Advancing Computational Methods for Mass Spectrometry-based Proteomics, Metabolomics, and Analysis of Multi-omics Datasets PDF Download
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Author: Hamid Hamzeiy
Publisher:
ISBN:
Category : Mass spectrometry
Languages : en
Pages :
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Book Description
Author: Hamid Hamzeiy
Publisher:
ISBN:
Category : Mass spectrometry
Languages : en
Pages :
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Book Description
Author: Susmita Datta
Publisher: Springer
ISBN: 3319458094
Category : Medical
Languages : en
Pages : 294
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Book Description
This book presents an overview of computational and statistical design and analysis of mass spectrometry-based proteomics, metabolomics, and lipidomics data. This contributed volume provides an introduction to the special aspects of statistical design and analysis with mass spectrometry data for the new omic sciences. The text discusses common aspects of design and analysis between and across all (or most) forms of mass spectrometry, while also providing special examples of application with the most common forms of mass spectrometry. Also covered are applications of computational mass spectrometry not only in clinical study but also in the interpretation of omics data in plant biology studies. Omics research fields are expected to revolutionize biomolecular research by the ability to simultaneously profile many compounds within either patient blood, urine, tissue, or other biological samples. Mass spectrometry is one of the key analytical techniques used in these new omic sciences. Liquid chromatography mass spectrometry, time-of-flight data, and Fourier transform mass spectrometry are but a selection of the measurement platforms available to the modern analyst. Thus in practical proteomics or metabolomics, researchers will not only be confronted with new high dimensional data types—as opposed to the familiar data structures in more classical genomics—but also with great variation between distinct types of mass spectral measurements derived from different platforms, which may complicate analyses, comparison, and interpretation of results.
Author: Fahad Saeed
Publisher: Springer Nature
ISBN: 3031019601
Category : Science
Languages : en
Pages : 146
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Book Description
To date, processing of high-throughput Mass Spectrometry (MS) data is accomplished using serial algorithms. Developing new methods to process MS data is an active area of research but there is no single strategy that focuses on scalability of MS based methods. Mass spectrometry is a diverse and versatile technology for high-throughput functional characterization of proteins, small molecules and metabolites in complex biological mixtures. In the recent years the technology has rapidly evolved and is now capable of generating increasingly large (multiple tera-bytes per experiment) and complex (multiple species/microbiome/high-dimensional) data sets. This rapid advance in MS instrumentation must be matched by equally fast and rapid evolution of scalable methods developed for analysis of these complex data sets. Ideally, the new methods should leverage the rich heterogeneous computational resources available in a ubiquitous fashion in the form of multicore, manycore, CPU-GPU, CPU-FPGA, and IntelPhi architectures. The absence of these high-performance computing algorithms now hinders scientific advancements for mass spectrometry research. In this book we illustrate the need for high-performance computing algorithms for MS based proteomics, and proteogenomics and showcase our progress in developing these high-performance algorithms.
Author: Conrad Bessant
Publisher: Royal Society of Chemistry
ISBN: 1782626735
Category : Science
Languages : en
Pages : 429
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Book Description
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.
Author: Ingvar Eidhammer
Publisher: John Wiley & Sons
ISBN: 9780470724293
Category : Medical
Languages : en
Pages : 296
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Book Description
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.
Author: Ingvar Eidhammer
Publisher: John Wiley & Sons
ISBN: 111849377X
Category : Mathematics
Languages : en
Pages : 290
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Book Description
The definitive introduction to data analysis in quantitative proteomics This book provides all the necessary knowledge about mass spectrometry based proteomics methods and computational and statistical approaches to pursue the planning, design and analysis of quantitative proteomics experiments. The author’s carefully constructed approach allows readers to easily make the transition into the field of quantitative proteomics. Through detailed descriptions of wet-lab methods, computational approaches and statistical tools, this book covers the full scope of a quantitative experiment, allowing readers to acquire new knowledge as well as acting as a useful reference work for more advanced readers. Computational and Statistical Methods for Protein Quantification by Mass Spectrometry: Introduces the use of mass spectrometry in protein quantification and how the bioinformatics challenges in this field can be solved using statistical methods and various software programs. Is illustrated by a large number of figures and examples as well as numerous exercises. Provides both clear and rigorous descriptions of methods and approaches. Is thoroughly indexed and cross-referenced, combining the strengths of a text book with the utility of a reference work. Features detailed discussions of both wet-lab approaches and statistical and computational methods. With clear and thorough descriptions of the various methods and approaches, this book is accessible to biologists, informaticians, and statisticians alike and is aimed at readers across the academic spectrum, from advanced undergraduate students to post doctorates entering the field.
