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Low-Abundance Proteome Discovery

Low-Abundance Proteome Discovery
  • Author : Egisto Boschetti,Pier Giorgio Righetti
  • Publisher :Unknown
  • Release Date :2013-03-26
  • Total pages :364
  • ISBN : 9780124045965
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Summary : Low-Abundance Proteome Discovery addresses the most critical challenge in biomarker discovery and progress: the identification of low-abundance proteins. The book describes an original strategy developed by the authors that permits the detection of protein species typically found in very low abundance and that may yield valuable clues to future discoveries. Known as combinatorial peptide ligand libraries, these new methodologies are one of the hottest topics related to the study of proteomics and have applications in medical diagnostics, food quality, and plant analysis. The book is written for university and industry scientists starting proteomic studies of complex matrices (e.g., biological fluids, biopsies, recalcitrant plant tissues, foodstuff, and beverage analysis), researchers doing wet chemistry, and graduate-level students in the areas of analytical and biochemistry, biology, and genetics. Covers methodologies for enhancing the visibility of low-abundance proteins which, until now, has been the biggest challenge in biomarker progress Includes detailed protocols that address real-life needs in laboratory practice Addresses all applications, including human disease, food and beverage safety, and the discovery of new proteins/peptides of importance in nutraceutics Compiles the research and analytic protocols of the two scientists who are credited with the discovery of these landmark methodologies, also known as combinatorial peptide ligand libraries, for the identification of low-abundance proteins

Proteomic and Metabolomic Approaches to Biomarker Discovery

Proteomic and Metabolomic Approaches to Biomarker Discovery
  • Author : Haleem J. Issaq,Timothy D. Veenstra
  • Publisher :Unknown
  • Release Date :2019-10-24
  • Total pages :504
  • ISBN : 9780128197882
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Summary : Proteomic and Metabolomic Approaches to Biomarker Discovery, Second Edition 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. This second edition has been fully updated and revised to address recent advances in MS and NMR instrumentation, high-field NMR, proteomics and metabolomics for biomarker validation, clinical assays of biomarkers and clinical MS and NMR, identifying microRNAs and autoantibodies as biomarkers, MRM-MS assay development, top-down MS, glycosylation-based serum biomarkers, cell surface proteins in biomarker discovery, lipodomics for cancer biomarker discovery, and strategies to design studies to identify predictive biomarkers in cancer research. Addresses the full range of proteomic and metabolomic methods and technologies used for biomarker discovery and validation Covers all steps involved in biomarker discovery, from study design to study execution Serves as a vital resource for biochemists, biologists, analytical chemists, bioanalytical chemists, clinical and medical technicians, researchers in pharmaceuticals and graduate students

Skeletal Biology and Medicine

Skeletal Biology and Medicine
  • Author : Mone Zaidi
  • Publisher :Unknown
  • Release Date :2010-05-03
  • Total pages :352
  • ISBN : STANFORD:36105133215082
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Summary : As part of the Annals of the New York Academy of Sciences series, this volume examines mechanisms involved in bone development and restructuring, including cellular and mechanical triggers, receptors, and signalling pathways. This volume also examines other factors associated with bone and musculoskeletal health, including physiological systems and disease states such as the immune system, inflammation, diabetes, infection and cancer. This book is ideal for Graduate students, medical students, researchers and clinicians in with an interest in anatomy, physiology, developmental biology, immunology, and musculoskeletal health NOTE: Annals volumes are available for sale as individual books or as a journal. For information on institutional journal subscriptions, please visit www.blackwellpublishing.com/nyas. ACADEMY MEMBERS: Please contact the New York Academy of Sciences directly to place your order (www.nyas.org). Members of the New York Academy of Science receive full-text access to the Annals online and discounts on print volumes. Please visit http://www.nyas.org/MemberCenter/Join.aspx for more information about becoming a member.

