Functional Proteomics

by Thompson, Julie D.; Schaeffer-reiss, Christine; Ueffing, Marius

• ISBN13: 9781617378607
• ISBN10: 1617378607
• Edition: Reprint
• Format: Paperback
• Copyright: 2010-12-16
• Publisher: Humana Pr Inc

Summary

As the emerging field of proteomics continues to expand at an extremely rapid rate, the relative quantification of proteins, targeted by their function, becomes its greatest challenge. Complex analytical strategies have been designed that allow comparative analysis of large proteomes, as well as in depth detection of the core proteome or the interaction network of a given protein of interest. In Functional Proteomics: Methods and Protocols, expert researchers describe the latest protocols being developed to address the problems encountered in high-throughput proteomics projects, with emphasis on the factors governing the technical choices for given applications. The case studies within the volume focus on the following three crucial aspects of the experimental design: 1) the strategy used for the selection, purification and preparation of the sample to be analyzed by mass spectrometry, 2) the type of mass spectrometer used and the type of data to be obtained from it, and 3) the method used for the interpretation of the mass spectrometry data and the search engine used for the identification of the proteins in the different types of sequence data banks available. As a part of the highly successful Methods in Molecular Biology series, the chapters compile step-by-step, readily reproducible laboratory protocols, lists of the necessary materials and reagents, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, Functional Proteomics: Methods and Protocols is an ideal resource for all scientists pursuing this developing field and its multitudinous data. Book jacket.

Table of Contents

Preface	p. v
Contributors	p. xiii
Introduction
A Brief Summary of the Different Types of Mass Spectrometers Used in Proteomics	p. 3
Experimental Setups and Considerations to Study Microbial Interactions	p. 17
Proteomics
Plant Proteomics	p. 29
Methods for Human CD8+ T Lymphocyte Proteome Analysis	p. 45
Label-Free Proteomics of Serum	p. 67
Flow Cytometric Analysis of Cell Membrane Microparticles	p. 79
Protein Expression Profiling
Exosomes	p. 97
Toward a Full Characterization of the Human 20S Proteasome Subunits and Their Isoforms by a Combination of Proteomic Approaches	p. 111
Free-Flow Electrophoresis of the Human Urinary Proteome	p. 131
Versatile Screening for Binary Protein-Protein Interactions by Yeast Two-Hybrid Mating	p. 145
Native Fractionation lsolation of Native Membrane-Bound Protein Complexes from Porcine Rod Outer Segments Using Isopycnic Density Gradient Centrifugation	p. 161
Mapping of Signaling Pathways by Functional Interaction Proteomics	p. 177
Selection of Recombinant Antibodies by Eukaryotic Ribosome Display	p. 193
Production of Protein Arrays by Cell-Free Systems	p. 207
Nondenaturing Mass Spectrometry to Study Noncovalent Protein/Protein and Protein/Ligand Complexes: Technical Aspects and Application to the Determination of Binding Stoichiometrics	p. 217
Protein Processing Characterized by a Gel-Free Proteomics Approach	p. 245
Identification and Characterization of N-Glycosylated Proteins Using Proteomics	p. 263
Protein Analysis
Data Standards and Controlled Vocabularies for Proteomics	p. 279
The Pride Proteomics Identifications Database: Data Submission, Query, and Dataset Comparison	p. 287
Searching the Protein Interaction Space Through the Mint Database	p. 305
PepSeeker: Mining Information from Proteomic Data	p. 319
Toward High-Throughput and Reliable Peptide Identification via Ms/Ms Spectra	p. 333
MassSorter: Peptide Mass Fingerprinting Data Analysis	p. 345
Database Similarity Searches	p. 361
Protein Multiple Sequence Alignment	p. 379
Discovering Biomedical Knowledge from the Literature	p. 415
Protein Subcellular Localization Prediction Using Artificial Intelligence Technology	p. 435
Protein Functional Annotation by Homology	p. 465
Designability and Disease	p. 491
Prism: Protein-Protein Interaction Prediction by Structural Matching	p. 505
Prediction of Protein Interaction Based on Similarity of Phylogenetic Trees	p. 523
Large Multiprotein Structures Modeling and Simulation: The Need for Mesoscopic Models	p. 537
Dynamic Pathway Modeling of Signal Transduction Networks: A Domain-Oriented Approach	p. 559
Index	p. 579
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