Author: Kazuki Saito
Publisher: Springer Science & Business Media
ISBN: 3540297820
Category : Science
Languages : en
Pages : 351
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Book Description
Metabolomics – which deals with all metabolites of an organism – is a rapidly-emerging sector of post-genome research fields. It plays significant roles in a variety of fields from medicine to agriculture and holds a fundamental position in functional genomics studies and their application in plant biotechnology. This volume comprehensively covers plant metabolomics for the first time. The chapters offer cutting-edge information on analytical technology, bioinformatics and applications. They were all written by leading researchers who have been directly involved in plant metabolomics research throughout the world. Up-to-date information and future developments are described, thereby producing a volume which is a landmark of plant metabolomics research and a beneficial guideline to graduate students and researchers in academia, industry, and technology transfer organizations in all plant science fields.
Author: Ling Hao
Publisher:
ISBN:
Category :
Languages : en
Pages : 439
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Book Description
Quantitative analysis of endogenous biomolecules offers a wealth of clues to understand cell biology and disease mechanisms. Mass spectrometry (MS) has become a foremost technology for the study of biomolecules and their dynamic alterations involved in disease processes. This dissertation is devoted to the development of novel and improved MS-based metabolomic and proteomic methodologies and the application to human disease studies. Specifically, both label-free and stable isotope labeling strategies have been developed for the analysis of metabolites, peptides, and proteins in various biological systems. Label-free methods provide straightforward measurements of biomolecules and are combined with advanced bioinformatics tools for biomarker discovery. Stable isotope labeling, particularly custom DiLeu, iDiLeu, and mdDiLeu tags, offers high-throughput and accurate quantification of biomolecules. Novel online software platform has also been developed for automated omics data analysis. The advancements of analytical methodologies in this work have been mainly achieved on standard flow liquid chromatography (LC)-MS, nanoflow LC-MS, and capillary electrophoresis (CE)-MS platforms. Comprehensive metabolomic and proteomic studies have been successfully applied to disease biomarker discovery for human Preclinical Alzheimer's Disease and Lower Urinary Tract Symptoms in human and mouse models.
Author: Nicholas William Kwiecien
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
The research described in this dissertation presents novel computational algorithms and strategies for (1) improving the assignment of molecular identities to analytes profiled by high-resolution gas chromatography-mass spectrometry (GC/MS), (2) performing relative quantitation of large sets of metabolites across expansive sets of mass spectrometry data files, (3) disseminating processed mass spectrometry data and post hoc statistical results in web-based platforms, and (4) monitoring mass spectrometer performance via a web-based data processing and analysis tool. An overview of the aforementioned computational strategies and developed software tools is presented in Chapter 1. A novel algorithm for leveraging accurate mass--afforded by high-resolution GC/MS systems--to discriminate between putative identifications assigned to profiled small molecules is described in Chapter 2. In Chapter 3, an algorithm and accompanying software suite designed to enable untargeted quantitation of small molecules across expansive sets of raw GC/MS data files is described. In Chapter 4, these algorithms are employed as part of a larger study wherein 174 single gene deletion strains of yeast were comprehensively profiled at the proteomic, metabolomic, and lipidomic levels. These multi-omic data were then integrated through various analysis planes in order to define functions of uncharacterized mitochondrial proteins. Chapter 5 details numerous web-based data visualization utilities developed for various projects designed to enable researchers to more rapidly interrogate MS data sets at depth. In Chapter 6, the development of a web-based mass spectrometry data deposition, processing, and visualization tool for automated quality control analysis is described.
Author: Sastia Prama Putri
Publisher: CRC Press
ISBN: 1482223775
Category : Science
Languages : en
Pages : 284
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Book Description
Mass Spectrometry-Based Metabolomics: A Practical Guide is a simple, step-by-step reference for profiling metabolites in a target organism. It discusses optimization of sample preparation for urine, serum, blood, tissue, food, and plant and animal cell samples. Encompassing three different technical fields-biology, analytical chemistry, and informa
