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Acceleration And Improvement Of Protein Identification By Mass Spectrometry
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Author :Willy Vincent Bienvenut Publisher :Springer Science & Business Media ISBN 13 :1402033192 Total Pages :314 pages Book Rating :4.4/5 (2 download)
Book Synopsis Acceleration and Improvement of Protein Identification by Mass Spectrometry by : Willy Vincent Bienvenut
Download or read book Acceleration and Improvement of Protein Identification by Mass Spectrometry written by Willy Vincent Bienvenut and published by Springer Science & Business Media. This book was released on 2005-12-05 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: At present where protein identification and characterisation using mass spectrometry is a method of choice, this book is presenting a review of basic proteomic techniques. The second part of the book is related to the novel high throughput protein identification technique called the 'molecular scanner'. Several protein identification techniques are described, especially the peptide mass fingerprint with MALDI-MS based method. E.g. ionisation process, matrix available, signal reproducibility and suppression effect, as well as date treatment for protein identification using bioinformatics tools.
Author :Willy Vincent Bienvenut Publisher :Springer Science & Business Media ISBN 13 :9781402033186 Total Pages :324 pages Book Rating :4.0/5 (331 download)
Book Synopsis Acceleration and Improvement of Protein Identification by Mass Spectrometry by : Willy Vincent Bienvenut
Download or read book Acceleration and Improvement of Protein Identification by Mass Spectrometry written by Willy Vincent Bienvenut and published by Springer Science & Business Media. This book was released on 2005-04-19 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt: At present where protein identification and characterisation using mass spectrometry is a method of choice, this book is presenting a review of basic proteomic techniques. The second part of the book is related to the novel high throughput protein identification technique called the 'molecular scanner'. Several protein identification techniques are described, especially the peptide mass fingerprint with MALDI-MS based method. E.g. ionisation process, matrix available, signal reproducibility and suppression effect, as well as date treatment for protein identification using bioinformatics tools.
Book Synopsis Computational Acceleration of Mass-spectrometry Based Protein Identification Algorithms Using Field-programmable Gate Arrays by :
Download or read book Computational Acceleration of Mass-spectrometry Based Protein Identification Algorithms Using Field-programmable Gate Arrays written by and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Protein Analysis using Mass Spectrometry by : Mike S. Lee
Download or read book Protein Analysis using Mass Spectrometry written by Mike S. Lee and published by John Wiley & Sons. This book was released on 2017-06-19 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents Practical Applications of Mass Spectrometry for Protein Analysis and Covers Their Impact on Accelerating Drug Discovery and Development Covers both qualitative and quantitative aspects of Mass Spectrometry protein analysis in drug discovery Principles, Instrumentation, Technologies topics include MS of peptides, proteins, and ADCs , instrumentation in protein analysis, nanospray technology in MS protein analysis, and automation in MS protein analysis Details emerging areas from drug monitoring to patient care such as Identification and validation of biomarkers for cancer, targeted MS approaches for biomarker validation, biomarker discovery, and regulatory perspectives Brings together the most current advances in the mass spectrometry technology and related method in protein analysis
Book Synopsis Computer-Supported Cooperative Work by : Uwe M. Borghoff
Download or read book Computer-Supported Cooperative Work written by Uwe M. Borghoff and published by Springer Science & Business Media. This book was released on 2000-07-14 with total page 1342 pages. Available in PDF, EPUB and Kindle. Book excerpt: A detailed introduction to interdisciplinary application area of distributed systems, namely the computer support of individuals trying to solve a problem in cooperation with each other but not necessarily having identical work places or working times. The book is addressed to students of distributed systems, communications, information science and socio-organizational theory, as well as to users and developers of systems with group communication and cooperation as top priorities.
