With the great cellular and therapeutic importance of plasma membrane proteins, unbiased technologies such as proteomics become even more vital as they have the power to define patterns of membrane protein expression characteristic of distinct states of cellular development, differentiation or disease, and thereby identify novel markers of, or targets for intervention in, disease. In Membrane Proteomics: Methods and Prools, leading experts in the field compile a laboratory bench resource which provides a comprehensive toolkit of proven methods. The volume delves into various modifications to standard two-dimensional gel electrophoresis prools as well as liquid chromatographic methods, prools for the enrichment of diverse classes of plasma membrane proteins, in silico approaches, and cutting-edge techniques for quantitative membrane protein profiling. Written in the highly successful Methods in Molecular Biology™ series format, chapters include brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory prools, and notes on troubleshooting and avoiding known pitfalls.
Comprehensive and easy-to-use, Membrane Proteomics: Methods and Prools is an ideal guide for investigators wishing to apply state of the art membrane proteomic methodologies in their own research programs.
Table of Contents
Section I: In silico Methods for Prediction of Membrane Protein Hydrophobicity and Topology 1. Online Tools for Predicting Integral Membrane Proteins Henry Bigelow and Burkhard Rost 2. In silico Identification of Novel G Protein Coupled Receptors Matthew N. Davies and Darren R. Flower 3. Transcriptome-Based Identification of Candidate Membrane Proteins Edward J. Evans, Lawrence Hene, Mai Vuong, S. Hussain I. Abidi, and Simon J. Davis Section II: Extraction and Purification of Membrane Proteins Subsection 1: Plant Membrane Proteins 4. Separation of Thylakoid Membrane Proteins by Sucrose Ultracentrifugation Gradient or Blue Native-SDS-PAGE Two Dimensional Electrophoresis Gian Maria D’Amici, Christian G. Huber, and Lello Zolla Subsection 2: Prokaryotic Membrane Proteins 5. Extraction of Yeast Mihondrial Membrane Proteins by Solubilization and Detergent/Polymer Aqueous Two-Phase Partitioning Henrik Everberg, Niklas Gustavsson, and Folke Tjerneld 6. 16-BAC/SDS-PAGE Analysis of Membrane Proteins of Yeast Mihondria Purified by Free Flow Electrophoresis Ralf J. Braun, Norbert Kinkl, Hans Zischka, and Marius Ueffing Subsection 3: Mammalian Membrane Proteins 7. Sequential Detergent Extraction Prior to Mass Spectrometry Analysis Fiona M. McCarthy, Amanda M. Cooksey, and Shane C. Burgess 8. Enrichment of Brain Plasma Membranes by Affinity Two-Phase Partitioning Jens Schindler and Hans Gerd Nothwang 9. Prool to Enrich and Analyze Plasma Membrane Proteins Jacek R. Wisniewski 10. Proteomic Analysis of the Lymphocyte Plasma Membrane Using Cell SurfaceBiotinylation and Solution-Phase Iso-Electric Focusing Matthew J. Peirce, Andrew P. Cope, and Robin Wait 11. Identification of Target Membrane Proteins as Detected by Phage Antibodies Cecile A.W. Geuijen, Arjen Q. Bakker, and John de Kruif 12. Membrane Protease Degradomics: Proteomic Identification and Quantification of Cell Surface Protease Substrates Georgina S. Butler, Richard A. Dean, Derek Smith, and Christopher M. Overall 13. Purification of Basolateral Integral Membrane Proteins by Cationic Colloidal Silica-Based Apical Membrane Subtraction Robert J.A. Goode and Richard J. Simpson 14. Moving Closer to the Lipid Raft Proteome Using Quantitative Proteomics Leonard J. Foster 15. Use of Sequential Chemical Extractions to Purify Nuclear Membrane Proteins for Proteomics Identification Nadia Korfali, Elizabeth A.L. Fairley, Selene K. Swanson, Laurence Florens, and Eric C. Schirmer 16. Isolation of Extracellular Membranous Vesicles for Proteomic Analysis Rommel A. Mathias, Justin W. Lim, Hong Ji, and Richard J. Simpson Section III: Separation of Membrane Proteins 17. Enrichment of Human Platelet Membranes for Proteomic Analysis David W. Greening, Kristen M. Glenister, Rosemary L. Sparrow, and Richard J. Simpson 18. Detergents and Chaotropes for Protein Solubilization before Two-Dimensional Electrophoresis Thierry Rabilloud 19. Two-Dimensional Separation of Membrane Proteins by 16-BAC-SDS-PAGE Hans Gerd Nothwang and Jens Schindler Section IV: Identification and Quantification of Membrane Proteins 20. MudPIT Analysis: Application to Human Heart Tissue Kelli G. Kline and Christine C. Wu