., Herzig, S., Wolfrum, C. & Prokesch, A., 15 Feb 2024, In: Nature Communications. 15, 1, p. 1-21 21 p., 1391.

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Afucosylated broadly neutralizing antibodies enhance clearance of HIV-1 infected cells through cell-mediated killing

de Taeye, S. W., Schriek, A. I., Umotoy, J. C., Grobben, M., Burger, J. A., Sanders, R. W., Vidarsson, G., Wuhrer, M., Falck, D., Kootstra, N. A. & van Gils, M. J., 9 Aug 2024, In: Communications Biology. 7, 1, 11 p., 964.

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Antigen-specific Fab profiling achieves molecular-resolution analysis of human autoantibody repertoires in rheumatoid arthritis

Stork, E. M., van Rijswijck, D. M. H., van Schie, K. A., Hoek, M., Kissel, T., Scherer, H. U., Huizinga, T. W. J., Heck, A. J. R., Toes, R. E. M. & Bondt, A., 10 Apr 2024, In: Nature Communications. 15, 1, 12 p., 3114.

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Assessment of IgG-Fc glycosylation from individual RhD-specific B cell clones reveals regulation at clonal rather than clonotypic level

de Graaf, E. L., Larsen, M. D., van der Bolt, N., Visser, R., Verhagen, O. J. H. M., Hipgrave Ederveen, A. L., Koeleman, C. A. M., van der Schoot, C. E., Wuhrer, M. & Vidarsson, G., Mar 2024, In: Immunology. 171, 3, p. 428-439 12 p.

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Assessment of Kinome-wide Activity Remodeling Upon Picornavirus Infection

Veth, T. S., Nouwen, L. V., Zwaagstra, M., Lyoo, H., Wierenga, K. A., Westendorp, B., Altelaar, M. A. F. M., Berkers, C., van Kuppeveld, F. J. M. & Heck, A. J. R., May 2024, In: Molecular and Cellular Proteomics. 23, 5, 100757.

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Asymmetric N-Glycosylation in the Tailpiece of Recombinant IgA1.

Peris-Díaz, M. D., Deslignière, E., Jager, S., Mokiem, N., Barendregt, A., Bondt, A. & Heck, A. J. R., 18 Dec 2024, In: Journal of the American Chemical Society. 146, 50, p. 34720-34732 13 p.

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Axonal endoplasmic reticulum tubules control local translation via P180/RRBP1-mediated ribosome interactions

Koppers, M., Özkan, N., Nguyen, H. H., Jurriens, D., McCaughey, J., Nguyen, D. T. M., Li, C. H., Stucchi, R., Altelaar, M., MacGillavry, H. D., Kapitein, L. C., Hoogenraad, C. C. & Farías, G. G., 19 Aug 2024, In: Developmental Cell. 59, 16, p. 2053-2068.e9 26 p.

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CAMSAPs and nucleation-promoting factors control microtubule release from γ-TuRC

Rai, D., Song, Y., Hua, S., Stecker, K., Monster, J. L., Yin, V., Stucchi, R., Xu, Y., Zhang, Y., Chen, F., Katrukha, E. A., Altelaar, M., Heck, A. J. R., Wieczorek, M., Jiang, K. & Akhmanova, A., Mar 2024, In: Nature Cell Biology. 26, 3, p. 404-420 17 p.

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Complex N-glycans are important for interspecies transmission of H7 influenza A viruses

Spruit, C. M., Palme, D. I., Li, T., Ríos Carrasco, M., Gabarroca García, A., Sweet, I. R., Kuryshko, M., Maliepaard, J. C. L., Reiding, K. R., Scheibner, D., Boons, G.-J., Abdelwhab, E. M. & de Vries, R. P., Apr 2024, In: Journal of Virology. 98, 4, 21 p., e0194123.