Book Synopsis Computational Methods to Improve and Validate Peptide Identifications in Proteomics by : Lei Wang (Computer scientist)
Download or read book Computational Methods to Improve and Validate Peptide Identifications in Proteomics written by Lei Wang (Computer scientist) and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the rapid development of mass spectrometry technology in the past decade and the recent large-scale proteomics projects, massive and highly redundant tandem mass spectra (MS/MS) are being generated at an unprecedented speed. Hundreds of publications have been made for proteomics studies, yet computational methods which can efficiently identify and analyze the sheer amount of proteomic MS/MS data are still outstanding. The thesis aims to provide systematic approaches to studying MS/MS data from three aspects: spectral clustering, spectral library searching and validation of peptide-spectrum matchings (PSMs).I first introduce a rapid algorithm accelerated by Locality Sensitive Hashing (LSH) techniques to reduce the redundancy in proteomics datasets via clustering similar spectra. The proposed method demonstrates 7-11X performance improvement in running time while retaining superior sensitivity and accuracy when compared to the state of the art spectral clustering algorithms. In addition to the reduction of repetition of similar spectra, the time to search protein database, i.e. a commonly used technique for peptide identification, can be greatly shortened when using the consensus spectra that usually exhibit higher quality than the raw spectra. As a result, It can be demonstrated that more peptide identifications were obtained at the same low false discovery rate (FDR).The second chapter delves into spectral library searching, a complementary approach to database searching for peptide identifications on MS/MS spectra. LSH techniques ensure that similar spectra are placed into the same buckets, whereas spectra with low pairwise similarity are scattered into different buckets. Each input experimental spectrum can then be compared against a subset of highly similar spectra, thus diminishing the unnecessary spectral similarity computation between the input spectrum and all possible combinations of candidate peptides. The identified peptides overlap with those reported by other existing algorithms to a great extent. More importantly, the acceleration rate in the running time of proposed algorithm compared to existing ones increases with the growing size of spectral libraries.Redundancy in large scale proteomic datasets are exploited to further improve the searching results by eliminating the false PSMs examined through a post-processing step. Despite the success of data searching algorithms in proteomics, the peptide identification results usually contain a small fraction of incorrect peptide assignments. Target decoy approach was introduced in previous work to assess the quality of identifications, by searching spectrum against both target and decoy sequences. I formalize the method to improve peptide identifications by removing false PSMs in a probabilistic post-processing approach. As a result, as low as 0.8\\% FDR can be obtained on the remaining PSMs previously reported at 1\\% FDR level and up to 38\\% more unique peptides can be reported at the expected FDR level.I anticipate the computational methods developed in the dissertation can advance the proteomics research field by improving the protein identification through database searching, spectral library searching and validating the searching outputs in a subsequent step. Although the algorithms were evaluated for proteomics studies, they can be extended to small molecules such as natural products, lipids and glycoconjugates. These algorithms can also be generalized to the identification of experimental MS/MS spectra from a molecule of specific interest in massive omic datasets.
Book Synopsis The Encyclopedia of Mass Spectrometry by :
Download or read book The Encyclopedia of Mass Spectrometry written by and published by Newnes. This book was released on 2015-12-04 with total page 407 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume 9: Historical Perspectives, Part A: The Development of Mass Spectrometry of The Encyclopedia of Mass Spectrometry describes and analyzes the development of many aspects of Mass Spectrometry. Beginning with the earliest types of Mass Analyzers, Historical Perspectives explores the development of many different forms of analytical processes and methods. The work follows various instruments and interfaces, to the current state of detectors and computerization. It traces the use of Mass Spectrometry across many different disciplines, including Organic Chemistry, Biochemistry, and Proteomics; Environmental Mass Spectrometry; Forensic Science; Imaging; Medical Monitoring and Diagnosis; Earth and Planetary Sciences; and Nuclear Science. Finally, the book covers the history of manufacturers and societies as well as the professionals who form the Mass Spectrometry community. Also available: Volume 9: Historical Perspectives, Part B: Notable People in Mass Spectrometry briefly reviews the lives and works of many of the major people who carried out this development. Preserves the history and development of Mass Spectrometry for use across scientific fields Written and edited by Mass Spectrometry experts Coordinates with Volume 9: Historical Perspectives, Part B: Notable People in Mass Spectrometry, a collection of short biographies on many of the major people who carried out this development
Book Synopsis Mass Spectrometry of Proteins and Peptides by : John R. Chapman
Download or read book Mass Spectrometry of Proteins and Peptides written by John R. Chapman and published by Springer Science & Business Media. This book was released on 2008-02-05 with total page 539 pages. Available in PDF, EPUB and Kindle. Book excerpt: Little more than three years down the line and I am already writing the Preface to a second volume to follow Protein and Peptide Analysis by Mass . What has happened in between these times to make this second venture worthwhile? New types of mass spectrometric instrumentation have appeared so that new techniques have become possible and existing techniques have become much more feasible. More particularly, however, the newer ionization te- niques, introduced for the analysis of high molecular weight materials, have now been thoroughly used and studied. As a result, there has been an en- mous improvement in the associated sample handling technology so that these methods are now routinely applied to much smaller sample amounts as well as to more intractable samples. Again, this particular community of mass spectrometry users has both increased in number and diversified. And, riding this wave of acceptance, leaders in the field have set their sights on more complex problems: molecular interaction, ion structures, quantitation, and kinetics are just a few of the newer areas reported in Mass Spectrometry of Proteins and Peptides. As with the first volume, one purpose of this collection, Mass Spectr- etry of Proteins and Peptides, is to show the reader what can be done by the application of mass spectrometry, and perhaps even to encourage the reader to venture down new paths.
