Computational Strategies for the Generation and Analysis of Mass Spectrometry-based Lipidomics Data

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ISBN 13 :
Total Pages : 200 pages
Book Rating : 4.:/5 (123 download)

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Book Synopsis Computational Strategies for the Generation and Analysis of Mass Spectrometry-based Lipidomics Data by : Paul Daniel Hutchins

Download or read book Computational Strategies for the Generation and Analysis of Mass Spectrometry-based Lipidomics Data written by Paul Daniel Hutchins and published by . This book was released on 2019 with total page 200 pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation describes advances in the analysis of mass spectrometry-based lipid measurements and their use to ascribe function to uncharacterized proteins. Despite their biochemical significance, lipids' structural complexity and diversity render their comprehensive characterization challenging. Chapter 1 outlines the use of mass spectrometry (MS) for lipid analysis, the unique analytical challenges created by lipid's combinatorial composition, and the data analysis steps required for robust lipid identification. Chapter 2 describes an open-source software suite which automates lipid identification using lipid-optimized algorithms - significantly reducing hands-on processing time for large lipidomic datasets. Chapter 3 discusses an algorithm to extract lipid fragmentation rules directly from experimental tandem mass spectra (MS/MS) and generate accurate in silico spectral libraries with minimal manual annotation. Although these two software tools significantly streamline lipid data processing, the quality and quantity of lipid identifications depend heavily on MS acquisition parameters optimized for the specific sample. A computational strategy for simulation of MS lipid data acquisition across different method parameters was developed to accelerate this time-consuming process and is outlined in Chapter 4. In Chapter 5, the described lipid data analysis tools are utilized as part of a multi-omic analysis of 106 CRISPR gene-deletion strains for the functional classification of uncharacterized mitochondrial proteins. Finally, Chapter 6 discusses potential solutions to the inherent challenges of lipidomics analysis and its potential as a vital systems biology tool.

Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry

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Publisher : Springer
ISBN 13 : 3319458094
Total Pages : 294 pages
Book Rating : 4.3/5 (194 download)

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Book Synopsis Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry by : Susmita Datta

Download or read book Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry written by Susmita Datta and published by Springer. This book was released on 2016-12-15 with total page 294 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Computational Approaches for Improved Identification, Quantitation, and Interpretation of Mass Spectrometry-based "omics" Data

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ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (11 download)

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Book Synopsis Computational Approaches for Improved Identification, Quantitation, and Interpretation of Mass Spectrometry-based "omics" Data by : Nicholas William Kwiecien

Download or read book Computational Approaches for Improved Identification, Quantitation, and Interpretation of Mass Spectrometry-based "omics" Data written by Nicholas William Kwiecien and published by . This book was released on 2016 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

High-Performance Algorithms for Mass Spectrometry-Based Omics

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Publisher : Springer Nature
ISBN 13 : 3031019601
Total Pages : 146 pages
Book Rating : 4.0/5 (31 download)

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Book Synopsis High-Performance Algorithms for Mass Spectrometry-Based Omics by : Fahad Saeed

Download or read book High-Performance Algorithms for Mass Spectrometry-Based Omics written by Fahad Saeed and published by Springer Nature. This book was released on 2022-09-02 with total page 146 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Lipidomics

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Publisher : John Wiley & Sons
ISBN 13 : 1118893123
Total Pages : 48 pages
Book Rating : 4.1/5 (188 download)

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Book Synopsis Lipidomics by : Xianlin Han

Download or read book Lipidomics written by Xianlin Han and published by John Wiley & Sons. This book was released on 2016-05-02 with total page 48 pages. Available in PDF, EPUB and Kindle. Book excerpt: Covers the area of lipidomics from fundamentals and theory to applications Presents a balanced discussion of the fundamentals, theory, experimental methods and applications of lipidomics Covers different characterizations of lipids including Glycerophospholipids; Sphingolipids; Glycerolipids and Glycolipids; and Fatty Acids and Modified Fatty Acids Includes a section on quantification of Lipids in Lipidomics such as sample preparation; factors affecting accurate quantification; and data processing and interpretation Details applications of Lipidomics Tools including for Health and Disease; Plant Lipidomics; and Lipidomics on Cellular Membranes

Data Analysis in Proteomics Novel Computational Strategies for Modeling and Interpreting Complex Mass Spectrometry Data

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ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (68 download)

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Book Synopsis Data Analysis in Proteomics Novel Computational Strategies for Modeling and Interpreting Complex Mass Spectrometry Data by :

