Proteomic Profiling and Analytical Chemistry

Dr. Pawel Ciborowski obtained an MS in Biochemistry from Warsaw University and a PhD in Bacteriology/Biochemistry in 1983 from the National Institute of Hygiene in Warsaw. After spending two years as the Alexander von Humboldt Fellow at the University of Cologne and two years as Visiting Scientist at the University of Lund, he came to the University of Pittsburgh. Since 2003, he has been a faculty member at the University of Nebraska Medical Center where he conducts his own research and directs the Mass Spectrometry and Proteomics Core Facility and teaches courses in biochemistry, mass spectrometry, and proteomics. He is the author of over 70 papers and reviews, as well as several contributions to books and textbooks. His research is focused on the correlation of structure and function of proteins, their receptors and the impact of posttranslational modifications on their functions in understanding molecular mechanisms of pathological processes and applications of this information in designing new strategies for disease prevention, early diagnosis, and control. Using state-of-the-art techniques in proteomics, he is investigating the structure and function of proteins which are involved in (i) response to changes in cell's environment, (ii) response to stimuli such as tissue injury, infection, drug treatment, and (iii) during malignant transformation. Dr. Jerzy Silberring obtained a PhD in Chemistry in 1978 at Jagiellonian University, Kraków, Poland. He received a Docent of Biochemistry title at the University of Uppsala in 1991, and became a full professor of biochemistry at the Jagiellonian University in 2001. He spent 10 years at the Uppsala University and Karolinska Institute in Stockholm. He is the author of over 200 papers and reviews mainly on proteolytic enzymes, neuropeptides, neurobiology of pain and drug dependence, proteomics, and mass spectrometry. His investigations have contributed to our understanding of the regulation of neuropeptides and their fragments, discovery of novel peptides, and applications of mass spectrometry. He teaches biochemistry, neurobiology of behavior, and drug dependence at the AGH University of Science and Technology, Jagiellonian University, and the Centre of Polymer and Carbon Materials, Polish Academy of Sciences.

• Preface1. IntroductionJerzy Silberring and Pawel Ciborowski2. BiomoleculesAriel Burns, Pawel Olszowy and Pawel Ciborowski3. General Strategies for Proteomic Sample PreparationPiotr Suder, Peter Novak, Vladimir Havlicek and Anna Bodzon-Kulakowska4. Protein Extraction and PrecipitationPetr Novak and Vladimir Havlicek5. Online and Offline Sample FractionationMarek Smoluch, Przemyslaw Mielczarek, Anna Drabik and Jerzy Silberring6. Immunoaffinity Depletion of High-Abundant Proteins for Proteomic Sample Preparation                               Jayme Wiederin and Pawel Ciborowski7. Gel Electrophoresis Anna Drabik, Anna Bodzon-Kulakowska and Jerzy Silberring8. Quantitative Measurements in Proteomics: Mass SpectrometryAnna Drabik and Jerzy Silberring9. SWATH-MS: Data Acquisition and AnalysisKristin Frederick and Pawel Ciborowski10. Top-Down ProteomicsCory Boone and Jiri Adamec11. Proteomic Database Search and Analytical Quantification for Mass SpectrometryMelinda Wojtkiewicz, Jayme Wiederin and Pawel Ciborowski12. Design and Statistical Analysis of Mass-Spectrometry-Based Quantitative Proteomics DataFang Yu, Fang Qiu and Jane Meza13: Principles of Analytical ValidationJo-Ellyn McMillan14.Validation in Proteomics and Regulatory AffairsJerzy Silberring, Melinda Wojtkiewicz and Pawel Ciborowski