The membranes surrounding cells and organelles constitute their interface with the local environment. The functions of membrane proteins include cell/cell and cell/extracellular matrix recognition, the reception and transduction of extracellular signals, and the tra- port of proteins, solutes and water molecules. Abnormal membrane protein expression has profound biological effects and may, for example, underlie phenotypic and functional differences between normal and tumour cells. Moreover the accessibility, particularly of plasma proteins traversing the plasma membrane of cells, makes them of particular ut- ity to the therapeutic intervention in disease. Indeed, it is estimated that of all currently licensed pharmaceuticals, approximately 70% target proteins resident in the plasma m- brane. In theory, unbiased technologies such as proteomics have the power to de?ne 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. However, although about 25% of open reading frames in fully sequenced genomes are estimated to encode integral membrane proteins, global analysis of membrane protein expression has proved problematic. Membrane protein analysis poses unique challenges at the level of extraction, solubilization, and separation in particular, and to a lesser extent of identi?cation and quantitation. These challenges have, however, fostered creativity, in- vation, and technical advances, many of which are brought together in Membrane P- teomics.

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 Mitochondrial 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 Mitochondria 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. Protocol to Enrich and Analyze Plasma Membrane Proteins Jacek R. Wisniewski 10. Proteomic Analysis of the Lymphocyte Plasma Membrane Using Cell Surface Biotinylation 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 21. Liquid Chromatography MALDI MS/MS for Membrane Proteome Analysis Nan Wang, Bryce Young, and Liang Li 22. Cysteinyl-Tagging of Integral Membrane Proteins for Proteomic Analysis Using Liquid Chromatography-Tandem ...