Download or read book Data Analysis in Proteomics Novel Computational Strategies for Modeling and Interpreting Complex Mass Spectrometry Data written by and published by . This book was released on 2008 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Contemporary proteomics studies require computational approaches to deal with both the complexity of the data generated, and with the volume of data produced. The amalgamation of mass spectrometry -- the analytical tool of choice in proteomics -- with the computational and statistical sciences is still recent, and several avenues of exploratory data analysis and statistical methodology remain relatively unexplored. The current study focuses on three broad analytical domains, and develops novel exploratory approaches and practical tools in each. Data transform approaches are the first explored. These methods re-frame data, allowing for the visualization and exploitation of features and trends that are not immediately evident. An exploratory approach making use of the correlation transform is developed, and is used to identify mass-shift signals in mass spectra. This approach is used to identify and map post-translational modifications on individual peptides, and to identify SILAC modification-containing spectra in a full-scale proteomic analysis. Secondly, matrix decomposition and projection approaches are explored; these use an eigen-decomposition to extract general trends from groups of related spectra. A data visualization approach is demonstrated using these techniques, capable of visualizing trends in large numbers of complex spectra, and a data compression and feature extraction technique is developed suitable for use in spectral modeling. Finally, a general machine learning approach is developed based on conditional random fields (CRFs). These models are capable of dealing with arbitrary sequence modeling tasks, similar to hidden Markov models (HMMs), but are far more robust to interdependent observational features, and do not require limiting independence assumptions to remain tractable. The theory behind this approach is developed, and a simple machine learning fragmentation model is developed to test the hypothesis that reproducible sequence-specific intens.

Computational Methods for Mass Spectrometry Proteomics

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Publisher : John Wiley & Sons
ISBN 13 : 9780470724293
Total Pages : 296 pages
Book Rating : 4.7/5 (242 download)

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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 John Wiley & Sons. This book was released on 2008-02-28 with total page 296 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.

Lipidomics and Bioactive Lipids: Mass Spectrometry Based Lipid Analysis

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Publisher : Elsevier
ISBN 13 : 0080554881
Total Pages : 432 pages
Book Rating : 4.0/5 (85 download)

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Book Synopsis Lipidomics and Bioactive Lipids: Mass Spectrometry Based Lipid Analysis by :

Download or read book Lipidomics and Bioactive Lipids: Mass Spectrometry Based Lipid Analysis written by and published by Elsevier. This book was released on 2007-11-26 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume in the well-established Methods in Enzymology series features methods for the study of lipids using mass spectrometry techniques. Articles in this volume cover topics such as Qualitative Analysis and Quantitative Assessment of Changes in Neutral Glycerol Lipid Molecular Species within Cells; Glycerophospholipid identification and quantitation by electrospray ionization mass spectrometry; Detection and Quantitation of Eicosanoids via High Performance Liquid Chromatography/Electrospray Ionization Mass Spectrometry; Structure-specific, quantitative methods for "lipidomic" analysis of sphingolipids by tandem mass spectrometry; Analysis of Ubiquinones, Dolichols and Dolichol Diphosphate-Oligosaccharides by Liquid Chromatography Electrospray Ionization Mass Spectrometry; Extraction and Analysis of Sterols in Biological Matrices by High-Performance Liquid Chromatography Electrospray Ionization Mass Spectrometry; The Lipid Maps Initiative in Lipidomics; Basic analytical systems for lipidomics by mass spectrometry in Japan; The European Lipidomics Initiative Enabling technologies; Lipidomic analysis of Signaling Pathways; Bioinformatics for Lipidomics; Mediator Lipidomics: Search Algorithms for Eicosanoids, Resolvins and Protectins; A guide to biochemical systems modeling of sphingolipids for the biochemist; and Quantitation and Standardization of Lipid Internal Standards for Mass Spectroscopy.

Mass Spectrometry-Based Lipidomics

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Publisher : Humana
ISBN 13 : 9781071614129
Total Pages : 314 pages
Book Rating : 4.6/5 (141 download)

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Book Synopsis Mass Spectrometry-Based Lipidomics by : Fong-Fu Hsu

Download or read book Mass Spectrometry-Based Lipidomics written by Fong-Fu Hsu and published by Humana. This book was released on 2022-05-20 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed volume covers conventional MS-based “shotgun lipidomics” by which samples are introduced by infusion or loop injection, as well as LC-MS-based lipidomics, which are becoming increasingly important due to the ever-increasing demand for a complete and precise lipid analysis of the complex and diversified lipids in nature. The volume features protocols applying chemical reactions, the on-line photochemical reactions combined with various MS methods for comprehensive characterization of various lipid classes, and quantification of specific and rare lipids. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Mass Spectrometry-Based Lipidomics: Methods and Protocols serves as an invaluable guide for biochemists and mass spectroscopists who are interested in lipid studies.

