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Development Of An Experimental And Computational Platform For Enhanced Characterization Of Modified Peptides And Proteins In Environmental Proteomics
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Book Synopsis Development of an Experimental and Computational Platform for Enhanced Characterization of Modified Peptides and Proteins in Environmental Proteomics by : Ritin Sharma
Download or read book Development of an Experimental and Computational Platform for Enhanced Characterization of Modified Peptides and Proteins in Environmental Proteomics written by Ritin Sharma and published by . This book was released on 2014 with total page 186 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the last decade, mass spectrometry based proteomics has been established as the front-runner in systems-level protein expression studies. However, with the field progressing into research of more and more complex samples, novel challenges have been raised with respect to efficient protein extraction and computational matching. In this dissertation, various aspects in the proteomics workflow, including experimental and computational approaches, have been developed, optimized and systematically evaluated. In this work, some of the critical factors with respect to proteomics sample preparation, like available biomass, detergent removal methods, and intact protein fractionation to achieve deeper proteome measurements were evaluated. The presented work will help the broader scientific community to carefully design proteomics experiments especially in biomass limited samples. A second major area of focus in this dissertation is comprehensive characterization of post-translational modifications (PTMs) in different biological systems. PTMs are critical for functioning of both the prokaryotic and eukaryotic species and this dissertation will highlight some of the experimental strategies to explore the diversity of PTMs in microbial isolates via application of alternate protease and multiple fragmentation schemes. The PTM discovery approach will be further extended into a complex eukaryotic model trees species Populus trichocarpa using recently developed sequence tagging methods to carryout broad scale PTM search and a complete blind PTM search. Although the work presented in this dissertation mainly revolves around prokaryotic and eukaryotic species involved in environmental proteomics, the general considerations outlined in this work can be extended to every proteomics pipeline. Thus this dissertation will benefit the scientific community in carefully designing experiments before embarking on any research project involving mass spectrometry.
Book Synopsis An Integrated Experimental and Computational Approach to Proteomics: Scaling from High Resolution Qualitative Analysis to Quantitative Measurements with Confidence Evaluation by : Chongle Pan
Download or read book An Integrated Experimental and Computational Approach to Proteomics: Scaling from High Resolution Qualitative Analysis to Quantitative Measurements with Confidence Evaluation written by Chongle Pan and published by . This book was released on 2006 with total page 283 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the research described here, a substantial advancement in both qualitative and quantitative proteomic measurements was achieved using an integrated experiment and computational approach. The improved proteomic measurements can help elucidate a range of biological processes.
Book Synopsis Integrated Computational and Experimental Platform for Characterizing Protein Isoforms and PTMs in Microbial Systems by Top-down FT-ICR Mass Spectrometry by : Heather Marie Connelly
Download or read book Integrated Computational and Experimental Platform for Characterizing Protein Isoforms and PTMs in Microbial Systems by Top-down FT-ICR Mass Spectrometry written by Heather Marie Connelly and published by . This book was released on 2006 with total page 251 pages. Available in PDF, EPUB and Kindle. Book excerpt: The goals of this dissertation research were to develop an integrated computational and experimental platform for characterizing protein isoforms and post translational modifications (PTMs) in microbial systems by top-down FT-ICR mass spectrometry. To accomplish this goal, we employed methodologies of microbial growth, intact protein and protein complex extractions, followed by sample preparation and then progressed to identification of the instrumentation needed to integrate the top-down and bottom-up proteomics methodologies used in these studies. Emphasis is placed on the development of integrated top-down and bottom-up informatics and the challenges faced in the integration of these two large mass spectrometry data sets and extraction of relevant biological data. We then illustrate how top-down and bottom-up methods can be applied to the analysis of complex protein mixtures, protein complexes, and microbial proteomes. Through the work of this dissertation we have contributed to the advancement of top-down proteomics by providing an experimental platform which will aid in the analysis of intact proteins and their associated PTMs and isoforms, as well as providing a computational method that allows for the integration of top-down and bottom-up data sets.
