Publications

2017 – Scientific Publications

 

  • Nieuwenhuis J, Adamopoulos A, Bleijerveld OB, Mazouzi A, Stickel E, Celie P, Altelaar M, Knipscheer P, Perrakis A, Blomen VA, Brummelkamp TR. (2017) Vasohibins encode tubulin detyrosinating activity. Science. Accepted. [PubMed]
  • Simonetta M, de Krijger I, Serrat J, Moatti N, Fortunato D, Hoekman L, Bleijerveld OB, Altelaar AFM, Jacobs JJL. (2017) H4K20me2 distinguishes pre-replicative from post-replicative chromatin to appropriately direct DNA repair pathway choice by 53BP1-RIF1-MAD2L2. Cell Cycle. Accepted. [PubMed]
  • Brockmann M, Blomen VA, Nieuwenhuis J, Stickel E, Raaben M, Bleijerveld OB, Altelaar AF, Jae TJ and Brummelkamp TR, (2017) Genetic wiring maps of single cell protein states reveal an off-switch for GPCR signaling. Nature, 546, 307–311. [PubMed]
  • Kai Jiang, Lenka Rezabkova, Shasha Hua, Qingyang Liu, Guido Capitani, A. F. Maarten Altelaar, Albert J. R. Heck, Richard A. Kammerer, Michel O. Steinmetz and Anna Akhmanova (2017) Microtubule minus-end regulation at spindle poles by microcephaly related proteins ASPM and katanin. Nature Cell Biology, 19(5), 480-492. [PubMed]
  • Frese CK, Mikhaylova M, Stucchi R, Gautier V, Liu Q, Mohammed S, Heck AJ, Altelaar AF, Hoogenraad CC. (2017) Quantitative Map of Proteome Dynamics during Neuronal Differentiation. Cell Reports 18(6), 1527-1542. [PubMed]
  • Vega FM, Gautier V, Fernandez-Ponce CM, Extremera MJ, Altelaar AF, Millan J, Tellez JC, Hernandez-Campos JA, Conejero R, Bolivar J, Pardal R, Garcia-Cózar FJ, Aguado E, Heck AJ, Duran-Ruiz MC. (2017) The atheroma plaque secretome stimulates the mobilization of endothelial progenitor cells ex vivo. Journal of Molecular and Cellular Cardiology 105: 12-23. [PubMed]
  • Mäkelä MR, Bouzid O, Robl D, Post H, Peng M, Heck A, Altelaar M, de Vries RP. (2017) Cultivation of Podospora anserina on soybean hulls results in an efficient enzyme cocktail for plant biomass hydrolysis. New Biotechnology 37(Pt B): 162-171. [PubMed]
  • Tsiatsiani L, Giansanti P, Scheltema RA, van den Toorn H, Overall CM, Altelaar AF, Heck AJ. (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. [PubMed]
  • Post H, Penning R, Fitzpatrick MA, Garrigues LB, Wu W, MacGillavry HD, Hoogenraad CC, Heck AJ, Altelaar AF. (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. [PubMed]
  • Niklasson M, Maddalo G, Sramkova Z, Mutlu E, Wee S, Sekyrova P, Schmidt L, Fritz N, Dehnisch I, Kyriatzis G, Krafcikova M, Carson BB, Feenstra JM, Marinescu VD, Segerman A, Haraldsson M, Gustavsson AL, Hammarström LG, Jenmalm Jensen A, Uhrbom L, Altelaar AF, Linnarsson S, Uhlén P, Trantirek L, Vincent CT, Nelander S, Enger PØ, Andäng M. (2017) Membrane-Depolarizing Channel Blockers Induce Selective Glioma Cell Death by Impairing Nutrient Transport and Unfolded Protein/Amino Acid Responses. Cancer Research Accepted [PubMed]

 

2016 – Scientific Publications

 

