Proteomic Profiling and Analytical Chemistry: The Crossroads, Second Edition helps scientists without a strong background in analytical chemistry to understand principles of the multistep proteomic experiment necessary for its successful completion. It also helps researchers who do have an analytical chemistry background to break into the proteomics field. Highlighting points of junction between proteomics and analytical chemistry, this resource links experimental design with analytical measurements, data analysis, and quality control. This targeted point of view will help both biologists and chemists to better understand all components of a complex proteomic study.
The book provides detailed coverage of experimental aspects such as sample preparation, protein extraction and precipitation, gel electrophoresis, microarrays, dynamics of fluorescent dyes, and more. The key feature of this book is a direct link between multistep proteomic strategy and quality control routinely applied in analytical chemistry. This second edition features a new chapter on SWATH-MS, substantial updates to all chapters, including proteomic database search and analytical quantification, expanded discussion of post-hoc statistical tests, and additional content on validation in proteomics.
- Covers the analytical consequences of protein and peptide modifications that may have a profound effect on how and what researchers actually measure
- Includes practical examples illustrating the importance of problems in quantitation and validation of biomarkers
- Helps in designing and executing proteomic experiments with sound analytics
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1. IntroductionJerzy Silberring and Pawel Ciborowski
2. BiomoleculesAriel Burns, Pawel Olszowy and Pawel Ciborowski
3. General Strategies for Proteomic Sample PreparationPiotr Suder, Peter Novak, Vladimir Havlicek and Anna Bodzon-Kulakowska
4. Protein Extraction and PrecipitationPetr Novak and Vladimir Havlicek
5. Online and Offline Sample FractionationMarek Smoluch, Przemyslaw Mielczarek, Anna Drabik and Jerzy Silberring
6. Immunoaffinity Depletion of High-Abundant Proteins for Proteomic Sample PreparationJayme Wiederin and Pawel Ciborowski
7. Gel ElectrophoresisAnna Drabik, Anna Bodzon-Kulakowska and Jerzy Silberring
8. Quantitative Measurements in Proteomics: Mass SpectrometryAnna Drabik and Jerzy Silberring
9. SWATH-MS: Data Acquisition and AnalysisKristin Frederick and Pawel Ciborowski
10. Top-Down ProteomicsCory Boone and Jiri Adamec
11. Proteomic Database Search and Analytical Quantification for Mass SpectrometryMelinda Wojtkiewicz, Jayme Wiederin and Pawel Ciborowski
12. Design and Statistical Analysis of Mass-Spectrometry-Based Quantitative Proteomics DataFang Yu, Fang Qiu and Jane Meza
13: Principles of Analytical ValidationJo-Ellyn McMillan
14.Validation in Proteomics and Regulatory AffairsJerzy Silberring, Melinda Wojtkiewicz and Pawel Ciborowski
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.