Proteomics: Targeted Technology, Innovations and Applications
"many excellent chapters" (Doodys)
Caister Academic Press
Manuel Fuentes and Joshua LaBaer
University of Salamanca, Spain and Arizona State University, USA; respectively
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Targeted proteomics is a technology for detecting proteins of interest with high sensitivity, quantitative accuracy and reproducibility. The analysis of a pre-defined group of proteins provides precise, quantitative and sensitive data to scientists and clinicians and can provide information on a subset of proteins important for their biological function.
In this book a panel of high-profile authors provides an overview of targeted proteomics in biomedical science. The book is focused on current, state-of-the-art technology and applications and is a valuable source of information for everyone working in this field. The first part of the book provides detailed examples of the application of targeted proteomics in biomarker discovery and pathogenesis. The second part is focused on the various tools used in targeted proteomics including bioinformatics approaches while the final section is dedicated to biobanks, a vital aspect of targeted proteomics.
This volume is highly recommended for anyone interested in proteomics, disease pathogenesis, clinical protein science and biomarker discovery.
"presents real-world examples of using targeted proteomics for biomarker discovery. It also describes the difference between targeted and discovery proteomics and gives practical advice on planning and analyzing data from a targeted proteomics experiment. There are many excellent chapters ... useful for anyone interested in entering the field of targeted proteomics." from Doodys
Table of contents
1. Serum Proteomics for Studying Disease Pathogenesis and Identification of Disease Biomarkers
Parvez Syed, Sandipan Ray, Kishore Gollapalli and Sanjeeva Srivastava
It is important to understand the disease pathogenesis and host immune response for making a correct therapeutic decision. Most of the diseases manifest at the protein level and hence analyzing changes at protein level gives an insight into the pathophysiological condition of the patients. However, identifying such subtle differences in protein expression is not an easy task. Over the decades, various proteomic techniques have been developed to perform serum proteome analysis. In this chapter we discuss the application of gel-, mass spectrometry- and array-based methods for the serum proteome analysis and identification of protein biomarkers. Advancement in proteomic technologies has shown the capability of enhancing the diagnostic potential of the existing diagnostic tools and help in assessing the risk factor. We also discuss the challenges associated with serum proteome profiling using these proteomic approaches.
2. Serum Profiling by Targeted Proteomics for Biomarker Discovery
Paula Diez, Maria Gonzalez-Gonzalez, Noelia Dasilva, Ricardo Jara-Acevedo, Alberto Orfao and Manuel Fuentes
Personalised medicine is one of the most important goals in medical research. Advances in detection and treatment of diseases have improved during the last decades, but there are still difficulties regarding the response to therapies depending on individual profiles. With the purpose of elucidating the best methods to deal with pathologies, various disciplines have emerged. Proteomics appears as the most promising in biomarker discovery. Detecting proteins with biomarker utility may be essential for a better diagnosis and prognosis. In this review we describe several targeted proteomic quantification methodologies. In addition, we summarize studies in cancer, auto-immune and metabolic diseases in which mass spectrometry approaches have been employed for biomarker discovery.
3. Targeted Proteomics. Applications in the Study of Liver Disorders
Fernando J. Corrales
Liver diseases afflict currently more than 10% of the world population and their incidence is increasing. Although the main risk factors are known and the population at risk is routinely monitored, new biomarkers are urgently needed to allow early diagnosis and more effective therapeutic interventions. As proteins are the cellular tools used to perform most of the biological processes, proteomics, among all the commonly known as -omics technologies, is expected to provide, a closer envision of cellular functions and seminal information to understand human physiology in health and disease. Large-scale comparative proteomics have provided in the last few years great amounts of data that partially outline the principal pathogenic mechanisms of some liver diseases and point out to potential biomarkers. However, the stringent validation of the emerging hypotheses and the detection of covalently modified protein species of clinical relevance that usually represent a sub-stoichiometric and very low abundant fraction in complex biological matrices are still bottlenecks in translational research. Targeted proteomic approaches based on mass spectrometry and affinity-based enrichment methods will surely contribute to fill the gap between the discovery of large lists of candidate proteins and the evaluation of their clinical use on suitable sample cohorts.