Mass Spectrometry-Based Lipidomics

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Publisher : Humana
ISBN 13 : 9781071614099
Total Pages : 314 pages
Book Rating : 4.6/5 (14 download)

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Book Synopsis Mass Spectrometry-Based Lipidomics by : Fong-Fu Hsu

Download or read book Mass Spectrometry-Based Lipidomics written by Fong-Fu Hsu and published by Humana. This book was released on 2021-05-29 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed volume covers conventional MS-based “shotgun lipidomics” by which samples are introduced by infusion or loop injection, as well as LC-MS-based lipidomics, which are becoming increasingly important due to the ever-increasing demand for a complete and precise lipid analysis of the complex and diversified lipids in nature. The volume features protocols applying chemical reactions, the on-line photochemical reactions combined with various MS methods for comprehensive characterization of various lipid classes, and quantification of specific and rare lipids. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Mass Spectrometry-Based Lipidomics: Methods and Protocols serves as an invaluable guide for biochemists and mass spectroscopists who are interested in lipid studies.

Mass Spectrometry for Lipidomics

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Publisher : John Wiley & Sons
ISBN 13 : 3527836500
Total Pages : 897 pages
Book Rating : 4.5/5 (278 download)

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Book Synopsis Mass Spectrometry for Lipidomics by : Michal Holcapek

Download or read book Mass Spectrometry for Lipidomics written by Michal Holcapek and published by John Wiley & Sons. This book was released on 2023-03-07 with total page 897 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass Spectrometry for Lipidomics All-in-one guide to successful lipidomic analysis, combining the latest advances and best practices from academia, industry, and clinical research Mass Spectrometry for Lipidomics presents a systematic overview of lipidomic analysis, covering established standards of lipid analysis, available technology, and key lipid classes, as well as applications in basic research, medicine, pharma, and the food industry. Through connecting recent technological advances with key application areas, this unique guide bridges the gap between academia and industry by translating the vast body of knowledge that has been gained in the past decade into much-needed practical advice for novices as well as routine users. Edited by the president and vice-president of the International Lipidomics Society with contributions from the top experts in lipid analysis, Mass Spectrometry for Lipidomics covers a wide range of key topics, including: Aspects of sample preparation, separation methods, different mass spectrometry modes, as well as identification and quantitation, including the use of bioinformatics tools for data analysis Identification, quantitation and profiling of lipids in different types of biological samples Analytical approaches for all major classes of biological lipids, from fatty acids to phospholipids to sterols Novel applications in biological research, clinical diagnostics, as well as food and crop science For analytical chemists, biochemists, clinical chemists, and analytical laboratories and hospitals, Mass Spectrometry for Lipidomics presents a comprehensive and authoritative overview of the subject, with unmatched expertise from practicing professionals actively involved in the latest research.

High-Throughput Metabolomics

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Publisher : Humana
ISBN 13 : 9781493992355
Total Pages : 459 pages
Book Rating : 4.9/5 (923 download)

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Book Synopsis High-Throughput Metabolomics by : Angelo D'Alessandro

Download or read book High-Throughput Metabolomics written by Angelo D'Alessandro and published by Humana. This book was released on 2019-05-23 with total page 459 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed volume focuses on recent technological, computational, and biostatistical advances in the field of high-throughput metabolomics. Chapters encompass methods, platforms, and analytical strategies for steady state measurements and metabolic flux analysis with stable isotope-labeled tracers, in biological matrices of clinical relevance and model organisms. Mass spectrometry-based or orthogonal methods are discussed, along with computational and statistical methods to address data sparsity in high-throughput metabolomics approaches. As a part of the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, High-Throughput Metabolomics: Methods and Protocols provides tools that can bring about the next generation of clinical biochemistry in a cost-effective, rigorous fashion, exponentially advancing our capacity to investigate nature while hastening the advent of personalized medicine.