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Contactin 2 homophilic adhesion structure and conformational plasticity

Chataigner, L. M. P., Thärichen, L., Beugelink, J. W., Granneman, J. C. M., Mokiem, N. J., Snijder, J., Förster, F. & Janssen, B. J. C., 4 Jan 2024, In: Structure. 32, 1, p. 60-73.e5

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Development of a Versatile Cancer Vaccine Format Targeting Antigen-Presenting Cells Using Proximity-Based Sortase A-Mediated Ligation of T-Cell Epitopes

Wang, A. Z., Brink, H. J., Bouma, R. G., Affandi, A. J., Nijen Twilhaar, M. K., Heijnen, D. A. M., van Elk, J., Maaskant, J. J., Konijn, V. A. L., Stolwijk, J. G. C., Kalay, H., Olesek, K., van Kooyk, Y., van der Schoot, J. M. S., Bentlage, A. E. H., Scheeren, F. A., Verdoes, M., Vidarsson, G., Kuijl, C. P. & den Haan, J. M. M., 20 Nov 2024, In: Bioconjugate Chemistry. 35, 11, p. 1805-1814 10 p.

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Direct Comparison of the Hinge-Cleaving Proteases IgdE and BdpK for LC-MS-Based IgG1 Clonal Profiling

van Rijswijck, D. M. H., Bondt, A., de Kat, N., Lood, R. & Heck, A. J. R., 9 Jan 2024, In: Analytical Chemistry. 96, 1, p. 23-27 5 p.

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Dual-Probe Activity-Based Protein Profiling Reveals Site-Specific Differences in Protein Binding of EGFR-Directed Drugs

van Bergen, W., Zuna, K., Fiala, J., Pohl, E. E., Heck, A. J. R. & Baggelaar, M. P., 16 Aug 2024, In: ACS Chemical Biology. 19, 8, p. 1705-1718 14 p.

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Dual role of proliferating cell nuclear antigen monoubiquitination in facilitating Fanconi anemia-mediated interstrand crosslink repair

Shah, R., Aslam, M. A., Spanjaard, A., de Groot, D., Zurcher, L. M., Altelaar, M., Hoekman, L., Pritchard, C. E. J., Pilzecker, B., van den Berk, P. C. M. & Jacobs, H., 2 Jul 2024, In: PNAS Nexus. 3, 7, 14 p., pgae242.

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Epidermal growth factor receptor (EGFR) is a target of the tumor-suppressor E3 ligase FBXW7

Boretto, M., Geurts, M. H., Gandhi, S., Ma, Z., Staliarova, N., Celotti, M., Lim, S., He, G. W., Millen, R., Driehuis, E., Begthel, H., Smabers, L., Roodhart, J., van Es, J., Wu, W. & Clevers, H., 19 Mar 2024, In: Proceedings of the National Academy of Sciences of the United States of America. 121, 12, e2309902121.

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Fast and Accurate Disulfide Bridge Detection

Heissel, S., He, Y., Jankevics, A., Shi, Y., Molina, H., Viner, R. & Scheltema, R. A., May 2024, In: Molecular and Cellular Proteomics. 23, 5, 12 p., 100759.

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Gene and protein sequence features augment HLA class I ligand predictions

Bresser, K., Nicolet, B. P., Jeko, A., Wu, W., Loayza-Puch, F., Agami, R., Heck, A. J. R., Wolkers, M. C. & Schumacher, T. N., 11 Jun 2024, In: Cell Reports. 43, 6, 23 p., 114325.

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Generation of human antibodies targeting human platelet antigen (HPA)-1a

Oosterhoff, J. J., Linty, F., Visser, R., de Vos, T., Hofstede-van Egmond, S., van de Weerd, M., Porcelijn, L., de Haas, M., van der Schoot, E. & Vidarsson, G., May 2024, In: Transfusion. 64, 5, p. 893-905 13 p.

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Genotype-dependent N-glycosylation and newly exposed O-glycosylation affect plasmin-induced cleavage of histidine-rich glycoprotein (HRG)

Zou, Y., Pronker, M. F., Damen, J. M. A., Heck, A. J. R. & Reiding, K. R., Jan 2024, In: Journal of Biological Chemistry. 300, 3, 12 p., 105683.

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Higher-order structure and proteoforms of co-occurring C4b-binding protein assemblies in human serum

Kadavá, T., Hevler, J. F., Kalaidopoulou Nteak, S., Yin, V. C., Strasser, J., Preiner, J. & Heck, A. J. R., Jul 2024, In: EMBO Journal. 43, 14, p. 3009-3026 18 p.