  • Vlaming H, Molenaar TM, van Welsem T, Poramba-Liyanage DW, Smith DE, Velds A, Hoekman L, Korthout T, Hendriks S, Altelaar AFM, van Leeuwen F. (2016) Direct screening for chromatin status on DNA barcodes in yeast delineates the regulome of H3K79 methylation by Dot1. Elife 5. pii: e18919. [PubMed]
  • Isogai T, van der Kammen R, Bleijerveld OB, Goerdayal SS, Argenzio E, Altelaar AF, Innocenti M. (2016) Quantitative Proteomics Illuminates a Functional Interaction Between mDia2 and the Proteasome. Journal of Proteome Research 15(12):4624-4637. [PubMed]
  • Wu J, de Heus C, Liu Q, Bouchet BP, Noordstra I, Jiang K, Hua S, Martin M, Yang C, Grigoriev I, Katrukha EA, Altelaar AF, Hoogenraad CC, Qi RZ, Klumperman J, Akhmanova A. (2016) Molecular Pathway of Microtubule Organization at the Golgi Apparatus. Developmental Cell 39(1):44-60. [PubMed]
  • Groot Kormelink T, Arkesteijn GJ, van de Lest CH, Geerts WJ, Goerdayal SS, Altelaar MA, Redegeld FA, Nolte-‘t Hoen EN, Wauben MH. (2016) Mast Cell Degranulation Is Accompanied by the Release of a Selective Subset of Extracellular Vesicles That Contain Mast Cell-Specific Proteases. Journal of Immunology pii: 1600614. [PubMed]
  • FC Bach, SAH de Vries, FM Riemers, J Boere, FWM van Heel, M van Doeselaar, SS Goerdayal, PGJ Nikkels, K Benz, LB Creemers, AF Maarten Altelaar, BP Meij, K Ito, MA Tryfonidou (2016) Soluble and pelletable factors in porcine, canine and human notochordal cell-conditioned medium: implications for IVD regeneration European Cells and Materials 32, 163-180. [PubMed]
  • van Herwijnen MJ, Zonneveld MI, Goerdayal S, Nolte-‘t Hoen EN, Garssen J, Stahl B, Altelaar AF, Redegeld FA, Wauben MH. (2016) Comprehensive proteomic analysis of human milk-derived extracellular vesicles unveils a novel functional proteome distinct from other milk components. Molecular & Cellular Proteomics pii: mcp.M116.060426. [PubMed]
  • Zuko A, Oguro-Ando A, Post H, Taggenbrock RL, van Dijk RE, Altelaar AF, Heck AJ, Petrenko AG, van der Zwaag B, Shimoda Y, Pasterkamp RJ, Burbach JP. Association of Cell Adhesion Molecules Contactin-6 and Latrophilin-1 Regulates Neuronal Apoptosis. Frontiers in Molecular Neuroscience 2016 Dec 15;9:143. [PubMed]
  • Bouchet BP, Gough RE, Ammon YC, van de Willige D, Post H, Jacquemet G, Altelaar AM, Heck AJ, Goult BT, Akhmanova A. (2016)  Talin-KANK1 interaction controls the recruitment of cortical microtubule stabilizing complexes to focal adhesions. Elife 5. pii: e18124. [PubMed]
  • Kemper K, Krijgsman O, Kong X, Cornelissen-Steijger P, Shahrabi A, Weeber F, van der Velden DL, Bleijerveld OB, Kuilman T, Kluin RJ, Sun C, Voest EE, Ju YS, Schumacher TN, Altelaar AF, McDermott U, Adams DJ, Blank CU, Haanen JB, Peeper DS. (2016) BRAFV600E Kinase Domain Duplication Identified in Therapy-Refractory Melanoma Patient-Derived Xenografts. Cell Reports 16(1):263-277. [PubMed]
  • Schmidlin T, Garrigues L, Lane CS, Mulder TC, van Doorn S, Post H, de Graaf EL, Lemeer S, Heck AJ, Altelaar AF. (2016) Assessment of SRM, MRM3 and DIA for the targeted analysis of phosphorylation dynamics in non-small cell lung cancer. Proteomics 16(15-16):2193-2205. [PubMed]
  • Guerreiro AC, Penning R, Raaijmakers LM, Axman IM, Heck AJ, Altelaar AF. (2016) Monitoring light/dark association dynamics of multi-protein complexes in cyanobacteria using size exclusion chromatography-based proteomics. Journal of Proteomics 142: 33-44. [PubMed]
  • Parreira JR, Bouraada J, Fitzpatrick MA, Silvestre S, Bernardes da Silva A, Marques da Silva J, Almeida AM, Fevereiro P, Altelaar AF, Araújo SS. (2016) Differential proteomics reveals the hallmarks of seed development in common bean (Phaseolus vulgaris L.). Journal of Proteomics pii: S1874-3919. [PubMed]

 

2015 – Scientific Publications

 

  • Najim Ameziane, et al. (2015) A novel Fanconi anaemia subtype associated with a dominant-negative mutation in RAD51 Nature Communications, 6, 8829. [PubMed]
  • van Beuningen SF, Will L, Harterink M, Chazeau A, van Battum EY, Frias CP, Franker MA, Katrukha EA, Stucchi R, Vocking K, Antunes AT, Slenders L, Doulkeridou S, Sillevis Smitt P, Altelaar AF, Post JA, Akhmanova A, Pasterkamp RJ, Kapitein LC, de Graaff E, Hoogenraad CC. (2015)  TRIM46 Controls Neuronal Polarity and Axon Specification by Driving the Formation of Parallel Microtubule Arrays. Neuron 88(6):1208-1226. [PubMed]
  • Elkon R, Loayza-Puch F, Korkmaz G, Lopes R, van Breugel PC, Bleijerveld OB, Altelaar AFM, Wolf E, Lorenzin F, Eilers M, Agami R. (2015) Myc coordinates transcription and translation to enhance transformation and suppress invasiveness. EMBO Reports 16(12): 1723-1736. [PubMed]
  • Thierry Schmidlin, Arjen J. Boender, Christian K. Frese, Albert J. R. Heck, Roger A. H. Adan, and A. F. Maarten Altelaar (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. [PubMed]
  • Linsey M. Raaijmakers, Piero Giansanti, Patricia A. Possik, Judith Mueller, Daniel S. Peeper, Albert J. R. Heck, and A. F. Maarten Altelaar (2015) PhosphoPath: Visualization of Phosphosite-centric Dynamics in Temporal Molecular Networks. Journal of Proteome Research 14(10):4332-4341. [PubMed]
  • de Graaf, Erik L, Kaplon, Joanna, Mohammed, Shabaz, Vereijken, Lisette A M, Duarte, Daniel P, Redondo-Gallego, Laura, Heck, Albert J R, Peeper, Daniel S & Altelaar, A F Maarten (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. [PubMed]
  • Brunner, Andrea M., Lössl, Philip, Liu, Fan, Huguet, Romain, Mullen, Christopher, Yamashita, Masami, Zabrouskov, Vlad, Makarov, Alexander, Altelaar, A. F Maarten & Heck, Albert J R (2015). Benchmarking multiple fragmentation methods on an orbitrap fusion for top-down phospho-proteoform characterization. Analytical Chemistry 87 (8), 4152-4158. [PubMed]
  • Vogel, Celia J., Smit, Marjon A., Maddalo, Gianluca, Possik, Patricia A., Sparidans, Rolf W., van der Burg, Sjoerd H., Verdegaal, Els M., Heck, Albert J R, Samatar, Ahmed A., Beijnen, Jos H., Altelaar, A. F Maarten & Peeper, Daniel 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. [PubMed]
  • Gray, Andrew N, Egan, Alexander J F, Van’t Veer, Inge L, Verheul, Jolanda, Colavin, Alexandre, Koumoutsi, Alexandra, Biboy, Jacob, Altelaar, A F Maarten, Damen, Mirjam J, Huang, Kerwyn Casey, Simorre, Jean-Pierre, Breukink, Eefjan, den Blaauwen, Tanneke, Typas, Athanasios, Gross, Carol A & Vollmer, Waldemar (07-05-2015). Coordination of peptidoglycan synthesis and outer membrane constriction during Escherichia coli cell division. eLife 4:e07118. [PubMed]
  • Balluff, Benjamin, Frese, Christian K., Maier, Stefan K., Schöne, Cédrik, Kuster, Bernhard, Schmitt, Manfred, Aubele, Michaela, Höfler, Heinz, Deelder, André M., Heck, Albert J R, Hogendoorn, Pancras C W, Morreau, Johannes, Altelaar, A. F Maarten, Walch, Axel & McDonnell, Liam A. (2015). De novo discovery of phenotypic intratumour heterogeneity using imaging mass spectrometry. Journal of Pathology 235 (1), 3-13. [PubMed]
  • Stulemeijer, Iris J E, De Vos, Dirk, Van Harten, Kirsten, Joshi, Onkar K., Blomberg, Olga, Van Welsem, Tibor, Terweij, Marit, Vlaming, Hanneke, De Graaf, Erik L., Altelaar, A. F Maarten, Bakker, Barbara M. & Van Leeuwen, Fred (2015). Dot1 histone methyltransferases share a distributive mechanism but have highly diverged catalytic properties. Scientific Reports 5. 9824. [PubMed]
  • Götzke, Hansjörg, Muheim, Claudio, Altelaar, A.F. Maarten, Heck, Albert J.R., Maddalo, Gianluca & Daley, Daniel O. (01-01-2015). Identification of putative substrates for the periplasmic chaperone YfgM in Escherichia coli using quantitative proteomics. Molecular & Cellular Proteomics 14 (1), 216-226. [PubMed]
  • Jansen, Robert S, Addie, Ruben, Merkx, Remco, Fish, Alexander, Mahakena, Sunny, Bleijerveld, Onno B, Altelaar, Maarten, IJlst, Lodewijk, Wanders, Ronald J, Borst, P & van de Wetering, Koen (2015). N-lactoyl-amino acids are ubiquitous metabolites that originate from CNDP2-mediated reverse proteolysis of lactate and amino acids. Proceedings of the National Academy of Sciences USA 112 (21), 6601-6606. [PubMed]
  • Isogai, Tadamoto, Van Der Kammen, Rob, Goerdayal, Soenita S., Heck, Albert J. R., Altelaar, A. F. Maarten & Innocenti, Metello (01-04-2015). Proteomic analyses uncover a new function and mode of action for mouse homolog of diaphanous 2 (mDia2). Molecular & Cellular Proteomics 14 (4), 1064-1078. [PubMed]
  • Benoit, Isabelle, Zhou, Miaomiao, Duarte, Alexandra Vivas, Downes, Damien J., Todd, Richard B., Kloezen, Wendy, Post, Harm, Heck, Albert J. R., Altelaar, A. F. Maarten & de Vries, Ronald P. (2015). Spatial differentiation of gene expression in Aspergillus niger colony grown for sugar beet pulp utilization. Scientific Reports 5 9824. [PubMed]
  • Patyshakuliyeva, Aleksandrina, Post, Harm, Zhou, Miaomiao, Jurak, Edita, Heck, Albert J R, Hildén, Kristiina S., Kabel, Mirjam A., Mäkelä, Miia R., Altelaar, Maarten AF & De Vries, Ronald P. (2015). Uncovering the abilities of Agaricus bisporus to degrade plant biomass throughout its life cycle. Environmental Microbiology 17 (8), 3098-3109. [PubMed]

 

 

2014 – Scientific Publications

 

  • Smit, Marjon A, Maddalo, Gianluca, Greig, Kylie, Raaijmakers, Linsey M, Possik, Patricia A, van Breukelen, Bas, Cappadona, Salvatore, Heck, Albert Jr, Altelaar, A. F Maarten & Peeper, Daniel S (2014). ROCK1 is a potential combinatorial drug target for BRAF mutant melanoma. Molecular Systems Biology 10 (12), 772. [PubMed]
  • de Graaf, Erik L, Kaplon, Joanna, Zhou, Houjiang, Heck, Albert J R, Peeper, Daniel S & Altelaar, A.F.M. (2014). Phosphoproteome dynamics in onset and maintenance of oncogene-induced senescence. Molecular & Cellular Proteomics 13 (8), 2089-2100. [PubMed]
  • Castano-Cerezo, Sara, Bernal, Vicente, Post, Harm, Fuhrer, Tobias, Cappadona, Salvatore, Sanchez-Diaz, Nerea C., Sauer, Uwe, Heck, Albert J. R., Altelaar, A. F. Maarten & Canovas, Manuel (2014). Protein acetylation affects acetate metabolism, motility and acid stress response in Escherichia coli. Molecular Systems Biology 10, 762. [PubMed]
  • Jiang, Kai, Hua, Shasha, Mohan, Renu, Grigoriev, Ilya, Yau, Kah Wai, Liu, Qingyang, Katrukha, Eugene A, Altelaar, A F Maarten, Heck, Albert J R, Hoogenraad, Casper C & Akhmanova, Anna (10-02-2014). Microtubule minus-end stabilization by polymerization-driven CAMSAP deposition. Developmental Cell 28 (3), 295-309. [PubMed]
  • de Graaf, Erik L, Giansanti, Piero, Altelaar, A F Maarten & Heck, Albert 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. [PubMed]
  • Guerreiro, Ana C L, Benevento, Marco, Lehmann, Robert, van Breukelen, Bas, Post, Harm, Giansanti, Piero, Altelaar, Adrianus, Axmann, Ilka M & Heck, Albert 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. [PubMed]
  • Vlaming, Hanneke, van Welsem, Tibor, de Graaf, Erik L, Ontoso, David, Altelaar, A F Maarten, San-Segundo, Pedro A, Heck, Albert J R & van Leeuwen, Fred (2014). Flexibility in crosstalk between H2B ubiquitination and H3 methylation in vivo. EMBO Reports 15 (10), 1077-84. [PubMed]
  • Klaubauf, Sylvia, Narang, Hari Mander, Post, Harm, Zhou, Miaomiao, Brunner, Kurt, Mach-Aigner, Astrid R, Mach, Robert L, Heck, Albert J R, Altelaar, A F Maarten & de Vries, Ronald 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. [PubMed]

 

2013 – Scientific Publications

 

  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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 4, 1408. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]

 

2012 – Scientific Publications

 

  • 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 USA 109, 407-412. [PubMed]
  • Altelaar, A.F.M. & Heck, A.J.R. (2012). Trends in ultrasensitive proteomics. Current Opinion in Chemical Biology, 16, 206-213. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]

 

2011 – Scientific Publications

 

  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]

 

2010 – Scientific Publications

 

  • 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. Analyst 135, 2643-2652. [PubMed]
  • Altelaar, A.F.M. & Piersma, S.R. (2010).Cellular imaging using matrix-enhanced and metal-assisted SIMS. Methods in Molecular Biology, 656, 197-208. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]

 

2009 – Scientific Publications

 

  • Klerk, L.A., Altelaar, A.F.M., Froesch, M., McDonnell, L.A. & Heeren, R.M.A. (2009). Fast and automated large-area imaging MALDI mass spectrometry in microprobe and microscope mode. International journal of mass spectrometry (285), 19-25.
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • Altelaar, A.F.M. & Heeren, R.M.A. (2009). Tissue analysis with high-resolution imaging mass spectrometry. Methods in molecular biology (492), 295-308. [PubMed]

 

2008 – Scientific Publications

 