Neuroproteomics

Neuroproteomics
  • Author : Andrew K. Ottens,Kevin K.W. Wang
  • Publisher :Unknown
  • Release Date :2009-08-05
  • Total pages :321
  • ISBN : UOM:39015075683261
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Summary : With the development of polypeptide ionization processes for mass spectrometry and the rapid processing of large-scale datasets with bioinformatics, researchers now have the tools necessary to propel neuroproteomics research to new levels. In Neuroproteomics: Methods and Protocols, experts in the neurological and analytical sciences present experimental details for applying proteomics to the study of the central nervous system (CNS) and its dysfunction through trauma and disease. Divided into four convenient sections, this collection covers CNS animal models used for neuroproteomics research, methods for separating and analyzing discrete subcomponents of the neuroproteome, large-scale approaches for CNS proteome characterization and quantification, as well as methods that evaluate biofluids and translate neuroproteomic results into clinical platforms. 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 cutting-edge, Neuroproteomics: Methods and Protocols includes the clear "how-to" information needed to critically assess what can be accomplished in the field and how to best perform and evaluate neuroproteomic experiments in one’s own research.

American Biotechnology Laboratory

American Biotechnology Laboratory
  • Author : Anonim
  • Publisher :Unknown
  • Release Date :2008
  • Total pages :229
  • ISBN : STANFORD:36105123660420
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Summary :

Comparative Proteomic Profiling and Biomarker Discovery in Complex Biological Samples by Mass Spectrometry

Comparative Proteomic Profiling and Biomarker Discovery in Complex Biological Samples by Mass Spectrometry
  • Author : Anonim
  • Publisher :Unknown
  • Release Date :2012
  • Total pages :498
  • ISBN : OCLC:830677438
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Summary : Advances in mass spectrometry (MS) technology have made MS-based proteomics a promising tool for protein profiling and biomarker discovery. However, MS analyses of biological samples are challenging due to their vast complexity and large dynamic range. Because disease identifying biomarkers are likely low abundance proteins, it is imperative to remove high abundance proteins or apply enrichment techniques during sample preparation to detect and improve coverage of low abundance proteins. In addition, the complexity of the digested biological samples can be reduced by applying multiple orthogonal separations prior to LC-MS/MS such as multidimensional protein identification technology (MudPIT). In this dissertation, the major objectives include the following: (1) method development of sample preparation and chromatographic separation for MS-based quantitative proteomics, and (2) their applications in large-scale protein characterization in complex biological samples for differential expression analysis and biomarker discovery will be discussed. First, MudPIT combined with ESI-MS/MS was optimized for global proteome profiling in naïve and interleukin-2 (IL-2)-activated natural killer cells to identify IL-2 regulated proteins that elucidate new pathways associated with IL-2 signaling. A similar strategy was also applied to the comparative secretome analysis in rat vascular smooth muscle cells (VSMCs) stimulated by transforming growth factor-beta; (TGF-beta), which led to the identification of secreted proteins that may be associated with TGF-beta; signaling in VSMCs. In a third project, lectin affinity chromatography (LAC) was utilized in sample preparation of mouse plasma affected by prion disease to specifically enrich glycoproteins that may prove to be important biomarkers for prion diseases. The combination of LAC and MudPIT significantly reduced sample complexity and led to the discovery of a panel of potential biomarkers including the validation of serum amyloid P-component (SAP). Furthermore, PNGase F digestion analysis confirmed that the glycosylated form of SAP could be used as a potential diagnostic biomarker for prion diseases. Collectively, the work included in this thesis extends the capability of mass spectrometry as a powerful analytical tool for large-scale proteomic analysis in complex biological samples to identify disease biomarkers or biomolecules involved in critical cellular processes.

Genetic Engineering & Biotechnology News

Genetic Engineering & Biotechnology News
  • Author : Anonim
  • Publisher :Unknown
  • Release Date :2009
  • Total pages :229
  • ISBN : PSU:000061849341
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Summary :

Archives of Pathology & Laboratory Medicine

Archives of Pathology & Laboratory Medicine
  • Author : Anonim
  • Publisher :Unknown
  • Release Date :2008
  • Total pages :229
  • ISBN : NWU:35558005698572
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Summary :

Methods and Techniques in Drug Discovery

Methods and Techniques in Drug Discovery
  • Author : John Sterling,Ellyn J. T. D. Kerr,Shannon Simons
  • Publisher :Unknown
  • Release Date :2005
  • Total pages :266
  • ISBN : STANFORD:36105114585073
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Summary :

Proteomic and Metabolomic Approaches to Biomarker Discovery

Proteomic and Metabolomic Approaches to Biomarker Discovery
  • Author : Haleem J Issaq,Timothy D. Veenstra
  • Publisher :Unknown
  • Release Date :2013-05-20
  • Total pages :488
  • ISBN : 9780123947956
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Summary : 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

