Cover Page The handle http://hdl.handle.net/1887/25784 holds various files of this Leiden University dissertation. Author: Nicolardi, Simone Title: Development of ultrahigh resolution FTICR mass spectrometry methods for clinical proteomics Issue Date: 2014-05-20 Development of ultrahigh resolution FTICR mass spectrometry methods for clinical proteomics Simone Nicolardi ISBN: 978-94-6182-435-6 The research described in this thesis was financially supported by the Center for Translational Molecular Medicine (CTMM). Printing: OffPage, Amsterdam Copyright © 2014 by S. Nicolardi. All rights reserved. No part of this book may be reproduced, stored in a retrieval system or transmitted in any form or by any means, without prior permission of the author. Development of ultrahigh resolution FTICR mass spectrometry methods for clinical proteomics proefschrift ter verkrijging van de graad van Doctor aan de Universiteit Leiden, op gezag van Rector Magnificus prof.mr. C.J.J.M. Stolker, volgens besluit van het College voor Promoties te verdedigen op dinsdag 20 mei 2014, klokke 15.00 uur door Simone Nicolardi geboren op 28 juni 1981, te Gagliano del Capo, Italië PROMOTIECOMMISSIE Promotores: Prof.dr. A.M. Deelder Prof.dr. R.A.E.M. Tollenaar Co-promotor: Dr. Y.E.M. van der Burgt Overige Leden: Prof.dr. G.A. Meijer Dept.of Pathology, VU University Medical Center (VUMC), The Netherlands Prof.dr. R. Cramer Dept. of Chemistry, University of Reading, United Kingdom Prof.dr. H.J. Tanke Prof.dr. F. Koning Prof.dr. A. van der Laarse TABLE OF CONTENTS Introduction 7 Chapter 1 Standardized and automated solid-phase extraction procedures for high-throughput proteomics of body fluids 29 Chapter 2 Precision profiling and identification of human serum peptides using Fourier transform ion cyclotron resonance mass spectrometry 51 Chapter 3 Quality control based on isotopic distributions for high-throughput MALDI-TOF and MALDI-FTICR serum peptide profiling 69 Chapter 4 Identification of human serum peptides in Fourier transform ion cyclotron resonance precision profiles 95 Chapter 5 Mapping O-glycosylation of apolipoprotein C-III in MALDIFT-ICR protein profiles 109 Chapter 6 Identification of new Apolipoprotein-CIII glycoforms with ultrahigh resolution MALDI-FTICR mass spectrometry of human sera 131 Chapter 7 Serum biomarker signatures of pancreatic cancer using MALDI-FTICR peptide and protein profiles 161 General Discussion 191 Summary 205 Samenvatting 210 Acknowledgements 214 Curriculum vitae 216 List of publications 217