Cover Page The handle http://hdl.handle.net/1887/28508 holds various files of this Leiden University dissertation. Author: Peironcely Miguel, Julio Eduardo Title: Automated de novo metabolite identification with mass spectrometry and cheminformatics Issue Date: 2014-09-03 Acknowledgements 181 Acknowledgements There are many persons have helped me to finish this thesis, and it is a nice challenge to properly thank all of them. This journey started with Eelke, Andreas, Michael and Prof. Ijzerman. They offered me the most exciting research project a master student could dream of and ignited my love for research and motivated me to go for a PhD. During this PhD I learned a lot from my (abundant) PhD supervisors. They turned me into a better scientist. I appreciate very much that they stayed patient when facing my temperament. With their optimism and their continuous questions they helped me a lot. They opened my eyes that a PhD student should create something new and that that is going to be tough. I would like to thank the students I was lucky to supervise, Remco, Bart and Anja. You brought new insights in my research and helped me to be more accountable. I only wish I could have offered you longer projects. My special thanks to the colleagues that contributed with their lab work: Piotr, Richard, Marco and Justin. Without you acquiring MSn trees I would have had nothing to test my tools with. Michael thanks for enlightening me computationally and doing it with a smile and for the updates in the app world. I would also like to thank Loes and Anneke for supporting me in all a PhD student needs. Special thanks to the ABS/NMC crew for all support and discussions during coffee breaks. My gratitude goes all the way to 182 Acknowledgements Evry, France, where Pablo and Davide welcomed me every time I was visiting them. Davide, thanks for teaching me how to cook proper risotto and for offering a temporary home when necessary. If there is a person that deserves credit for a lot of this thesis is Miquel. He helped me scientifically and personally during four years. Moltes gracies mestre, ho hem aconseguit!! Thanks to my dearest friends Alvaro, Laura and Juan Carlos, no hay dia que no os eche de menos, gambiteros. My gratitude goes also to Jordi and Lisa for keeping my social life alive … i pels sopars vegetarians per llepar-‐se’n els dits. Special thanks go to my daily support groups where I can vent my frustrations, La Tertulia and Club M, who needs a psychologist with such great friends? Long time ago, after my first BSc year I was doubting whether a university study was the right thing for me. Now I am allowed to defend my PhD thesis. This transformation has only been possible with the encouragement and good values my parents provided me: gràcies papa, gracias mama, os quiero. And above everybody, there is Lin. What a ride these years have been. I would not have achieved this without you. You offered me your patience, sweetness and understanding day in and day out. Esta tesis es para ti, Gatita. 183 184 Curriculum vitae 185 Curriculum vitae Julio Eduardo Peironcely Miguel was born on 9 December 1982 in Barcelona, Catalonia, Spain. He completed his BSc in Computer Science in 2006 at Universitat Autonoma de Barcelona. In September 2006 he joined the MSc Bioinformatics offered jointly by Leiden and TU Delft universities. During his studies, he developed an interest in research using and developing software for life sciences. He started with the data integration of different microarray experiments, under the supervision of Dr. F. Verbeek. He continued between January and September 2008, with a research project between the Medicinal Chemistry group (supervisors Dr. A. Bender and Dr. E. vd Horst) and the Leiden Institute For Advanced Computer Science (LIACS) (supervisor Dr. M. Emerich). In this project he devised a new way to measure the similarity of GPCR receptors according to their sequence similarity and their ligand similarity. From October 2008 till December 2012 he performed the work presented in this thesis as PhD student in Analytical Biosciences at Leiden University (supervisor Prof. Dr. T. Hankemeier and Dr. T. Reijmers), TNO Quality of Life (supervisors Dr. L. Coulier and Dr. I. Bobbeldijk-‐Pastorova) and the Institute Of Systems and Synthetic Biology at Evry University (supervisor Prof. Dr. J-‐L. Faulon). During his PhD, Julio was appointed visiting scientist at the Institute Of Applied Mathematics (IPAM) at the University of California Los Angeles (UCLA). Currently Julio works as a data scientist in industry where he continues to use his computational research skills and ingenuity to solve new types of challenges. 186 Publications 187 Publications 1. Peironcely JE, Reijmers T, Coulier L, Bender A, Hankemeier T: Understanding and Classifying Metabolite Space and Metabolite-‐Likeness. PLoS ONE 2011, 6:e28966. 2. Peironcely JE, Rojas-‐Cherto M, Fichera D, Reijmers T, Coulier L, Faulon J-‐L, Hankemeier T: OMG: open molecule generator. Journal of Cheminformatics 2012, 4:21. 3. Peironcely JE, Rojas-‐Cherto M, Tas A, Vreeken R, Reijmers T, Coulier L, Hankemeier T: An Automated Pipeline For De Novo Metabolite Identification Using Mass Spectrometry-‐Based Metabolomics. Analytical Chemistry 2013, 7:3576–3583. 4. Peironcely JE*, Jaghoori MM*, Tas A, Reijmers T, Coulier L, Faulon J-‐L, Hankemeier T: De Novo Identification of Metabolites With Open Molecule Generator For Metabolomics. In preparation Not part of this thesis 5. Doddareddy MR, Westen GJP Van, Horst E Van Der, Peironcely JE, Ijzerman AP, Emmerich M, Jenkins JL, Bender A: Chemogenomics : Looking at Biology through the Lens of Chemistry. Analysis 2009. 6. Van der Horst E*, Peironcely JE*, Ijzerman AP, Beukers MW, Lane JR, Van Vlijmen HWT, Emmerich MTM, Okuno Y, Bender A: A novel chemogenomics analysis of G protein-‐coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-‐orphanization. BMC bioinformatics 2010, 11:316. 188 Publications 7. Horst E Van Der, Peironcely JE, Westen GJP Van, Hoven OO Van Den, Galloway WRJD, Spring DR, Wegner JK, Vlijmen HWT Van, Ijzerman AP, Overington JP, Bender A: Chemogenomics Approaches for Receptor Deorphanization and Extensions of the Chemogenomics Concept to Phenotypic Space. Curr. Top. Med. Chem. 2011, 44. 8. Rojas-‐Chertó M, Peironcely JE, Kasper PT, Van der Hooft JJJ, De Vos RCH, Vreeken R, Hankemeier T, Reijmers T: Metabolite Identification Using Automated Comparison of High-‐Resolution Multistage Mass Spectral Trees. Analytical Chemistry 2012, 84:5524–5534. 9. Rojas-‐Chertó M, Van Vliet M, Peironcely JE, Van Doorn R, Kooyman M, Beek T Te, Van Driel M a, Hankemeier T, Reijmers T: MetiTree: a web application to organize and process high resolution multi-‐stage mass spectrometry metabolomics data. Bioinformatics 2012, 28:2707–2709. 10. Kirchmair J, Howlett A, Peironcely JE, Murrell DS, Williamson MJ, Adams SE, Hankemeier T, Van Buren L, Duchateau G, Klaffke W, Glen RC: How Do Metabolites Differ from Their Parent Molecules and How Are They Excreted? Journal of Chemical Information and Modeling 2013, 53:354–367. 11. Jaghoori MM, Jongmans S-‐STQ, De Boer F, Peironcely JE, Faulon J-‐L, Reijmers T, Hankemeier T: PMG: Multi-‐core Metabolite Identification. Electronic Notes in Theoretical Computer Science 2013, 299:53–60. *Authors contributed equally 189
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