Functional proteomics : methods and protocols

A brief summary of the different types of mass spectrometers used in proteomics / Christine Schaeffer-Reiss -- Experimental setups and considerations to study microbial interactions / Petter Melin -- Plant proteomics / Eric Sarnighausen and Ralf Reski -- Methods for human CD8+ T lymphocyte proteome analysis / Lynne Thadikkaran ... [et al.] -- Label-free proteomics of serum / Natalia Govorukhina, Peter Horvatovich, and Rainer Bischoff -- Flow cytometric analysis of cell membrane microparticles / Monique P. Gelderman and Jan Simak -- Exosomes / Joost P.J.J. Hegmans, Peter J. Gerber, and Bart N. Lambrecht -- Toward a full characterization of the human 20S proteasome subunits and their isoforms by a combination of proteomic approaches / Sandrine Uttenweiler-Joseph ... [et al.] -- Free-flow electrophoresis of the human urinary proteome / Mikkel Nissum and Robert Wildgruber -- Versatile screening for binary protein-protein interactions by yeast two-hybrid mating / Stef J.F. Letteboer and Ronald Roepman -- Native fractionation : isolation of native membrane-bound protein complexes from porcine rod outer segments using isopycnic density gradient centrifugation / Magdalena Swiatek-de Lange, Bernd Müller, and Marius Ueffing -- Mapping the signaling pathways by functional interaction proteomics / Alex von Kriegsheim, Christian Preisinger, and Walter Kolch -- Selection of recombinant antibodies by eukaryotic ribosome display / Mingyue He and Michael J. Taussig -- Production of protein arrays by cell-free systems / Mingyue He and Michael J. Taussig -- Nondenaturing mass spectrometry to study noncovalent protein/protein and protein/ligand complexes : technical aspects and application to the determination of binding stoichiometries / Sarah Sanglier ... [et al.]. Protein processing characterized by a gel-free proteomics approach / Petra Van Damme ... [et al.] -- Identification and characterization of N-glycosylated proteins using proteomics / David S. Selby ... [et al.] -- Data standards and controlled vocabularies for proteomics / Lennart Martens, Luisa Montecchi Palazzi, and Henning Hermjakob -- The PRIDE proteomics identifications database : data submission, query, and dataset comparison / Philip Jones and Richard Côté -- Searching the protein interaction space through the MINT database / Andrew Chatr-aryamontri ... [et al.] -- PepSeeker : mining information from proteomic data / Jennifer A. Siepen, Julian N. Selley, and Simon J. Hubbard -- Toward high-throughput and reliable peptide identification via MS/MS spectra / Jian Liu -- MassSorter : peptide mass fingerprinting data analysis / Ingvar Eidhammer, Harald Barsnes and Svein-Ole Mikalsen -- Database similarity searches / Frédéric Plewniak -- Protein multiple sequence alignment / Chuong B. Do and Kazutaka Katoh -- Discovering biomedical knowledge from the literature / Jasmin Šaríc, Henriette Engelken, and Uwe Reyle -- Protein subcellular localization prediction using artificial intelligence technology / Rajesh Nair and Burkhard Rost -- Protein functional annotation by homology / Raja Mazumder, Sona Vasudevan, and Anastasia N. Nikolskaya -- Designability and disease / Philip Wong and Dmitrij Frishman -- Prism : protein-protein interaction prediction by structural matching / Ozlem Keskin, Ruth Nussinov, and Attila Gursoy -- Prediction of protein interaction based on similarity of phylogenetic trees / Florencio Pazos ... [et al.] -- Large multiprotein structures modeling and simulation : the need for mesoscopic models / Antoine Coulon, Guillaume Beslon, and Olivier Gandrillon -- Dynamic pathway modeling of signal transduction networks : a domain-oriented approach / Holger Conzelmann and Ernst-Dieter Gilles