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Author: Muaaz Gul Awan Publisher: ISBN: Category : Data reduction Languages : en Pages : 98
Book Description
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.
Author: Muaaz Gul Awan Publisher: ISBN: Category : Data reduction Languages : en Pages : 98
Book Description
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.
Author: Fahad Saeed Publisher: Springer Nature ISBN: 3031019601 Category : Science Languages : en Pages : 146
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: Daniela Cecconi Publisher: ISBN: 9781071616413 Category : Proteomics Languages : en Pages : 326
Book Description
This thorough book collects methods and strategies to analyze proteomics data. It is intended to describe how data obtained by gel-based or gel-free proteomics approaches can be inspected, organized, and interpreted to extrapolate biological information. Organized into four sections, the volume explores strategies to analyze proteomics data obtained by gel-based approaches, different data analysis approaches for gel-free proteomics experiments, bioinformatic tools for the interpretation of proteomics data to obtain biological significant information, as well as methods to integrate proteomics data with other omics datasets including genomics, transcriptomics, metabolomics, and other types of data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice that will ensure high quality results in the lab. Authoritative and practical, Proteomics Data Analysis serves as an ideal guide to introduce researchers, both experienced and novice, to new tools and approaches for data analysis to encourage the further study of proteomics.
Author: Gary Siuzdak Publisher: ISBN: 9780974245126 Category : Bioengineering Languages : en Pages : 0
Book Description
Covers the basic concepts in mass spectrometry as well as advanced topics including protein identification/protein structural analysis, carbohydrate and oligonucleotide analysis. Topics also include pharmacokinetics, high throughput screening, and the recent development of mass spectrometry in clinical diagnosis.
Author: Bogusław Buszewski Publisher: Springer Nature ISBN: 3030956601 Category : Science Languages : en Pages : 1091
Book Description
This book presents an authoritative review of analytical methods used for diagnostics, medical therapy and for forensic purposes. Divided into 4 parts, the book discusses new challenges in bioanalytics, covers bioanalysis as a source of clinical, pharmaceutical and forensic information, explores natural resources as a source of biologically active compounds, and offers new analytical strategies and equipment solutions. Written by interdisciplinary expert academics, this work will appeal to a wide readership of students, researchers and professionals interested in the fields of medicine, chemistry, pharmaceutical, life and health sciences, engineering and environmental protection. Clinicians and employees of forensic laboratories will also find this work instructive and informative.
Author: Pedro R. Cutillas Publisher: Humana Press ISBN: 9781607617815 Category : Science Languages : en Pages : 330
Book Description
With the development of new quantitative strategies and powerful bioinformatics tools to cope with the analysis of the large amounts of data generated in proteomics experiments, liquid chromatography with tandem mass spectrometry (LC-MS/MS) is making possible the analysis of proteins on a global scale, meaning that proteomics can now start competing with cDNA microarrays for the analysis of whole genomes. In LC-MS/MS in Proteomics: Methods and Applications, experts in the field provide protocols and up-to-date reviews of the applications of LC-MS/MS, with a particular focus on MS-based methods of protein and peptide quantification and the analysis of post-translational modifications. Beginning with overviews of the use of LC-M/MS in protein analysis, the book continues with topics such as protocols for the analysis of post-translational modifications, with particular focus on phosphorylation and glycosylation, popular techniques for quantitative proteomics, such as multiple reaction monitoring, metabolic labelling, and chemical tagging, biomarker discovery in biological fluids, as well as novel applications of LC-MS/MS. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective subjects, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, LC-MS/MS in Proteomics: Methods and Applications presents the techniques and concepts necessary in order to aid proteomic practitioners in the application of LC-MS/MS to essentially any biological problem.