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High throughput screening identifies repurposable drugs for modulation of innate and acquired immune responses

Ghorbanalipoor, S., Matsumoto, K., Gross, N., Heimberg, L., Krause, M., Veldkamp, W., Magens, M., Zanken, J., Neuschutz, K. J., De Luca, D. A., Kridin, K., Vidarsson, G., Chakievska, L., Visser, R., Kunzel, S., Recke, A., Gupta, Y., Boch, K., Vorobyev, A. & Kalies, K. & 3 others, Manz, R. A., Bieber, K. & Ludwig, R. J., Sept 2024, In: Journal of Autoimmunity. 148, 15 p., 103302.

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Human fetal brain self-organizes into long-term expanding organoids

Hendriks, D., Pagliaro, A., Andreatta, F., Ma, Z., van Giessen, J., Massalini, S., López-Iglesias, C., van Son, G. J. F., DeMartino, J., Damen, J. M. A., Zoutendijk, I., Staliarova, N., Bredenoord, A. L., Holstege, F. C. P., Peters, P. J., Margaritis, T., Chuva de Sousa Lopes, S., Wu, W., Clevers, H. & Artegiani, B., 1 Feb 2024, In: Cell. 187, 3, p. 712-732 21 p., e38.

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Human IgG Subclasses Differ in the Structural Elements of Their N-Glycosylation

Wang, W., Maliepaard, J. C. L., Damelang, T., Vidarsson, G., Heck, A. J. R. & Reiding, K. R., 27 Nov 2024, In: ACS Central Science. 10, 11, p. 2048-2058 11 p.

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IgG1 glycosylation highlights premature aging in Down syndrome

Streng, B., Van Coillie, J., Wildenbeest, J., Binnendijk, R., Smits, G., den Hartog, G., Wang, W., Nouta, J., Linty, F., Visser, R., Wuhrer, M., Vidarsson, G. & Bont, L., Jul 2024, In: Aging Cell. 23, 7, 10 p., e14167.

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Inceptor binds to and directs insulin towards lysosomal degradation in β cells

Siehler, J., Bilekova, S., Chapouton, P., Dema, A., Albanese, P., Tamara, S., Jain, C., Sterr, M., Enos, S. J., Chen, C., Malhotra, C., Villalba, A., Schomann, L., Bhattacharya, S., Feng, J., Akgün Canan, M., Ribaudo, F., Ansarullah, Burtscher, I. & Ahlbrecht, C. & 6 others, Plettenburg, O., Kurth, T., Scharfmann, R., Speier, S., Scheltema, R. A. & Lickert, H., 2024, In: Nature Metabolism. 6, 12, p. 2374–2390 17 p., e202206132.

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Integrative analysis of neuroblastoma by single-cell RNA sequencing identifies the NECTIN2-TIGIT axis as a target for immunotherapy

Wienke, J., Visser, L. L., Kholosy, W. M., Keller, K. M., Barisa, M., Poon, E., Munnings-Tomes, S., Himsworth, C., Calton, E., Rodriguez, A., Bernardi, R., van den Ham, F., van Hooff, S. R., Matser, Y. A. H., Tas, M. L., Langenberg, K. P. S., Lijnzaad, P., Borst, A. L., Zappa, E. & Bergsma, F. J. & 28 others, Strijker, J. G. M., Verhoeven, B. M., Mei, S., Kramdi, A., Restuadi, R., Sanchez-Bernabeu, A., Cornel, A. M., Holstege, F. C. P., Gray, J. C., Tytgat, G. A. M., Scheijde-Vermeulen, M. A., Wijnen, M. H. W. A., Dierselhuis, M. P., Straathof, K., Behjati, S., Wu, W., Heck, A. J. R., Koster, J., Nierkens, S., Janoueix-Lerosey, I., de Krijger, R. R., Baryawno, N., Chesler, L., Anderson, J., Caron, H. N., Margaritis, T., van Noesel, M. M. & Molenaar, J. J., 12 Feb 2024, In: Cancer Cell. 42, 2, p. 283-300.e8