Plant Proteomics

Plant Proteomics
  • Author : Jesus V Jorrin-Novo,Luis Valledor,Mari Angeles Castillejo,Maria-Dolores Rey
  • Publisher :Unknown
  • Release Date :2021-06-11
  • Total pages :417
  • ISBN : 1071605305
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Summary :

Discovery of PTPMT1, a Novel Mitochondrial Phosphatase Involved in ATP Production and Insulin Secretion in Pancreatic Beta Cells

Discovery of PTPMT1, a Novel Mitochondrial Phosphatase Involved in ATP Production and Insulin Secretion in Pancreatic Beta Cells
  • Author : David James Pagliarini
  • Publisher :Unknown
  • Release Date :2005
  • Total pages :258
  • ISBN : UCSD:31822018116012
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Summary :

Applied Genomics and Proteomics

Applied Genomics and Proteomics
  • Author : Anonim
  • Publisher :Unknown
  • Release Date :2003
  • Total pages :229
  • ISBN : CORNELL:31924099661708
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Summary :

N-terminal Plasma Profiling

N-terminal Plasma Profiling
  • Author : Gemma Rose Davidson
  • Publisher :Unknown
  • Release Date :2011
  • Total pages :229
  • ISBN : OCLC:847538933
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Summary : Blood is a highly accessible body fluid that is rich in biological information; it is widely accepted that this is the most popular diagnostic sample available within a clinical environment. The measurement of cellular and non-cellular blood components, including blood cells, electrolytes, metabolites, lipids and proteins can aid clinicians in establishing an individuals' health status and can also function to diagnose and monitor the progression of disease. An alteration in an individuals' physiological state, such as the presence/absence of disease, will often lead to an alteration in protein expression. The accurate identification and measurement of proteins found in the non-cellular component of blood, known as plasma, could provide key information relating to a multitude of biological processes. Blood plasma is considered to contain the most comprehensive proteome of the body, as it is in contact with every cell, tissue and organ. Enthused by the clinical potential of this biological fluid there has been a drive within the proteomics community to develop robust proteomic platforms for the analysis of the blood plasma proteome. Coupled with powerful technologies, such as chromatography and mass spectrometry, there has been some success. Initiatives, such as the human plasma proteome project (PPP) have strived to standardised and collate data across laboratories with the objective of the global analysis and quantification of the plasma proteins. Unfortunately, as yet the plasma proteome remains to a large degree undiscovered, or more suitably 'hidden'. Blood plasma contains many proteins from all parts of the body. Tensioned against these desirable features are two disadvantages that have thus far hindered most plasma proteomic studies: high complexity and large dynamic range. The quantitative dynamic range of the human plasma proteome spans over 10 orders of magnitude with a small number of high-abundance proteins dominating approximately 99% total protein concentration, with albumin alone constituting approximately 50% total plasma protein. The dominance of the plasma proteome by such high-abundance proteins has inhibited the ability of most proteomic studies to access those proteins considered low-abundance. This is especially problematic when one considers that those proteins that constitute approximately 1 % total plasma protein, such as tissue leakage proteins, are considered to be extremely important in protein biomarker discovery. The analytical challenges imposed by blood plasma have thus far hampered efforts to delve deep into the proteome; presently no analytical technique has been presented that can fully exploit the full potential of plasma for medicine and therapeutics. A reduction in analyte complexity and improvements in analytical instrumentation are the most common approaches to combat the complexity and dynamic range problems associated with the study of the plasma proteome. Although the selective removal of high-abundance proteins via immunodepletion is an attractive approach to address the dynamic range issue, many of the high-abundance plasma proteins, such as albumin, have been shown to associate with other proteins. Thus, selective depletion will lead to the non-specific removal of other proteins. Other strategies aim to selectively target specific amino acid residues for enrichment, however utilising such an approach might lead to the over or under-representation of certain proteins. A positional proteomics approach targets one of two locations common to all proteins; the N- terminus or the C-terminus. This investigation focuses on the adoption of a positional proteomics strategy to selectively enrich the N-terminal peptides of the human plasma proteins. A reduction in sample complexity is observed when compared to a traditional 'shot-gun' proteomic approach. The absolute measurement of proteins is particularly important for protein biomarker validation/verification and for the development of our own understanding of biological processes. The development ofa QconCAT protein that is a concatomer ofN-terminal peptides, each a surrogate for its parent plasma protein, has the potential to provide absolute measurement of N-terminal peptides in a multiplexed manner. Utilising highly sensitive and selective mass spectrometric techniques such as selected reaction monitoring (SRM) in combination with the N-terminal enrichment strategy and QconCAT technology there is potential to selectively target and quantify N- terminal peptides in a high-throughput manner. Utilising N-terminal enrichment as a tool for human plasma proteome analysis gives an insight into the magnitude of enzymatic processes that specifically target the N-terminal portion of a protein. Such exo- and endo- proteolytic activity could prove significant for biomarker research. Although dynamic range is still a major problem, the N-terminal enrichment strategy demonstrates its utility as a tool for profiling the human plasma N-terminome. The global analysis of the plasma proteome will most likely require a combination of proteomic approaches that will specifically target and enrich sub-sections of this unique proteome.