Book Synopsis Protein Sequencing and Identification Using Tandem Mass Spectrometry by : Michael Kinter
Download or read book Protein Sequencing and Identification Using Tandem Mass Spectrometry written by Michael Kinter and published by John Wiley & Sons. This book was released on 2005-04-12 with total page 321 pages. Available in PDF, EPUB and Kindle. Book excerpt: How to design, execute, and interpret experiments for protein sequencing using mass spectrometry The rapid expansion of searchable protein and DNA databases in recent years has triggered an explosive growth in the application of mass spectrometry to protein sequencing. This timely and authoritative book provides professionals and scientists in biotechnology research with complete coverage of procedures for analyzing protein sequences by mass spectrometry, including step-by-step guidelines for sample preparation, analysis, and data interpretation. Michael Kinter and Nicholas Sherman present their own high-quality, laboratory-tested protocols for the analysis of a wide variety of samples, demonstrating how to carry out specific experiments and obtain fast, reliable results with a 99% success rate. Readers will get sufficient experimental detail to apply in their own laboratories, learn about the proper selection and operation of instruments, and gain essential insight into the fundamental principles of mass spectrometry and protein sequencing. Coverage includes: * Peptide fragmentation and interpretation of product ion spectra * Basic polyacrylamide gel electrophoresis * Preparation of protein digests for sequencing experiments * Mass spectrometric analysis using capillary liquid chromatography * Techniques for protein identification by database searches * Characterization of modified peptides using tandem mass spectrometry And much more
Download or read book Neuroproteomics written by Oscar Alzate and published by CRC Press. This book was released on 2009-10-26 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this, the post-genomic age, our knowledge of biological systems continues to expand and progress. As the research becomes more focused, so too does the data. Genomic research progresses to proteomics and brings us to a deeper understanding of the behavior and function of protein clusters. And now proteomics gives way to neuroproteomics as we beg
Book Synopsis Genetics, Genomics and Breeding of Stone Fruits by : Chittaranjan Kole
Download or read book Genetics, Genomics and Breeding of Stone Fruits written by Chittaranjan Kole and published by CRC Press. This book was released on 2012-08-17 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt: The stone fruits—including peaches, apricots, almonds, plums, and cherries—have been bred and grown for thousands of years and today are significant agricultural crops in many local economies worldwide. This volume presents a comprehensive commentary on classical genetics and breeding, molecular mapping and breeding of agronomic traits, and the cloning of genes of interest. It also explores recent advances on omics sciences including structural and functional genomics, proteomics, nd metabolomics. The book enumerates the whole genome sequencing of the model fruit plant peach and discusses bioinformatic strategies and tools for stone fruit research
Book Synopsis Quantitative Proteomics by Mass Spectrometry by : Salvatore Sechi
Download or read book Quantitative Proteomics by Mass Spectrometry written by Salvatore Sechi and published by Springer Science & Business Media. This book was released on 2008-02-05 with total page 223 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is a compendium of cutting-edge protocols for quantitative proteomics, and presents the most significant methods used in the field today. The focus on mass spectrometry (MS) is integral. Attention is given to state-of-the-art techniques for the characterization of the phosphoproteome and tandem MS for detection of inborn errors of metabolism. This volume is an indispensable resource in the search for novel biomarkers.