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Into the dark serum proteome: personalized features of IgG1 and IgA1 repertoires in severe COVID-19 patients

Bondt, A., Hoek, M., Dingess, K., Tamara, S., de Graaf, B., Peng, W., den Boer, M. A., Damen, M., Zwart, C., Barendregt, A., van Rijswijck, D. M. H., Schulte, D., Grobben, M., Tejjani, K., van Rijswijk, J., Völlmy, F., Snijder, J., Fortini, F., Papi, A. & Volta, C. A. & 6 others, Campo, G., Contoli, M., van Gils, M. J., Spadaro, S., Rizzo, P. & Heck, A. J. R., Jan 2024, In: Molecular and Cellular Proteomics. 23, 1, p. 100690 13 p., 100690.

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LacdiNAc to LacNAc: remodelling of bovine α-lactalbumin N-glycosylation during the transition from colostrum to mature milk

Gazi, I., Reiding, K. R., Groeneveld, A., Bastiaans, J., Huppertz, T. & Heck, A. J. R., 13 Aug 2024, In: Glycobiology. 34, 9, 11 p., cwae062.

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Lipidome characterisation and sex-specific differences in type 1 and type 2 diabetes mellitus

Barranco-Altirriba, M., Alonso, N., Weber, R. J. M., Lloyd, G. R., Hernandez, M., Yanes, O., Capellades, J., Jankevics, A., Winder, C., Falguera, M., Franch-Nadal, J., Dunn, W. B., Perera-Lluna, A., Castelblanco, E. & Mauricio, D., 29 Mar 2024, In: Cardiovascular Diabetology. 23, 1, 13 p., 109.

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Longitudinal Fluctuations in Protein Concentrations and Higher-Order Structures in the Plasma Proteome of Kidney Failure Patients Subjected to a Kidney Transplant

Nteak, S., Vollmy, F., Lukassen, M., van den Toorn, H., den Boer, M., Bondt, A., van der Lans, S., Haas, P., van Zuilen, A., Rooijakkers, S. & Heck, A., 3 May 2024, In: Journal of Proteome Research. 23, 6, p. 2124–2136 13 p.

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MARS an improved de novo peptide candidate selection method for non-canonical antigen target discovery in cancer

Liao, H., Barra, C., Zhou, Z., Peng, X., Woodhouse, I., Tailor, A., Parker, R., Carre, A., Borrow, P., Hogan, M., Paes, W., Eisenlohr, L., Mallone, R., Nielsen, M. & Ternette, N., 22 Jan 2024, In: Nature Communications. 15, 1, 16 p., 661.

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Multimodal stimulation screens reveal unique and shared genes limiting T cell fitness

Lin, C. P., Levy, P. L., Alflen, A., Apriamashvili, G., Ligtenberg, M. A., Vredevoogd, D. W., Bleijerveld, O. B., Alkan, F., Malka, Y., Hoekman, L., Markovits, E., George, A., Traets, J. J. H., Krijgsman, O., van Vliet, A., Poźniak, J., Pulido-Vicuña, C. A., de Bruijn, B., van Hal-van Veen, S. E. & Boshuizen, J. & 14 others, van der Helm, P. W., Díaz-Gómez, J., Warda, H., Behrens, L. M., Mardesic, P., Dehni, B., Visser, N. L., Marine, J. C., Markel, G., Faller, W. J., Altelaar, M., Agami, R., Besser, M. J. & Peeper, D. S., 8 Apr 2024, In: Cancer Cell. 42, 4, p. 623-645 23 p., e10.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

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Not All Arms of IgM Are Equal: Following Hinge-Directed Cleavage by Online Native SEC-Orbitrap-Based CDMS

Yin, V., Desligniere, E., Mokiem, N., Gazi, I., Lood, R., de Haas, C., Rooijakkers, S. & Heck, A., 20 May 2024, In: Journal of the American Society for Mass Spectrometry. 35, 6, p. 1320–1329 10 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

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Biomolecular Mass Spectrometry and Proteomics

Research output

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