Author: Bin Liang Publisher: Elsevier ISBN: 0443141711 Category : Science Languages : en Pages : 671
Book Description
Water Security: Big Data-Driven Risk Identification, Assessment and Control of Emerging Contaminants contains the latest information on big data–driven risk detection and analysis, risk assessment and environmental health effect, intelligent risk control technologies, and global control strategy of emerging contaminants. First, this book highlights advances and challenges throughout the detection of emerging chemical contaminants (e.g., antimicrobials, microplastics) by sensors or mass spectrometry, as well as emerging biological contaminant (e.g., ARGs, pathogens) by a combination of next- and third-generation sequencing technologies in aquatic environment. Second, it discusses in depth the ecological risk assessment and environmental health effects of emerging contaminants. Lastly, it presents the most up-to-date intelligent risk management technologies. This book shares instrumental global strategy and policy analysis on how to control emerging contaminants. Offering interdisciplinary and global perspectives from experts in environmental sciences and engineering, environmental microbiology and microbiome, environmental informatics and bioinformatics, intelligent systems, and knowledge engineering, this book provides an accessible and flexible resource for researchers and upper level students working in these fields. Covers the detection, high-throughput analyses, and environmental behavior of the typical emerging chemical and biological contaminants Focuses on chemical and biological big data driven aquatic ecological risk assessment models and techniques Highlights the intelligent management and control technologies and policies for emerging contaminants in water environments
Author: Gerard Drewes Publisher: Humana Press ISBN: 9781617793639 Category : Science Languages : en Pages : 0
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: Alexander R. Ivanov Publisher: Springer Science & Business Media ISBN: 9400708289 Category : Science Languages : en Pages : 1081
Book Description
The aim of this book is to provide the researcher with important sample preparation strategies in a wide variety of analyte molecules, specimens, methods, and biological applications requiring mass spectrometric analysis as a detection end-point. In this volume we have compiled the contributions from several laboratories which are employing mass spectrometry for biological analysis. With the latest inventions and introduction of highly sophisticated mass spectrometry equipment sample preparation becomes an extremely important bottleneck of biomedical analysis. We have a goal of giving the reader several successful examples of sample preparation, development and optimization, leading to the success in analytical steps and proper conclusions made at the end of the day. This book is structured as a compilation of contributed chapters ranging from protocols to research articles and reviews. The main philosophy of this volume is that sample preparation methods have to be optimized and validated for every project, for every sample type and for every downstream analytical technique.
Author: A. Wallace Hayes Publisher: CRC Press ISBN: 1000875776 Category : Medical Languages : en Pages : 2143
Book Description
Hayes’ Principles and Methods of Toxicology has long been established as a reliable and informative reference for the concepts, methodologies, and assessments integral to toxicology. The new edition contains updated and new chapters with the addition of new authors while maintaining the same high standards that have made this book a benchmark resource in the field. Key Features: The comprehensive yet concise coverage of various aspects of fundamental and applied toxicology makes this book a valuable resource for educators, students, and professionals. Questions provided at the end of each chapter allow readers to test their knowledge and understanding of the material covered. All chapters have been updated and over 60 new authors have been added to reflect the dynamic nature of toxicological sciences New topics in this edition include Safety Assessment of Cosmetics and Personal Care Products, The Importance of the Dose/Rate Response, Novel Approaches and Alternative Models, Epigenetic Toxicology, and an Expanded Glossary. The volume is divided into 4 major sections, addressing fundamental principles of toxicology (Section I. "Principles of Toxicology"), major classes of established chemical hazards (Section II. "Agents"), current methods used for the assessment of various endpoints indicative of chemical toxicity (Section III. "Methods"), as well as toxicology of specific target systems and organs (Section IV. "Organ- and System-Specific Toxicology"). This volume will be a valuable tool for the audience that wishes to broaden their understanding of hazards and mechanisms of toxicity and to stay on top of the emerging methods and concepts of the rapidly advancing field of toxicology and risk assessment.
Author: Muaaz Gul Awan
Author: Muaaz Gul Awan
Author: Fahad Saeed
Author: Daniela Cecconi
Author: Gary Siuzdak
Author: Bogusław Buszewski
Author: Pedro R. Cutillas
Author: Bin Liang
Author: Gerard Drewes
Author: Alexander R. Ivanov
Author: A. Wallace Hayes