Book Synopsis Proteome Informatics by : Conrad Bessant
Download or read book Proteome Informatics written by Conrad Bessant and published by Royal Society of Chemistry. This book was released on 2016-11-15 with total page 429 pages. Available in PDF, EPUB and Kindle. Book excerpt: The field of proteomics has developed rapidly over the past decade nurturing the need for a detailed introduction to the various informatics topics that underpin the main liquid chromatography tandem mass spectrometry (LC-MS/MS) protocols used for protein identification and quantitation. Proteins are a key component of any biological system, and monitoring proteins using LC-MS/MS proteomics is becoming commonplace in a wide range of biological research areas. However, many researchers treat proteomics software tools as a black box, drawing conclusions from the output of such tools without considering the nuances and limitations of the algorithms on which such software is based. This book seeks to address this situation by bringing together world experts to provide clear explanations of the key algorithms, workflows and analysis frameworks, so that users of proteomics data can be confident that they are using appropriate tools in suitable ways.
Book Synopsis Peptide and Protein Design for Biopharmaceutical Applications by : Knud Jensen
Download or read book Peptide and Protein Design for Biopharmaceutical Applications written by Knud Jensen and published by John Wiley & Sons. This book was released on 2009-09-01 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt: Peptides serve as effective drugs in the clinic today. However the inherent drawbacks of peptide structures can limit their efficacy as drugs. To overcome this researchers are developing new methods to create ‘tailor-made’ peptides and proteins with improved pharmacological properties. Design of Peptides and Proteins provides an overview of the experimental and computational methods for peptide and protein design, with an emphasis on specific applications for therapeutics and biomedical research. Topics covered include: Computer modeling of peptides and proteins Peptidomimetics Design and synthesis of cyclic peptides Carbohydrates in peptide and protein design De novo design of peptides and proteins Medical development applications An extended case study – the design of insulin variants Design of Peptides and Proteins presents the state-of-the-art of this exciting approach for therapeutics, with contributions from international experts. It is an essential resource for academic and industrial scientists in the fields of peptide and protein drug design, biomedicine, biochemistry, biophysics, molecular modelling, synthetic organic chemistry and medicinal/pharmaceutical chemistry.
Book Synopsis Bioinformatic and Experimental Approaches for Deeper Metaproteomic Characterization of Complex Environmental Samples by : Ramsunder Mahadevan Iyer
Download or read book Bioinformatic and Experimental Approaches for Deeper Metaproteomic Characterization of Complex Environmental Samples written by Ramsunder Mahadevan Iyer and published by . This book was released on 2017 with total page 192 pages. Available in PDF, EPUB and Kindle. Book excerpt: The coupling of high performance multi-dimensional liquid chromatography and tandem mass spectrometry for characterization of microbial proteins from complex environmental samples has paved the way for a new era in scientific discovery. The field of metaproteomics, which is the study of protein suite of all the organisms in a biological system, has taken a tremendous leap with the introduction of high-throughput proteomics. However, with corresponding increase in sample complexity, novel challenges have been raised with respect to efficient peptide separation via chromatography and bioinformatic analysis of the resulting high throughput data. In this dissertation, various aspects of metaproteomic characterization, including experimental and computational approaches have been systematically evaluated. In this study, robust separation protocols employing strong cation exchange and reverse phase have been designed for efficient peptide separation thus offering excellent orthogonality and ease of automation. These findings will be useful to the proteomics community for obtaining deeper non-redundant peptide identifications which in turn will improve the overall depth of semi-quantitative proteomics. Secondly, computational bottlenecks associated with screening the vast amount of raw mass spectra generated in these proteomic measurements have been addressed. Computational matching of tandem mass spectra via conventional database search strategies lead to modest peptide/protein identifications. This seriously restricts the amount of information retrieved from these complex samples which is mainly due to high complexity and heterogeneity of the sample containing hundreds of proteins shared between different microbial species often having high level of homology. Hence, the challenges associated with metaproteomic data analysis has been addressed by utilizing multiple iterative search engines coupled with de novo sequencing algorithms for a comprehensive and in-depth characterization of complex environmental samples. The work presented here will utilize various sample types ranging from isolates and mock microbial mixtures prepared in the laboratory to complex community samples extracted from industrial waste water, acid-mine drainage and methane seep sediments. In a broad perspective, this dissertation aims to provide tools for gaining deeper insights to proteome characterization in complex environmental ecosystems.
Book Synopsis Microcharacterization of Proteins by : Roland Kellner
Download or read book Microcharacterization of Proteins written by Roland Kellner and published by John Wiley & Sons. This book was released on 2008-09-26 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteomics - the analysis of the whole set of proteins and their functions in a cell - is based on the revolutionary developments which have been achieved in protein analysis during the last years. The number of finished genome projects is growing and in parallel there is a dramatically increasing need to identify the products of revealed genes. Acting on a micro level modern protein chemistry increases our understanding of biological events by elucidating the relevant structure-function relationships. The second edition of the successful title Microcharacterization of Proteins presents a current overview of modern protein analysis: From sample preparation to sequence analysis, mass spectrometry and bioinformatics it informs about the tools needed in protein research. This makes the book indispensable for everyone involved in proteomics!
Book Synopsis Quantitative Characterization of Proteins and Post-translational Modifications in Complex Proteomes Using High-resolution Mass Spectrometry-based Proteomics by : Zhou Li (Researcher in biological systems)
Download or read book Quantitative Characterization of Proteins and Post-translational Modifications in Complex Proteomes Using High-resolution Mass Spectrometry-based Proteomics written by Zhou Li (Researcher in biological systems) and published by . This book was released on 2014 with total page 175 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry-based proteomics is focused on identifying the entire suite of proteins and their post-translational modifications (PTMs) in a cell, organism, or community. In particular, quantitative proteomics measures abundance changes of thousands of proteins among multiple samples and provides network-level insight into how biological systems respond to environmental perturbations. Various quantitative proteomics methods have been developed, including label-free, metabolic labeling, and isobaric chemical labeling. This dissertation starts with systematic comparison of these three methods, and shows that isobaric chemical labeling provides accurate, precise, and reproducible quantification for thousands of proteins. Based on these results, we applied this approach to characterizing the proteome of Arabidopsis seedlings treated with Strigolactones (SLs), a new class of plant hormones that modulate various developmental processes. Our study reveals that SLs regulate the expression of a range of proteins that have not been assigned to SL pathways, which provides novel targets for follow-up genetic and biochemical characterization of SL signaling. The same approach was also used to measure how elevated temperature impacts the physiology of individual microbial groups in an acid mine drainage (AMD) microbial community, and shows that related organisms differed in their abundance and functional responses to temperature. Elevated temperature repressed carbon fixation by two Leptospirillum genotypes, whereas carbon fixation was significantly up-regulated at higher temperature by a third member of this genus. Further, we developed a new proteomic approach that harnessed high-resolution mass spectrometry and supercomputing for direct identification and quantification of a broad range of PTMs from an AMD microbial community. We find that PTMs are extraordinarily diverse between different growth stages and highly divergent between closely related bacteria. The findings of this study motivate further investigation of the role of PTMs in the ecology and evolution of microbial communities. Finally, a computational approach has been developed to improve the sensitivity of phosphopeptide identification. Overall, the research presented in the dissertation not only reveals biological insights with existing quantitative proteomics methods, but also develops novel methodologies that open up new avenues in studying PTMs of proteins (e.g. PTM cross-talk).
Book Synopsis Computational Methods for Mass Spectrometry Proteomics by : Ingvar Eidhammer
Download or read book Computational Methods for Mass Spectrometry Proteomics written by Ingvar Eidhammer and published by Wiley-Interscience. This book was released on 2008-01-22 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteomics is the study of the subsets of proteins present in different parts of an organism and how they change with time and varying conditions. Mass spectrometry is the leading technology used in proteomics, and the field relies heavily on bioinformatics to process and analyze the acquired data. Since recent years have seen tremendous developments in instrumentation and proteomics-related bioinformatics, there is clearly a need for a solid introduction to the crossroads where proteomics and bioinformatics meet. Computational Methods for Mass Spectrometry Proteomics describes the different instruments and methodologies used in proteomics in a unified manner. The authors put an emphasis on the computational methods for the different phases of a proteomics analysis, but the underlying principles in protein chemistry and instrument technology are also described. The book is illustrated by a number of figures and examples, and contains exercises for the reader. Written in an accessible yet rigorous style, it is a valuable reference for both informaticians and biologists. Computational Methods for Mass Spectrometry Proteomics is suited for advanced undergraduate and graduate students of bioinformatics and molecular biology with an interest in proteomics. It also provides a good introduction and reference source for researchers new to proteomics, and for people who come into more peripheral contact with the field.
Book Synopsis Methods for Proteomic Characterization of Antibody Repertoires and de Novo Peptide Sequencing by : Andrew Pitchford Horton
Download or read book Methods for Proteomic Characterization of Antibody Repertoires and de Novo Peptide Sequencing written by Andrew Pitchford Horton and published by . This book was released on 2016 with total page 180 pages. Available in PDF, EPUB and Kindle. Book excerpt: Driven by the increased performance and availability of protein mass spectrometry and next generation sequencing technologies, research in proteomics and systems biology has expanded far beyond the study of model organisms. This heralds a deeper understanding of biology, the world, and human health. However, it also brings significant new challenges to the interpretation of sequencing and mass spectrometry data, the current software tools ill-suited for many modern studies. The first half of this dissertation explores some of these challenges and solutions in the context of a particularly demanding domain – that of serological antibody proteomics. Our team has developed a combined sequencing and proteomics approach for profiling the human serum antibody repertoire. This opens an unprecedented view into the nature of the adaptive immune system and provides insight on antibody repertoire dynamics in both health and disease. The platform also provides effective means to evaluate vaccine efficacy and identify potential antibody therapeutics. Chapter 1 reviews recent advances in and results from such molecular level characterization of the serum antibody repertoire. Detailed in the second chapter, challenges specific to antibody repertoire proteomics preclude the use of standard analysis methods and motivated our development of novel tools and approaches for interpreting serum repertoire proteomic data. I will shift focus in chapters 3 and 4 to present an experimental and computational workflow for accurate and full-length de novo peptide sequencing. We applied 351 nm ultraviolet photodissociation (UVPD) on chromophore-tagged peptides and developed software for sequencing the resultant UVPD mass spectra. Improvements described in chapter 4 enable the software to automatically learn from and interpret new types and combinations of spectra from the same precursor peptide. We demonstrate the effectiveness of this machine learning framework on CID/UVPD spectral pairs and obtain results, from low resolution spectra, comparable to current state of the art. Continued development of these de novo interpretation and sequencing methods, in part or in whole, may sidestep many of the remaining challenges facing repertoire proteomics, and successful application of these efforts promises further advancement in antibody repertoire characterization and understanding.
Book Synopsis Peptide Characterization and Application Protocols by : Gregg B. Fields
Download or read book Peptide Characterization and Application Protocols written by Gregg B. Fields and published by Humana Press. This book was released on 2010-11-19 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is dedicated to the characterization of peptides and their applications for the study of biochemical systems. The contributing authors are all leaders in the field of peptide research. Part I, Characterization, presents the most recent advances in select analytical techniques. Part II, Application, presents a variety of specific applications for synthetic peptides. This book is an indispensable aid in the pursuit of new directions in peptide research.
Book Synopsis New Tools for Enhanced Proteome Characterization by : Rachel M. Miller (Ph.D.)
Download or read book New Tools for Enhanced Proteome Characterization written by Rachel M. Miller (Ph.D.) and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are the key biological actors within cells, driving many biological processes integral for both healthy and diseased states. Understanding the depth of complexity represented within the proteome is crucial to our scientific understandingof cellular biology and to provide disease specific insights for clinical applications. Mass spectrometry-based proteomics is the premier method for proteome analysis, with the ability to both identify and quantify proteins. Although proteomics continues to grow as a robust field of bioanalytical chemistry, advances are still necessary to enable a more comprehensive view of the proteome. In this thesis, several new tools for the improvement of proteome characterization are described, seeking to not only increase the depth of proteome characterization, but also the precision of the results obtained. In Chapter 1, an overview of mass spectrometry-based proteomics is provided including specific background information for the different areas of proteomic analysis addressed in the chapters of this thesis. Chapter 2 introduces multi-protease protein inference and illustrates advantages of utilizing peptides from multiple proteolytic digests for protein inference. Chapter 3 describes an in silico digestion software tool called ProteaseGuru, designed to aid in the consideration of alternative proteases for bottom-up experiments. Chapter 4 establishes a software pipeline for the generation of sample-specific databases from PacBio long-read sequencing data. Chapter 5 describes the discovery and validation of dehydroamino acid residues within the HIV-1 virus. These uncommon post-translational modifications (PTMs) were initially discovered using global PTM discovery (GPTMD), and then subsequently validated using a chemical labeling strategy. All the works described throughout this thesis are summarized and future directions for the improvement of proteome characterization are outlined in Chapter 6.
Book Synopsis Modern Proteomics – Sample Preparation, Analysis and Practical Applications by : Hamid Mirzaei
Download or read book Modern Proteomics – Sample Preparation, Analysis and Practical Applications written by Hamid Mirzaei and published by Springer. This book was released on 2016-12-14 with total page 525 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume serves as a proteomics reference manual, describing experimental design and execution. The book also shows a large number of examples as to what can be achieved using proteomics techniques. As a relatively young area of scientific research, the breadth and depth of the current state of the art in proteomics might not be obvious to all potential users. There are various books and review articles that cover certain aspects of proteomics but they often lack technical details. Subject specific literature also lacks the broad overviews that are needed to design an experiment in which all steps are compatible and coherent. The objective of this book was to create a proteomics manual to provide scientists who are not experts in the field with an overview of: 1. The types of samples can be analyzed by mass spectrometry for proteomics analysis. 2. Ways to convert biological or ecological samples to analytes ready for mass spectral analysis. 3. Ways to reduce the complexity of the proteome to achieve better coverage of the constituent proteins. 4. How various mass spectrometers work and different ways they can be used for proteomics analysis 5. The various platforms that are available for proteomics data analysis 6. The various applications of proteomics technologies in biological and medical sciences This book should appeal to anyone with an interest in proteomics technologies, proteomics related bioinformatics and proteomics data generation and interpretation. With the broad setup and chapters written by experts in the field, there is information that is valuable for students as well as for researchers who are looking for a hands on introduction into the strengths, weaknesses and opportunities of proteomics.
Book Synopsis Development and Application of Mass Spectrometry-based Biophysical Approaches by : Ying Zhang
Download or read book Development and Application of Mass Spectrometry-based Biophysical Approaches written by Ying Zhang and published by . This book was released on 2015 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry (MS)-based biophysical approaches are new "tools" for protein characterization owing to its capability to analyze proteins and protein complexes that range in molecular weight from kDa to MDa. Protein characterization requires more than identifying the primary structure. More importantly, protein high order structures (i.e., secondary, tertiary and quaternary structures) are needed for biological studies. MS has become the major tool in studies of protein primary structure and post translational modifications (PTMs) over the past two decades. Because MS has high sensitivity and fast turnaround, more and more biophysical approaches rely on MS to generate information for protein higher order structures. One of the emerging biophysical approaches is MS-based protein footprinting. Protein surface regions can be covalently labeled by chemical reagents in a biologically relevant environment. These chemical labels can be read out by MS through either bottom-up or top-down MS proteomics analysis. The outcome provides protein conformational information. Among various chemical labeling strategies, hydrogen deuterium exchange (HDX) is one of the most commonly used approaches in MS-based protein biophysical studies. HDX-MS is introduced in Chapter 1 by covering the early developments and new applications especially in measuring interaction affinities. Although HDX-MS has been developed for decades, there are still many challenges in protein characterization that require new or improved HDX method development. One such challenge is characterization of protein aggregation. Protein aggregation leads to loss of protein function, and protein aggregates are implicated in several neurodegenerative diseases like Alzheimer's and Parkinson's diseases. A key issue in studies of protein aggregation is real-time monitoring under biologically relevant condition. We developed an HDX-MS-based approach by studying Alzheimer's disease related A[beta] aggregation, and we described this development in Chapter 2. A[beta] proteins are labeled by deuterium in a pulsed way during A[beta] aggregation. The extents of aggregations are monitored by MS as deuterium uptake. This pulsed HDX platform provides peptide-level information about A[beta] aggregation. Ligands (drug candidates) were also evaluated with this platform to determine how the drug candidates affect oligomerization (Chapter 3). Ligand interactions can induce protein conformational changes, which are required in various protein functions like signaling, enzyme activity. Such interactions are fundamental to all biological processes. One of the often used ligands in cells is calcium. Calcium interacts with a variety of calcium-binding proteins, most of which have conserved sequence that form EF-hand motifs to bind calcium. MS-HDX has been an important tool in studies of these typical calcium-binding proteins. Many proteins without an EF-hand motif also require calcium for their function. For example, protein-arginine deiminase (PAD) is an enzyme for arginine citrullination and binds calcium without EF-hand motif. We conducted differential HDX studies on PAD2 protein (Chapter 4). Multiple and cooperative calcium binding of PAD2 are detected by HDX. HDX was further extended by applying protein-ligand titration in an HDX experiment (i.e., Protein-ligand interactions by mass spectrometry, titration and H/D exchange, PLIMSTEX). The calcium binding affinity of each binding site can be elucidated by PLIMSTEX (Chapter 5). Protein aggregation or ligand-binding induced conformational changes can also be detected by