Novel Computational Techniques in Mass Spectrometry Based Proteomics

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Publisher :
ISBN 13 : 9783838332307
Total Pages : 144 pages
Book Rating : 4.3/5 (323 download)

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Book Synopsis Novel Computational Techniques in Mass Spectrometry Based Proteomics by : Lukas Mueller

Download or read book Novel Computational Techniques in Mass Spectrometry Based Proteomics written by Lukas Mueller and published by . This book was released on 2011-07 with total page 144 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Chemical Derivatization in Gas Chromatography

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Publisher : Elsevier
ISBN 13 : 0080858201
Total Pages : 247 pages
Book Rating : 4.0/5 (88 download)

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Book Synopsis Chemical Derivatization in Gas Chromatography by : J. Drozd

Download or read book Chemical Derivatization in Gas Chromatography written by J. Drozd and published by Elsevier. This book was released on 1986-07-01 with total page 247 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical Derivatization in Gas Chromatography

Metabolomics

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Publisher : CRC Press
ISBN 13 : 1498725279
Total Pages : 276 pages
Book Rating : 4.4/5 (987 download)

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Book Synopsis Metabolomics by : Ron Wehrens

Download or read book Metabolomics written by Ron Wehrens and published by CRC Press. This book was released on 2019-08-19 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metabolomics is the scientific study of the chemical processes in a living system, environment and nutrition. It is a relatively new omics science, but the potential applications are wide, including medicine, personalized medicine and intervention studies, food and nutrition, plants, agriculture and environmental science. The topics presented and discussed in this book are based on the European Molecular Biology Organization (EMBO) practical courses in metabolomics bioinformatics taught to those working in the field, from masters to postgraduate students, PhDs, postdoctoral and early PIs. The book covers the basics and fundamentals of data acquisition and analytical technologies, but the primary focus is data handling and data analysis. The mentioning and usage of a particular data analysis tool has been avoided; rather, the focus is on the concepts and principles of data processing and analysis. The material has been class-tested and includes lots of examples, computing and exercises. Key Features: Provides an overview of qualitative /quantitative methods in metabolomics Offers an introduction to the key concepts of metabolomics, including experimental design and technology Covers data handling, processing, analysis, data standards and sharing Contains lots of examples to illustrate the topics Includes contributions from some of the leading researchers in the field of metabolomics with extensive teaching experiences

High-performance Reductive Strategies for Big Data from LC-MS/MS Proteomics

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Publisher :
ISBN 13 :
Total Pages : 98 pages
Book Rating : 4.:/5 (113 download)

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Book Synopsis High-performance Reductive Strategies for Big Data from LC-MS/MS Proteomics by : Muaaz Gul Awan

Download or read book High-performance Reductive Strategies for Big Data from LC-MS/MS Proteomics written by Muaaz Gul Awan and published by . This book was released on 2019 with total page 98 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass Spectrometry (MS)-based proteomics utilizes high performance liquid chromatography in tandem with high-throughput mass spectrometers. These experiments can produce MS data sets with astonishing speed and volume that can easily reach peta-scale level, creating storage and computational problems for large-scale systems biology studies. Each spectrum output by a mass spectrometer may consist of thousands of peaks, which must all be processed to deduce the corresponding peptide. However, only a small percentage of peaks in a spectrum are useful for further processing, as most of the peaks are either noise or are not useful. Our experiments have shown that 90 to 95% of the peaks are not required for reliable results. This leads to a lot of redundant processing and causes a hindrance to high-throughput processing of big MS data. The existing pre-processing algorithms for noise-removal or spectra-denoising are limited in their data-reduction capability and are compute intensive; in most cases these pre-processing stages create an additional compute bottleneck in the software pipeline for proteomics. One method of attacking this problem would be by developing data-aware algorithms capable of minimizing the amount of redundant computations. Besides, owing to the continuous increase in the speed and size of proteomics data, high-performance computing solutions need to be introduced. In this study we propose a new data reduction algorithm, which exploits the high noise content of MS/MS data to its advantage and uses a weighted-random- sampling technique to reduce the number of computations drastically. Our results have shown a speed gain of over 100x with respect to the existing tools, while giving comparable accuracy on experimental data. To support rapid adoption and development of high-performance computing solutions in proteomics and big data studies in general, we introduce a template-based strategy for development of optimized GPU-based algorithms for omics data. Our proposed template outlines generic methods to tackle critical GPU-centric bottlenecks and provides details of implementing optimized and scalable GPU algorithms for a given big data problem. We demonstrate the application of this template by implementing a GPU version of our proposed data-reduction algorithm as a case-study. This study also explores the methods of benchmarking novel proteomics algorithms and introduces a highly configurable data simulator to generate user-controlled ground-truth data for assessing new algorithms.

Computational data analysis and bioinformatics in mass spectrometry based proteomics

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Publisher :
ISBN 13 :
Total Pages : 58 pages
Book Rating : 4.:/5 (768 download)

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Book Synopsis Computational data analysis and bioinformatics in mass spectrometry based proteomics by : Thomas Aarup Hansen

Download or read book Computational data analysis and bioinformatics in mass spectrometry based proteomics written by Thomas Aarup Hansen and published by . This book was released on 2010 with total page 58 pages. Available in PDF, EPUB and Kindle. Book excerpt: