Unraveling Signal Transduction Networks by High-resolution and Quantitative Mass-spectrometry-based Proteomics PDF Download
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Author: Maximiliane Hilger
Publisher:
ISBN:
Category :
Languages : en
Pages : 115
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Author: Maximiliane Hilger
Publisher:
ISBN:
Category :
Languages : en
Pages : 115
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Author: L. A. T. Meijer
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Author: Alejandro Wolf Yadlin
Publisher:
ISBN:
Category :
Languages : en
Pages : 272
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(cont.) Because our method was based on information dependent acquisition (IDA) the reproducibility of peptides identified across multiple analyses was low. To improve our methodology to permit both discovery of new phosphorylation sites and robust quantification of hundreds of nodes within a signaling network we combined IDA-analysis with multiple reaction monitoring (MRM) of selected precursor ions. MRM quantification of high resolution temporal profiles of the EGFR network provided 88% reproducibility across four different samples, as compared to 34% reproducibility by IDA only. In summary, we have developed a new robust mass spectrometry technique allowing site specific identification, quantification and monitoring of dynamic phosphorylation in the cell with high temporal resolution and under any number of biological conditions. Because the data obtained with this method is not sparse it is especially well suited to mathematical and computational analyses. The methodology is also broadly applicable to multiple signaling networks and to a variety of samples, including quantitative analysis of signaling networks in clinical samples.
Author: Stefan Hanke
Publisher:
ISBN:
Category :
Languages : en
Pages : 246
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Author: Zhou Li (Researcher in biological systems)
Publisher:
ISBN:
Category : Acid mine drainage
Languages : en
Pages : 175
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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).
Author: Timothy Gordon Curran
Publisher:
ISBN:
Category :
Languages : en
Pages : 163
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Mass spectrometry has become the tool of choice for proteomics. Its unrivaled coverage and reproducibility has positioned it head and shoulders above competing techniques for analyzing protein expression post-translational modification. With the increased popularity comes a flood of new research applications, each with its own biological motivations and goals. To ensure that mass spectrometry-based proteomics can be useful to as many biological questions as possible, it is of utmost importance to ensure high data quality. This research focuses on two general stages of the typical proteomics workflow and introduces tools to facilitate effective target screening, follow-up analysis, as well as more precise measurements. This new pipeline is then demonstrated in a case study of Epidermal Growth Factor Receptor (EGFR) signaling and phenotype prediction. The quantity of proteomic mass spectrometry data available from a single analysis has increased exponentially as new generations of instruments become quicker and more sensitive. This deluge of data leaves many tempted to forego time-intensive manual validation of database identified targets in favor of global data set quality statistics. Particularly in the realm of post-translational modifications, long lists of putative matches are often reported with little or no scan-specific validation. Such practices no longer provide assurance that any single identified target is indeed correct, leaving researchers vulnerable to expending vast resources chasing false positives. The argument is that manual validation is too time-intensive to be carried out for each and every identification. To remedy this problem we have introduced the Computer Assisted Manual Validation (CAMV) software package to expedite the procedure by preprocessing the database results so as to remove the tedious steps associated with the validation task and only recruit human judgment for the final quality decision. This approach has drastically decreased the time required for manual validation; a task that used to take weeks now is completed in hours. Another focus of this research is the development of a multiplex, multisite absolute quantification method, which has improved the quality of quantitative proteomic mass spectrometry data. Absolute site-specific data allows many more biological hypotheses to be directly tested with a single mass spectrometry experiment, including phosphorylation stoichiometry. This technique has been applied to the EGFR system to better understand signaling downstream of three distinct ligands. These ligands all bind the same receptor yet elicit different phenotypes, suggesting differential information processing. The analysis showed unique patterns of receptor phosphorylation present following sub-saturating ligand treatment. However, at saturating doses the same pattern of phosphorylation is produced regardless of ligand, but the magnitude of that pattern is still ligand-dependent. In this regime, the adaptor proteins were still able to retain ligand-specific phosphorylation patterns presumably responsible for differential phenotypes. The data set also permitted the identification of signals important for the regulation of only one of the two phenotypes examined.
Author: Gerard Drewes
Publisher: Humana Press
ISBN: 9781617793639
Category : Science
Languages : en
Pages : 0
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Book Description
The multidisciplinary science of chemical proteomics studies how small molecules of synthetic or natural origin bind to proteins and modulate their function. In Chemical Proteomics: Methods and Protocols, expert researchers in the field provide key techniques to investigate chemical proteomics focusing on analytical strategies, how probes are generated, techniques for the discovery of small molecule targets and the probing of target function, and small molecule ligand and drug discovery. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Chemical Proteomics : Methods and Protocols seeks to provide methodologies that will contribute to a wider application of chemical proteomics methods in biochemical and cell biological laboratories.
Author: John R. Griffiths
Publisher: John Wiley & Sons
ISBN: 1119045851
Category : Science
Languages : en
Pages : 414
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Book Description
Covers all major modifications, including phosphorylation, glycosylation, acetylation, ubiquitination, sulfonation and and glycation Discussion of the chemistry behind each modification, along with key methods and references Contributions from some of the leading researchers in the field A valuable reference source for all laboratories undertaking proteomics, mass spectrometry and post-translational modification research
Author: Hamid Mirzaei
Publisher: Springer
ISBN: 3319414488
Category : Science
Languages : en
Pages : 525
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Book Description
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.
Author: Thomas J. Hope
Publisher:
ISBN: 9781461496106
Category : AIDS (Disease)
Languages : en
Pages :
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