MS-HDX. One significant question in MS-based biophysical studies is how to generate structural information for proteins in the absence of a high resolution structure. In a newly developed platform, we combined a traditional structural biology approach, homology modeling, and MS-HDX to generate a structural model for diheme cytochrome c (DHCC) from Heliobacterium (Chapter 6), a protein for which solvent accessibility information from HDX experiment was used as the guide for homology modeling and used to generate a refined structural model of DHCC by using various computational approaches. In summary, we describe in this thesis development and application of several new, refined approaches of HDX and analyze protein aggregation, protein-ligand binding and unknown protein structures. We hope other scientists can apply these approaches to solve complicated and demanding biological problems that are difficult to investigate using traditional biophysical methods
Book Synopsis Characterization of the Extracellular Proteome of a Natural Microbial Community with an Integrated Mass Spectrometric/bioinformatic Approach by : Brian Keith Erickson
Download or read book Characterization of the Extracellular Proteome of a Natural Microbial Community with an Integrated Mass Spectrometric/bioinformatic Approach written by Brian Keith Erickson and published by . This book was released on 2010 with total page 177 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteomics comprises the identification and characterization of the complete suite of expressed proteins in a given cell, organism or community. The coupling of high performance liquid chromatography (LC) with high throughput mass spectrometry (MS) has provided the foundation for current proteomic progression. The transition from proteomic analysis of a single cultivated microbe to that of natural microbial assemblages has required significant advancement in technology and has provided greater biological understanding of microbial community diversity and function. To enhance the capabilities of a mass spectrometric based proteomic analysis, an integrated approach combining bioinformatics with analytical preparations and experimental data collection was developed and applied. This has resulted in a deep characterization of the extracellular fraction of a community of microbes thriving in an acid mine drainage system. Among the notable features of this relatively low complexity community, they exist in a solution that is highly acidic (pH 1) and hot (temperature 40°C), with molar concentrations of metals. The extracellular fraction is of particular interest due to the potential to identify and characterize novel proteins that are critical for survival and interactions with the harsh environment. The following analyses have resulted in the specific identification and characterization of novel extracellular proteins. In order to more accurately identify which proteins are present in the extracellular space, a combined computational prediction and experimental identification of the extracellular fraction was performed. Among the hundreds of proteins identified, a highly abundant novel cytochrome was targeted and ultimately characterized through high performance MS. In order to achieve deep proteomic coverage of the extracellular fraction, a metal affinity based protein enrichment utilizing seven different metals was developed and employed resulting in novel protein identifications. A combined top down and bottom up analysis resulted in the characterization of the intact molecular forms of extracellular proteins, including the identification of post-translational modifications. Finally, in order to determine the effectiveness of current MS methodologies, a software package was designed to characterize the> 100,000 mass spectra collected during an MS experiment, revealing that specific optimizations in the LC, MS and protein sequence database have a significant impact on proteomic depth.
Book Synopsis Advancing Bottom-up Proteomics and Ptm Characterization Via Development of Novel Mass Spectrometry-based Approaches by : Fengfei Ma (Ph.D.)
Download or read book Advancing Bottom-up Proteomics and Ptm Characterization Via Development of Novel Mass Spectrometry-based Approaches written by Fengfei Ma (Ph.D.) and published by . This book was released on 2018 with total page 335 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry (MS) has emerged as a central technology for biomedical research largely due to its capability to provide unprecedented insights into the compositions and structures of the proteome. Thousands of proteins and peptides can be characterized in a single experiment, shedding lights on the complex biological processes and enabling discovery of novel therapeutic targets. This dissertation is devoted to the development of novel liquid chromatography (LC)-MS based techniques to characterize proteins and decipher post-translational modifications (PTMs) qualitatively and quantitatively. Specifically, novel sample preparation strategy has been developed for improved sample recovery and unbiased extraction of different categories of proteins. State-of-the-art hybrid fragmentation methods have been established for large scale differentiation of 3- and 4- hydroxyproline isomers. Furthermore, an integrated pipeline for in-depth investigation of protein glycosylation has been developed and implemented. These innovative analytical methodologies have been successfully demonstrated and applied to comprehensive characterization of biological scaffolds and breast cancer cells, which provide valuable insights into multiple research areas including tissue engineering and cancer biology.
Book Synopsis Report on the proposed Umtata rural water supply scheme, district of Umtata by :
Download or read book Report on the proposed Umtata rural water supply scheme, district of Umtata written by and published by . This book was released on 1979 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
