The Evolution from Protein Chemistry to Proteomics

by Lundblad; Roger L.

• ISBN13: 9780849396786
• ISBN10: 0849396786
• Format: Hardcover
• Copyright: 2005-10-14
• Publisher: CRC Press

Summary

Largely driven by major improvements in the analytical capability of mass spectrometry, proteomics is being applied to broader areas of experimental biology, ranging from oncology research to plant biology to environmental health. However, while it has already eclipsed solution protein chemistry as a discipline, it is still essentially an extension of classical protein chemistry, owing much of its maturation to prior contributions. Unfortunately, this debt is not always evident in current literature.The Evolution from Protein Chemistry to Proteomics: Basic Science to Clinical Application, in providing a different perspective than other reviews, strengthens the connection between solution protein chemistry and proteomic technology. Towards this end, Roger Lundblad, a long-time leader in protein chemistry and a scientist who has worked in both academics and industry, brings together some seemingly disparate areas into a single volume. Discussing analytical proteomics, expression proteomics, and clinical proteomics (biomarker identification), he provides coverage that is uniquely rich in detail.Lundblad applies this detail to sample preparation for proteomic analysis, including preparation from blood and tissues. He also presents specifics on the prefractionation of samples used to identify specific subproteomes such as phosphoproteomes and glycoproteomes. Comprehensive reviews are provided covering the chemical modification of proteins, including its use for chemical proteomics. Special attention is given to challenges that impede the identification, validation, and development of biomarkers into clinically useful diagnostic analytes.A bestselling author, Lundblad utilizes classical protein chemistry literature in providing an intellectual basis for proteomics that merges current concepts with the existing literature, while providing the technical detail necessary for the effective commercialization of proteomics.

Table of Contents

A Brief Discussion of Proteomics --- Definition -- Concepts -- Illusions	1	(23)
Introduction and Definition of the Proteome and Proteomics	1	(8)
Division of Activities in Proteomics	9	(4)
Analytical Proteomics	9	(3)
Expression Proteomics	12	(1)
Biomarker Identification	12	(1)
References	13	(10)
An Overview of the Chemical Modification of Proteins	23	(70)
Introduction	23	(1)
Specific Chemical Modification of Proteins	24	(6)
Arginine	30	(3)
Cysteine	33	(4)
Cystine	37	(2)
Carboxyl Groups	39	(3)
Histidine	42	(2)
Amino Groups	44	(5)
Methionine	49	(1)
Tyrosine	50	(2)
Tryptophan	52	(3)
Chemical Cleavage of Peptide Bonds	55	(13)
Cross-linking of Proteins	68	(5)
In Vivo NonEnzymatic Chemical Modification	73	(9)
Oxidation	73	(1)
Nitric Oxide	73	(4)
Glycation	77	(5)
References	82	(11)
The Application of Site-Specific Chemical Modification to Proteomics: Chemical Proteomics	93	(68)
Introduction	93	(1)
Activity-Based Proteomics	94	(12)
Alkylfluorophosphonate Derivatives	96	(6)
Peptide Halomethyl Ketones	102	(2)
Other Functional Derivatives	104	(2)
Specific Modification of Proteins and Peptides for Proteomic Analysis	106	(7)
Other Clever Reagents	113	(1)
Stable Isotope Labeling --- Quantitative Proteomics	113	(8)
Other Clever Approaches to the Modification of Proteins for Proteomic Analysis	121	(4)
Labeling of Protein Prior to Fractionation --- Fluorescent Dyes	125	(12)
Enzymatic Modification of Targets for Proteomic Analysis	137	(1)
Protein Microarrays	138	(7)
References	145	(16)
Sample Preparation for Proteomic Studies	161	(34)
Introduction	161	(1)
Contribution of Sample Preparation to Experimental Variance	162	(1)
Biological Fluids	162	(1)
Cell and Tissue Extraction	163	(14)
Sample Stability Issues	177	(1)
Inhibition of Proteolysis	177	(5)
Quality Attributes for a Proteomic Sample	182	(1)
Determination of Protein Concentration in Proteomic Samples	182	(2)
Sample Quality	184	(1)
Conclusions	185	(1)
References	185	(10)
Prefractionation	195	(20)
Introduction	195	(2)
Blood and Serum	197	(2)
Removal of High-Abundance Proteins from Plasma and Serum	199	(2)
Tissue and Cell Samples --- Laser Capture Microdissection	201	(2)
Subproteomics	203	(1)
Affinity Selection	204	(1)
Conclusions	205	(1)
References	205	(10)
An Overview of Analytical Technologies Used in Proteomic Research	215	(24)
Introduction	215	(1)
Development in Protein Analytical Technology	216	(1)
Mass Spectrometry	217	(4)
Two-Hybrid Systems and Tandem-Affinity Purification --- Study of Protein--Protein Interactions	221	(2)
Two-Dimensional Gel Electrophoresis	223	(2)
ShotGun Proteomics/Multidimensional Protein Identification Technology (MuDPIT)	225	(2)
Surface Enhanced Laser Desorption/Ionization --- Mass Spectrometry (SELDI-MS)	227	(1)
Conclusions	228	(1)
References	228	(11)
Clinical Proteomics	239	(26)
Introduction	239	(5)
Clinical Proteomics --- Trends --- Diagnostics --- Biomarkers	244	(1)
Rheumatoid Arthritis and Osteoarthritis	245	(2)
Head and Neck Cancer	247	(1)
Specificity and Sensitivity --- CA125 and Other Markers	247	(6)
Clinical Proteomics by Technical Approach	253	(1)
Conclusions	254	(4)
References	258	(7)
Validation Issues in Proteomics and the Transition from Research to Diagnostic Development	265	(14)
Introduction	265	(1)
Issues Affecting Assay Variability	266	(1)
Index of Variability	267	(2)
Personalized Medicine	269	(1)
Assay Validation	269	(1)
Biomarkers in Toxicity and Environmental Health	270	(2)
Design Control	272	(1)
Conclusions	272	(1)
References	273	(6)
Index	279