Since the advent of microarray technology in the early 1990's, the development of highly multiplex genomics tools has greatly outpaced the field of proteomics in terms of the generation of useful platforms for basic research and clinical analysis. Yet, to deliver on the great promise of genomics tools that analyze nucleic acids, technologies that permit the analysis of protein-protein interactions on a comparable scale need to be developed. Our group and others have shown that whole-protein and peptide microarrays can provide large amounts of information about the protein interactions that underlie the human immune response in health and disease. Here we describe three novel proteomics microarray platforms and demonstrate that the arrays can be used to gain insight into the antibody-mediated immune response in a spectrum of human diseases. In the first study, we detail the generation of a protein microarray that allows the detection of antibodies that bind to the molecular communication factors of the immune system: cytokines, chemokines, growth factors, and other circulating proteins. Using these arrays, we identified novel targets of autoantibodies in systemic lupus erythematosus, which may delineate a unique subgroup of patients within the spectrum of lupus. In the second study, we describe influenza antigen microarrays that permitted the identification of antibody reactivity to specific influenza hemagglutinin epitopes associated with poor or effective response to the seasonal influenza vaccine. These arrays have potential for development into a clinical diagnostic tool capable of predicting an individual's ability to mount an effective antibody response to vaccination. Finally, we report the development of a silicon-based peptide microarray developed in collaboration with researchers at the Intel Corporation. These "Intel arrays" hold great potential for ultimately enabling highly parallel, real-time measurement of protein-protein interaction with myriad possible downstream applications. The technologies we have developed move the field of multiplex proteomic analysis forward on many fronts, and constitute valuable additions to the proteomics toolkit available to researchers and clinicians. Moreover, our work demonstrates that detailed analysis of protein-protein interaction is required to make more informed models of different states of human health and disease.

Written by recognized experts in the study of proteins, Proteomics for Biological Discovery begins by discussing the emergence of proteomics from genome sequencing projects and a summary of potential answers to be gained from proteome-level research. The tools of proteomics, from conventional to novel techniques, are then dealt with in terms of underlying concepts, limitations and future directions. An invaluable source of information, this title also provides a thorough overview of the current developments in post-translational modification studies, structural proteomics, biochemical proteomics, microfabrication, applied proteomics, and bioinformatics relevant to proteomics. Presents a comprehensive and coherent review of the major issues faced in terms of technology development, bioinformatics, strategic approaches, and applications Chapters offer a rigorous overview with summary of limitations, emerging approaches, questions, and realistic future industry and basic science applications Discusses higher level integrative aspects, including technical challenges and applications for drug discovery Accessible to the novice while providing experienced investigators essential information Proteomics for Biological Discovery is an essential resource for students, postdoctoral fellows, and researchers across all fields of biomedical research, including biochemistry, protein chemistry, molecular genetics, cell/developmental biology, and bioinformatics.

Microarrays play an increasingly significant role in drug discovery. The commercial landscape has changed dramatically over the past few years and researchers have made great advancements with regard to construction and use. Now in its second edition, Applying Genomic and Proteomic Microarray Technology in Drug Discovery highlights, describes, and evaluates current scientific research using microarray technology in genomic and proteomic applications. Updated and revised to reflect recent progress in the field, the second edition discusses: Expanded omics-driven applications, including the areas of metabolomics and chemical biology The commercialization of the microarray platform, with a historical perspective aimed at recognizing key technological developments Solid-supports (substrates) and surface chemistries currently used in the creation of nucleic acid and protein microarrays Different approaches to producing microarrays that achieve spot equality with the same number of molecules properly oriented The development of the gene expression microarray and representative applications The development of protein microarray technology, including its history and key applications Unique to this edition is a new chapter on multiplex assays that examines the development and applications of arrays across diverse platforms. It discusses applications for qPCR, multiplex lateral flow, and multiplex bead assays. It also presents platform-to-platform comparisons. Microarrays remain an invaluable tool for omics-based research not only in drug discovery, but in the life sciences, in clinical research, and for diagnostic applications worldwide. This volume presents the current state of the art on the utility of this technology to solve a host of important biological problems.

Due to their versatility, along with the diminishing costs of library synthesis and the growth of commercial support, peptide microarrays will likely expand beyond being just a research tool into an adaptable and powerful platform to be harnessed for wider drug discovery and point-of-care applications. In Peptide Microarrays: Methods and Protocols, experts in the field provide a cutting-edge view of peptide array technology, its applications, and technical issues. After examining how peptides can characterize proteins and clarify, at the amino acid level, the molecular recognition events in which they are involved, the volume goes on to cover topics such as the production and use of peptide arrays for enzyme and binding motifs characterization, epitope mapping, and diagnostics, the newest technological advancements, as well as software and web tools for the design of peptide arrays and for the analysis of output data. As a volume in the highly successful Methods in Molecular BiologyTM series, chapters include brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easy-to-use, Peptide Microarrays: Methods and Protocols promises to serve scientists with its unique insights and novel solutions in peptide array technology in order to advance this vital field.

Technologies collectively called omics enable simultaneous measurement of an enormous number of biomolecules; for example, genomics investigates thousands of DNA sequences, and proteomics examines large numbers of proteins. Scientists are using these technologies to develop innovative tests to detect disease and to predict a patient's likelihood of responding to specific drugs. Following a recent case involving premature use of omics-based tests in cancer clinical trials at Duke University, the NCI requested that the IOM establish a committee to recommend ways to strengthen omics-based test development and evaluation. This report identifies best practices to enhance development, evaluation, and translation of omics-based tests while simultaneously reinforcing steps to ensure that these tests are appropriately assessed for scientific validity before they are used to guide patient treatment in clinical trials.

Protein microarrays soon will become one of the major tools for realizing the goals of drug discovery research in the post-genome era. The book is aimed at life science researchers and scientists working in drug and pharma industry.

Proteomic and Metabolomic Approaches to Biomarker Discovery demonstrates how to leverage biomarkers to improve accuracy and reduce errors in research. Disease biomarker discovery is one of the most vibrant and important areas of research today, as the identification of reliable biomarkers has an enormous impact on disease diagnosis, selection of treatment regimens, and therapeutic monitoring. Various techniques are used in the biomarker discovery process, including techniques used in proteomics, the study of the proteins that make up an organism, and metabolomics, the study of chemical fingerprints created from cellular processes. Proteomic and Metabolomic Approaches to Biomarker Discovery is the only publication that covers techniques from both proteomics and metabolomics and includes all steps involved in biomarker discovery, from study design to study execution. The book describes methods, and presents a standard operating procedure for sample selection, preparation, and storage, as well as data analysis and modeling. This new standard effectively eliminates the differing methodologies used in studies and creates a unified approach. Readers will learn the advantages and disadvantages of the various techniques discussed, as well as potential difficulties inherent to all steps in the biomarker discovery process. A vital resource for biochemists, biologists, analytical chemists, bioanalytical chemists, clinical and medical technicians, researchers in pharmaceuticals, and graduate students, Proteomic and Metabolomic Approaches to Biomarker Discovery provides the information needed to reduce clinical error in the execution of research. - Describes the use of biomarkers to reduce clinical errors in research - Includes techniques from a range of biomarker discoveries - Covers all steps involved in biomarker discovery, from study design to study execution