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A Compendium of cutting-edge protocols for quantitative proteomics, and presents the most significant methods used in the field today. The focus on mass spectrometry (MS) is integral, as MS has, and will continue to be, an essential tool in proteomics for studying complex biological systems and human diseases. This volume, written and compiled by leading quantitative proteomic experts, is an indispensable resource in the search for novel biomarkers. Quantitative Proteomics by Mass Spectrometry presents several innovative MS quantitative procedures, including a variety of methods for introducing isotopic labels and quantifying post-translational modifications. Some of these methods include growing an organism in isotope-enriched media, performing trypsin proteolysis in the presence of 18O-water, reacting protein samples with isotopically labeled reagents, quantifying relative amount of proteins without the use of any isotopic labels. Attention is also given to state-of-the-art techniques for the characterization of the phosphoproteome and tandem MS for detection of inborn errors of metabolism. Specifically, the procedure for determinations of enzymatic activity could be used for large-scale screening of newborns. The protocols in this volume expand both the breadth and depth of readily available methods for quantitative proteomic researchers using MS.
Quantitative Proteomics by Mass Spectrometry Editor Salvatore Sechi Table of Contents 1. Preface by Salvatore Sechi: An Overview of Quantitative Proteomics by Mass Spectrometry. 2. Illarion V. Turko and Salvatore Sechi: Acrylamide - A Cysteine Alkylating Reagent for Quantitative Proteomics. 3. Jeffrey A. Ranish, Marjorie Brand and Ruedi Aebersold: Using stable isotope tagging and MS to characterize protein complexes and to detect changes in their composition. 4. Shao-En Ong and Matthias Mann: Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) for Quantitative Proteomics. 5. Toshitaka Sato, Yasushi Ishihama, Yoshiya Oda: Quantitative Proteomics of Mouse Brain, and Specific Protein-Interaction Studies using Stable Isotope Labeling. 6. Scott A. Gerber, Arminja N. Kettenbach, John Rush and Steven P. Gygi: The Absolute Quantification Strategy: Application to Phosphorylation Profiling of Human Separase Serine 1126. 7. Sushmita Mimi Roy and Christopher H. Becker: Quantification of proteins and metabolites by mass spectrometry without isotopic labeling. 8. Tao Liu, Wei-Jun Qian, David G. Camp, II, and Richard D. Smith: The Use of a Quantitative Cysteinyl-peptide Enrichment Technology for High-Throughput Quantitative Proteomics. 9. Fred E. Regnier: An isotope coding strategy for proteomics involving both amine and carboxyl group labeling 10. Catherine Fenselau and Xudong Yao: Proteolytic Labeling with 18O for Comparative Proteomics Studies: preparation of 18O-labeled peptides and the 18O/16O peptide mixture 11. Franti_ek Ture_ek, C. Ronald Scott, and Michael H. Gelb: Tandem mass spectrometry in the detection of inborn errors of metabolism and newborn screening. 12. Yu Lu, Patricia Bottari, Ruedi Aebersold, Franti_ek Ture_ek, and Michael H. Gelb: Absolute quantitation of proteins in complex mixtures by the Visible Isotope-Coded Affinity Tags method. 13. Michael J. MacCoss and Christine C. Wu.: Computational Analysis of Quantitative Proteomics Data using Stable Isotope Labeling. 14. Christine C. Wu and Michael J. MacCoss: Quantitative Proteomic Analysis of Mammalian Organisms Using Metabolically Labeled Tissues. 15. Zhang, Y., Wolf-Yadlin A., White F.M.: Quantitative Proteomic Analysis of Phosphotyrosine-Mediated Cellular Signaling Networks.