Book Synopsis Protein and Peptide Mass Spectrometry in Drug Discovery by : Michael L. Gross
Download or read book Protein and Peptide Mass Spectrometry in Drug Discovery written by Michael L. Gross and published by John Wiley & Sons. This book was released on 2011-09-26 with total page 484 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book that highlights mass spectrometry and its application in characterizing proteins and peptides in drug discovery An instrumental analytical method for quantifying the mass and characterization of various samples from small molecules to large proteins, mass spectrometry (MS) has become one of the most widely used techniques for studying proteins and peptides over the last decade. Bringing together the work of experts in academia and industry, Protein and Peptide Mass Spectrometry in Drug Discovery highlights current analytical approaches, industry practices, and modern strategies for the characterization of both peptides and proteins in drug discovery. Illustrating the critical role MS technology plays in characterizing target proteins and protein products, the methods used, ion mobility, and the use of microwave radiation to speed proteolysis, the book also covers important emerging applications for neuroproteomics and antigenic peptides. Placing an emphasis on the pharmaceutical industry, the book stresses practice and applications, presenting real-world examples covering the most recent advances in mass spectrometry, and providing an invaluable resource for pharmaceutical scientists in industry and academia, analytical and bioanalytical chemists, and researchers in protein science and proteomics.
Book Synopsis Protein Identification Via Assembly of Tandem Mass Spectra by : Adrian Lewis Guthals
Download or read book Protein Identification Via Assembly of Tandem Mass Spectra written by Adrian Lewis Guthals and published by . This book was released on 2015 with total page 108 pages. Available in PDF, EPUB and Kindle. Book excerpt: High-throughput proteomics is made possible by a combination of modern mass spectrometry instruments capable of generating many millions of tandem mass (MS2 or MS/MS) spectra on a daily basis and the increasingly sophisticated associated software for their automated identification. Despite the growing accumulation of collections of identified spectra and the regular generation of MS2 data from related peptides, the mainstream approach for peptide identification is still the nearly two decades old approach of matching one MS2 spectrum at a time against a database of protein sequences. These traditional approaches fail for the identification of spectra from unknown proteins such as antibodies or proteins from organisms with un-sequenced genomes. Furthermore, attempts to identify MS/MS spectra against large databases (e.g., the human microbiome or 6-frame translation of the human genome) face a search space that is 10-100 times larger than the human proteome, where it becomes increasingly challenging to separate between true and false peptide matches. First, we describe techniques to utilize networks of spectra from related peptides to rigorously compute the joint spectral probability of multiple spectra being matched to peptides with overlapping sequences, thus improving peptide identification by 30-62% against large search spaces. We then introduce methods that dramatically improve de novo sequencing of unknown proteins using novel spectral network assembly algorithms and incorporating alternative MS/MS acquisition protocols. Finally, we describe an interesting end-goal biological problem for which the described advances in de novo sequencing can usher in a new era of therapeutic drug discovery.
Book Synopsis Protein Mass Spectrometry by : Julian Whitelegge
Download or read book Protein Mass Spectrometry written by Julian Whitelegge and published by Elsevier. This book was released on 2008-10-09 with total page 563 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is designed to be a central text for young graduate students interested in mass spectrometry as it relates to the study of protein structure and function as well as proteomics. It is a definite must-have work for:- libraries at academic institutions with Master and Graduate programs in biochemistry, molecular biology, structural biology and proteomics- individual laboratories with interests covering these areas - libraries and individual laboratories in the pharmaceutical and biotechnology industries.*Serves as an essential reference to those working in the field*Incorporates the contributions of prominent experts *Features comprehensive coverage and a logical structure
Book Synopsis Mass Spectrometry: Modified Proteins and Glycoconjugates by : A.L. Burlingame
Download or read book Mass Spectrometry: Modified Proteins and Glycoconjugates written by A.L. Burlingame and published by Gulf Professional Publishing. This book was released on 2005-12-13 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides comprehensive treatment of tools and proper usage for the identification of proteins, affinity chromatography and studies the complexity of protein machines and assemblages, assignment of the most common protein posttranslational modifications (phosphorylation and glycosylation) and glycolipidomics. *Part 2 of 2 volumes about Mass Spectrometry *Discusses peptide and protein cleanup and preparation requirements for mass spectrometry *Explains protein enzymic and chemical digestion strategies *Includes case studies of protein assemblages and machines
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.