4. Targeted Proteomics for Chronic Lymphocytic Leukemia
Rafael Góngora, Paula Díez, Nieves Ibarrola, Rosa M. Dégano, Alberto Orfao and Manuel Fuentes
Chronic lymphocytic leukemia (CLL) is the most common leukemia in Western countries. It is a blood and bone marrow disease that progresses slowly. Traditionally, flow cytometry has been the diagnosis tool of choice due to the wide knowledge in markers field. Other strategies, such as fluorescent in situ hybridisation, have allowed chromosomal studies related to CLL. Numerous markers such as Zap70 protein or CD38 have been recently established as possible identifiers of the disease. For this, the need of proteomics approaches is evident. In this chapter we introduce basic information about the disease and its features, as well as the most relevant strategies in proteomics area leading to a better understanding of CLL.
5. Protein Microarrays: A Versatile Tool for Scientific Discovery
Johnathan Neiswinger, Jiang Qian and Heng Zhu
Over the last quarter century, protein microarray technology has emerged as a prominent field in scientific study. The versatility of the platform, coupled with the ability to characterize thousands of proteins in a parallel and high-throughput manner, has resulted in great strides in our knowledge database. Microarrays consist of three classes, analytical, functional, and reverse-phase, all of which have their own place in biomedical research. Much progress in this technology has been made over the last decade as new methods, particularly in microarray fabrication, have been developed. This chapter will give an overview of new and founding technologies, complete with a series of examples from both the basic and clinical research fields, including: microarray fabrication, detection methods (label-dependent and independent), binding interactions, post-translational modifications (PTMs), host-microbe interactions, and cancer research.
6. Bioinformatics Challenges in Targeted Proteomics
Lars Gustav Malmström
Targeted proteomics is becoming an important technology since it is capable of producing quantitative data with high reproducibility and accuracy for several proteins in a single experiment. The user needs to specify in great detail what to measure and the produced data is analyzed using techniques that have been specially developed for this technology. Targeted proteomics is therefore fundamentally dependent on an extensive set of software tools at almost every step. This chapter describes the bioinformatics challenges in targeted proteomics and suggests possible tools which can be used in each step.
7. Standardized Formats, Report Information Guidelines, Mass Spectrometry-based Repositories and Application Programming Interfaces for Implementing Data Standards in Proteomics
J. Alberto Medina-Aunon and Juan P. Albar
This chapter focuses on the standardization of proteomics data. Sharing and detailed description of proteomics experimental results to enable verification by other scientists are fundamental principles of scientific research. However, the vast heterogeneity of data formats provided by equipment vendors has hindered the progress in this field, making difficult the verification of published results. The Human Proteome Organization initiative on proteomics standards (HUPO-PSI) has worked on the definition of standards for proteomics data representation as well as in the description of the guidelines that state the minimum information that should be included when reporting a proteomics experiment (MIAPE). Such minimum information must describe the complete experiment, including both experimental protocols and data processing methods, allowing a critical evaluation of the whole process and the potential repetition of the work. In this chapter we describe the standardization work performed by the HUPO-PSI, focusing on the MIAPE guidelines and the XML data formats. In addition, main proteomics data repositories are described as well as the application programming interphases (APIs) required for the integration of data standards into laboratory pipelines. Finally, bioinformatics tools for converting raw data into proteomics data standards and data analysis tools for inspection, validation, reporting and statistics are analyzed.
8. Clinical Protein Science and Targeted Mass Spectrometric Assays: New Frontiers in Disease Link and Biobanking
Ákos Végvári and György Marko-Varga
Today's societies have to reach out for improved healthcare solutions due to the increased number of patients and changed disease profiles represented by the dominance of cardiovascular and neurodegenerative diseases as well as various forms of cancer that require customized therapies. There is an extensive need for diagnostic and therapeutic biomarkers that may also become targets for drug developments in the future. Modern analytical platforms headed by mass spectrometry offer enhanced sensitivity as well as novel methodologies with extreme specificity to identify and quantify these potential protein markers in clinical studies, which is in the focus of international research organized by the Human Proteome Organization. However, the complexity of clinical samples and the wide concentration range of proteins represent analytical tasks yet need to be accomplished. In this chapter we present the challenges the healthcare systems face nowadays and outline possible solutions using biobanking standardization, personalized medicine and mass spectrometric technologies with relevant examples.
How to buy this book
(EAN: 9781908230461 9781908230621 Subjects: [molecular microbiology] [genomics] [bioinformatics] [molecular biology] )