Recent success stories demonstrated that the combination of subcellular prefractionation methods with proteomic analysis is a very potent approach to simplify complex protein extracts from cells or tissues and to detect low abundance proteins. It also made clear that sophisticated strategies encompassing sample preparation, analytics and validation steps were required to fully exploit the potential of subcellular proteomics.
This volume summarizes the new developments that made subcellular proteomics a rapidly expanding area. It examines the different levels of subcellular organization and their specific methodologies. In addition, the book includes coverage of systems biology that deals with the integration of the data derived from these different levels to produce a synthetic description of the cell as a system. It also includes a survey of the most advanced technical developments in proteomics, which covers single cell analysis methods, molecular imaging and LC-MALDI. Written by a panel of leading experts in the field, this book represents an unprecedented attempt to reflect state-of-the-art methodology and also to convey both the mode of thinking and the hype of this discipline.
Table of contents
Introduction
Section 1: Membrane proteomics
Keynotes on membrane proteomics
Thierry Rabilloud
Two-dimensional BAC/SDS-PAGE for membrane proteomics
René P. Zahedi, Jan Moebius and Albert Sickmann
Microparticles: a new tool for plasma membrane sub-cellular proteomic
Laurent Miguet, Sarah Sanglier, Christine Schaeffer, Noelle Potier, Laurent Mauvieux and Alain Van Dorsselaer.
Lipid raft proteomics: more than just detergent-resistant membranes
Leonard J. Foster and Queenie W. T. Chan
Section 2: Organelle subproteomes
Organelle Proteome Variation Among Different Cell Types: Lessons from Nuclear Membrane Proteins
Deirdre M. Kavanagh, William E. Powell, Poonam Malik, Vassiliki Lazou and Eric C. Schirmer
Synaptosome Proteomics
Fengju Bai and Frank A. Witzmann
Proteomic analysis of secreted exosomes
Christine Olver and Michel Vidal
Section 3: Characterization of supramolecular protein complexes
From Protein-Protein Complexes to Interactomics
Vincent Collura and Guillaume Boissy
Supramolecular signalling complexes in the nervous system
Mark O. Collins and Seth G.N. Grant
Protein networks and complexes in photoreceptor cilia
Ronald Roepman and Uwe Wolfrum
Section 4: Subcellular systems biology
Systems Biology and the Reconstruction of the Cell: from molecular components to integral function
Frank J. Bruggeman, Sergio Rossell, Karen van Eunen, Jildau Bouwman, Hans V. Westerhoff and Barbara Bakker
Automated, Systematic Determination of Protein Subcellular Location using Fluorescence Microscopy
Elvira García Osuna and Robert F. Murphy
Systems biology of the Endoplasmic Reticulum stress response
Marie-Elaine Caruso and Eric Chevet
Section 5: Emerging technologies in proteomics
Systems Nanobiology: From Quantitative Single Molecule Biophysics to Microfluidic-Based Single Cell Analysis
Joerg Martini, Wibke Hellmich, Dominik Greif, Anke Becker, Thomas Merkle, Robert Ros, Alexandra Ros, Katja Toensing and Dario Anselmetti
Biophotonics applied to proteomics
Michel Faupel, Débora Bonenfant, Patrick Schindler, Eric Bertrand Dieter Mueller, Markus Stoeckli, Francis Bitsch, Tatiana Rohner, Dieter Staab and Jan Van Oostrum
Differential epitope identification of antibodies against intracellular domains of Alzheimer`s amyloid precursor protein using high resolution affinity- mass spectrometry
Xiaodan Tian, Madalina Maftei, Markus Kohlmann, Bernadette Allinquant and Michael Przybylski
LC-MALDI MS and MS/MS An Efficient Tool in Proteome Analysis
Dieter R. Mueller, Hans Voshol, Annick Waldt, Brigitte Wiedmann and Jan van Oostrum