Publicaties
2025
Wetenschappelijke publicaties
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. (2025).
Spatial organization of the sperm cell glycoproteome.
Molecular and Cellular Proteomics,
24(1), Article 100893.
[DOI] [Portal] 2024
Wetenschappelijke publicaties
Nteak, SK., Vollmy, F.
, Lukassen, MV., van den Toorn, H., den Boer, MA., Bondt, A., van der Lans, SPA., Haas, PJ., van Zuilen, AD., Rooijakkers, SHM.
, & Heck, AJR. (2024).
Longitudinal Fluctuations in Protein Concentrations and Higher-Order Structures in the Plasma Proteome of Kidney Failure Patients Subjected to a Kidney Transplant.
Journal of Proteome Research,
23(6), 2124–2136.
[DOI] [Portal]2023
Wetenschappelijke publicaties
Valverde, J. M., Dubra, G., Phillips, M., Haider, A., Elena-Real, C., Fournet, A., Alghoul, E., Chahar, D., Andrés-Sanchez, N., Paloni, M., Bernadó, P., van Mierlo, G.
, Vermeulen, M., van den Toorn, H., Heck, A. J. R., Constantinou, A., Barducci, A., Ghosh, K., Sibille, N.
, ... Altelaar, M. (2023).
A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation.
Nature Communications,
14(1), 1-23. Article 6316.
[DOI] [Repository] 2021
Wetenschappelijke publicaties
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.
[DOI] [Repository] 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.
[DOI] [Repository] Prust, N., van der Laarse, S. A. M., van den Toorn, H., van Sorge, N. M., & Lemeer, S. (2021).
In depth characterization of the Staphylococcus aureus phosphoproteome reveals new targets of Stk1.
Molecular and Cellular Proteomics,
20, 1-12. Article 100034.
[DOI] [Repository] 2020
Wetenschappelijke publicaties
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.
[DOI] [Repository] 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.
[DOI] [Repository] 2019
Wetenschappelijke publicaties
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.
[DOI] [Repository] 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.
[DOI] [Repository] 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.
[DOI] [Repository] de Graaf, S. C.
, Klykov, O., Van den Toorn, H., & Scheltema, R. A. (2019).
Cross-ID: Analysis and Visualization of Complex XL-MS Driven Protein Interaction Networks.
Journal of Proteome Research,
18(2), 642-651.
[DOI] [Repository]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.
[DOI] [Repository] 2017
Wetenschappelijke publicaties
van den Toorn, H. W. P. (2017).
Computational proteomics: from numbers to biology. [Doctoral thesis 1 (Research UU / Graduation UU), Universiteit Utrecht]. Utrecht University.
[Repository] 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.
[DOI] [Repository] 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.
[DOI] [Repository] 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.
[DOI] [Repository] 2015
Wetenschappelijke publicaties
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.
[DOI] [Repository] 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.
[DOI] [Repository]2014
Wetenschappelijke publicaties
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.
[DOI] [Repository]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.
[DOI] 2013
Wetenschappelijke publicaties
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.
[DOI] 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.
[DOI] 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.
[DOI] [Repository] 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.
[DOI] [Repository]2012
Wetenschappelijke publicaties
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.
[DOI]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.
[DOI]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.
[DOI] Bleijerveld, O. B., Wijten, P., Cappadona, S., McClellan, E. A.
, Polat, A. N., Raijmakers, R., Sels, J. W., Colle, L. B., Grasso, S.
, van den Toorn, H. W. P., van Breukelen, B., Stubbs, A., Pasterkamp, G.
, Heck, A. J. R., Hoefer, I. E.
, & Scholten, A. (2012).
Deep Proteome Profiling of Circulating Granulocytes Reveals Bactericidal/Permeability-Increasing Protein as a Biomarker for Severe Atherosclerotic Coronary Stenosis.
Journal of Proteome Research,
11, 5235-5244.
http://www.ncbi.nlm.nih.gov/pubmed/23020738 2011
Wetenschappelijke publicaties
Van Den Toorn, H. W. P., Muñoz, J.
, Mohammed, S., Raijmakers, R., Heck, A. J. R., & Van Breukelen, B. (2011).
RockerBox: Analysis and filtering of massive proteomics search results.
Journal of Proteome Research,
10(3), 1420-1424.
[DOI] 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).
2010
Wetenschappelijke publicaties
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.
2009
Wetenschappelijke publicaties
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.
[DOI] 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.
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.
2006
Wetenschappelijke publicaties
Campilho, A. M., Garcia, B., van den Toorn, H. W. P., van Wijk, H. P. J., & Scheres, B. J. G. (2006). Time-lapse analysis of stem-cell divisions in the Arabidopsis thaliana root. Plant Journal, 48, 619-627.
2004
Wetenschappelijke publicaties
Scheres, B. J. G., van den Toorn, H. W. P., & Heidstra, R. (2004).
Root genomics: towards digital in situ hybridization.
Genome Biology,
5, 227.
[Repository]
