The goal and philosophy of sample preparation in biological mass spectrometry is to reveal the actual multicomponent molecular structure of a biological specimen that can be assessed by mass spectrometry tools. Unfortunately, sample preparation is often looked at as a necessary but "boring" step which does not warrant any efforts beyond a paragraph or two in a "Methods" section; it is believed not to be conducive to innovation, and does not elicit the enthusiasm of funding agencies. Nevertheless, in recent years, the attention to sample preparation methods has risen considerably, both in Academia and in the life science industry. The aim of this book is to provide the researcher with important sample preparation strategies for a wide variety of analyte molecules, specimens, methods, and biological applications demanding mass spectrometric analysis as the detection end-point. In this volume we have compiled contributions from several laboratories that employ mass spectrometry for biological analysis. With the latest inventions and the introduction of highly sophisticated mass spectrometry equipment, sample preparation has become an extremely important bottleneck of biomedical analysis. This book is structured as a compilation of contributed chapters ranging from step-by-step protocols to research articles and reviews. The main philosophy of this volume is that sample preparation methods have to be optimized and validated for every project, for every sample type and for every downstream analytical technique.

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Introduction: Sample Preparation - Boring but Important! Alexander Lazarev1 and Alexander R. Ivanov Section I. Traditional and improved techniques in sample preparation for proteomics 1. Gel-based and Gel-free Sample Preparation for LC-MS/MS Analysis; Xianyin Lai and Frank A. Witzmann 2. Manipulating the Mass Spectrometric Properties of Peptides through Selective Chemical Modification; David Arnott, Peter S. Liu, Patricia Molina, Lilian Phu, and Wendy N. Sandoval 3. Sample Preparation for 2D Electrophoresis and CE-based Proteomics; Judit M. Nagy, Alexandria Lipka, Fiona Pereira, Nicky Marlin, and Stuart Hassard 4. Filtration as a Sample Preparation Technique Prior to Mass Spectrometry: Selecting the Right Filtration Device; Vivek Joshi and Elena Chernokalskaya 5. Pressure-Assisted Lysis of Mammalian Cell Cultures Prior to Proteomic Analysis; Emily Freeman, Yelena Margolin, and Alexander R. Ivanov 6. Multiplexed Preparation of Biological Samples for Mass Spectrometry using Gel Electrophoresis; Jeremy L. Norris, Alan A. Doucette Section II. Methods for Improved Proteolytic Digestion 7. Development of an On-bead Digestion Procedure for Immunoprecipitated Proteins; Matthew J. Berberich, Jeffrey Kowalak, Anthony Makusky, Brian Martin, Detlef Vullhorst, Andres Buonanno, and Sanford Markey 8. Ultra-Fast Sample Preparation for High-Throughput Proteomics; Daniel Lopez-Ferrer, Kim K. Hixson, Mikhail E. Belov, and Richard D. Smith 9. Exploring the Capabilities of the Protein Identification by Unconventional Sample Preparation Approaches: LC/MALDI/On-target Digestion Approach and High Pressure-assisted In-gel Tryptic Digestion; Melkamu Getie-Kebtie and Michail A. Alterman Section III. Methods for Tissue, Cell, and Organelle Preparation and Analysis 10. Sample Preparation of Formalin-Fixed Paraffin-Embedded (FFPE) Tissue for Proteomic Analyses; Diem Tran, Mark Daniels, Ben Colson, Dikran Aivazian, Antonio Boccia, Ingrid Joseph, Steffan Ho, Steve French, Alex Buko, and Jing Wei 11. Brain Proteomics: Sample Preparation Techniques for the Analysis of Rat Brain Samples using Mass Spectrometry; Yoshinori Masuo, Misato Hirano, Junko Shibato, Hyung Wook Nam, Isabelle Fournier, Meriaux Celine, Maxence Wisztorski, Michel Salzet, Hideaki Soya, Ganesh Kumar Agrawal, and Randeep Rakwal 12. Subcellular Fractionation Using Step-Wise Density Extraction for Mass Spectrometry Analysis; WenKui Lan, Marc J. Horn, Fumihiko Urano, Andre Kopoyan, and Sun W. Tam Section IV. 2D Gel-based Proteomics 13. Two-dimensional Polyacrylamide Gel Electrophoresis; Aisling A. Robinson, Ciara A. McManus, and Michael J. Dunn 14. Quantitative Intact Proteomic Strategies to Detect Changes in Protein Modification and Genomic Variation; David B. Friedman 15. Two-dimensional Non-denaturing Gel Electrophoresis for Characterization of Proteins in Multi-molecular Particles by Mass Spectrometry; Susan T. Weintraub and Philip Serwer Section V. Sample Preparation and Analysis Techniques for Biological Fluids and Biomarker Discovery 16. Pre-Analytical Variables for Plasma and Serum Proteome Analyses; Craig A. Gelfand and Gilbert S. Omenn 17. Biomarker Discovery in Biological Fluids; Wasfi Alrawashdeh and Tatjana Crnogorac-Jurcevic 18. Sample Handling of Body Fluids for Proteomics; Joao A. Paulo, Ali R. Vaezzadeh, Darwin L. Conwell, Richard S. Lee, and Hanno Steen Section VI. Sample Preparation Methods in Plant Proteomics 19. Quantitative Plant Proteomics Using Hydroponic Isotope Labeling of Entire Plants (HILEP); Laurence V. Bindschedler, Celia J. Smith and Rainer Cramer 20. Efficient Strategies for Analysis of Low Abundance Proteins in Plant Proteomics; Olga A. Koroleva, Laurence V. Bindschedler 21. Plant Plasma Membrane Proteomics: Challenges and Possibilities; Anders Laurell Blom Moller, Katja Witzel, Annelies Vertommen, Vibeke Barkholt, Birte Svensson, Sebastien Carpentier, Hans-Peter Mock, and ...