  • Broersen, A., Liere, R., Altelaar, A.F.M., Heeren, R.M.A. & McDonnell, L.A. (2008). Automated, Feature-Based Image Alignment for High-Resolution Imaging Mass Spectrometry of Large Biological Samples. Journal of the American Society for Mass Spectrometry 19, 823-832. [PubMed]
  • 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. [PubMed]

2007 – Scientific Publications

 

  • Altelaar AF, Luxembourg SL, McDonnell LA, Piersma SR, Heeren RM. (2007) Imaging mass spectrometry at cellular length scales. Nature Protocols 2(5): 1185-96. [PubMed]
  • Altelaar, A.F.M., Taban, I., McDonnell, L.A., Verhaert, P.D.E.M., de Lange, R.P.J., Adan, R.A.H., Mooi, W.J., Heeren, R.M.A. & Piersma, S.R. (2007). High-resolution MALDI imaging mass spectrometry allows localization of peptide distributions at cellular length scales in pituitary tissue sections. International journal of mass spectrometry 260 (2-3), 203-211.
  • Taban, I., Altelaar, A.F.M., van der Burgt, Y.E.M., McDonnell, L.A. & Heeren, R.M.A. (2007). Imaging of Peptides in the Rat Brain Using MALDI-FTICR Mass Spectrometry. Journal of the American Society for Mass Spectrometry 18, 145-151) (7 p.). [PubMed]
  • Klinkert, I., McDonnell, L.A., Luxembourg, S.L., Altelaar, A.F.M., Amstalden, E.R., Piersma, S.R. & Heeren, R.M.A. (2007). Tools and strategies for visualization of large image datasets in high-resolution imaging mass spectrometry. Review of scientific instruments 78, 053716-1-053716-10. [PubMed]

 

2006 – Scientific Publications

 

  • Altelaar, A.F.M., Klinkert, I., Jalink, K., de Lange, R.P.J., Adan, R.A.H., Heeren, R.M.A. & Piersma, S.R. (2006). Gold-enhanced biomolecular surface imaging of cells and tissue by SIMS and MALDI mass spectrometry. Analytical Chemistry 78 (3), 734-742. [PubMed]
  • Altelaar, A.F.M., van Minnen, J., Heeren, R.M.A. & Piersma, S.R. (2006). The influence of the cholesterol microenvironment in tissue sections on molecular ionization efficiencies and distributions in ToF-SIMS. Applied surface science 252, 6702-6705.
  • Heeren, R.M.A., McDonnell, L.A., Amstalden, E.R., Luxembourg, S.L., Altelaar, A.F.M. & Piersma, S.R. (2006). Why don’t biologists use SIMS? A critical evaluation of imaging MS. Applied surface science 252, 6827-6835.

 

≤ 2005 – Scientific Publications

 

  • Altelaar, A.F.M., van Minnen, J., Jiménez, C.R., Heeren, R.M.A. & Piersma, S.R. (2005). Direct molecular imaging of Lymnaea stagnalis nervous tissue at subcellular spatial resolution by mass spectrometry. Analytical Chemistry 77, 735-741. [PubMed]
  • McDonnell, L.A., Piersma, S.R., Altelaar, A.F.M., Mize, T.H., Luxembourg, S.L., Verhaert, P.D.E.M., van Minnen, J. & Heeren, R.M.A. (2005). Subcellular imaging mass spectrometry of brain tissue. Journal of Mass Spectrometry 40, 160-168.
  • Gimeno RA, Altelaar AFM, Marcé RM, Borrull F. (2002) Determination of polycyclic aromatic hydrocarbons and polycyclic aromatic sulfur heterocycles by high-performance liquid chromatography with fluorescence and atmospheric pressure chemical ionization mass spectrometry detection in seawater and sediment samples. Journal of Chromatography A 958(1-2) 141-8. [PubMed]
  • Seifar RM, Altelaar AFM, Dijkstra RJ, Ariese F, Brinkman UAT, Gooijer C. (2000) Surface-enhanced resonance Raman spectroscopy as an identification tool in column liquid chromatography. Analytical Chemistry 72 5718-5724. [PubMed]

 

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