Proteomics in Cancer Research

Proteomics in Cancer Research
  • Author : Daniel C. Liebler
  • Publisher :Unknown
  • Release Date :2004
  • Total pages :216
  • ISBN : 0471444758
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Summary : Proteomics in Cancer Research covers both the basic principles of proteomics along with detailed presentations of new and emerging technology that represent promising breakthroughs in cancer prevention and treatment. The topics covered include: Basic concepts, including setting up a proteomics laboratory, mass spectrometry, protein separations, protein array technologies, and informatics tools Application of emerging technologies to proteomic analysis of cancer cells and tissues, including discussion of critical issues such as characteristics of cancer cell proteomes and protein-protein interactions Application of proteomics approaches in clinical cancer research and a forecast of future research and applications In most cases, applications of methods in basic and translational cancer research that are discussed in the text represent the first uses of these proteomics approaches to study any disease. Critical issues that readers in cancer research need to understand are covered in detail, including: Advantages and limitations of different technologies New approaches to the molecular classification of tumors Discovery of new biomarkers and imaging targets and development of new proteomic platforms for profiling and screening The unique proteomic features that characterize cancers offer new opportunities for disease prevention and treatment. Despite intense interest, however, proteomics is just beginning to become a part of the cancer research mainstream, as relatively few cancer researchers have training in proteomics methods and approaches. This book, therefore, is both a timely and an essential guide that will help readers understand key concepts of proteomics and use its methods to search for ways to both cure and prevent cancer.

Proteomic Profiling of Saliva for the Detection of Cancer

Proteomic Profiling of Saliva for the Detection of Cancer
  • Author : Prasanna Ramachandran
  • Publisher :Unknown
  • Release Date :2009
  • Total pages :522
  • ISBN : UCLA:L0099901654
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Summary :

Protein Purification

Protein Purification
  • Author : Jan-Christer Janson,Lars Rydén,Lars Ryden
  • Publisher :Unknown
  • Release Date :1998
  • Total pages :695
  • ISBN : 0471186260
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Summary : This is a state-of-the-art sourcebook on modern high-resolution biochemical separation techniques for proteins. It contains all the basic theory and principles used in protein chromatography and electrophoresis.

Genetic Engineering News

Genetic Engineering News
  • Author : Anonim
  • Publisher :Unknown
  • Release Date :2006
  • Total pages :229
  • ISBN : STANFORD:36105123646494
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Summary :

Proteome Research

Proteome Research
  • Author : M.R. Wilkins,R.D. Appel,K.L. Williams,D.F. Hochstrasser
  • Publisher :Unknown
  • Release Date :2008-02-05
  • Total pages :239
  • ISBN : 3540712410
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Summary : Proteomics is a multifaceted, interdisciplinary field which studies the complexity and dynamics of proteins in biological systems. It combines powerful separation and analytical technology with advanced informatics to understand the function of proteins in the cell and in the body. This book provides a clear conceptual description of each facet of proteomics, describes recent advances in technology and thinking in each area, and provides details of how these have been applied to a variety of biological problems. It is written by expert practitioners in the field, from industry, research institutions, and the clinic. It provides junior and experienced researchers with an invaluable proteomic reference, and gives fascinating glimpses of the future of this dynamic field.

Nature

Nature
  • Author : Sir Norman Lockyer
  • Publisher :Unknown
  • Release Date :2008
  • Total pages :229
  • ISBN : UOM:49015003426369
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Science

Science
  • Author : Anonim
  • Publisher :Unknown
  • Release Date :2009
  • Total pages :229
  • ISBN : UCSB:31205034615391
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Summary :