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Author: Michael Kinter Publisher: John Wiley & Sons ISBN: 0471231886 Category : Science Languages : en Pages : 321
Book Description
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
Author: Michael Kinter Publisher: John Wiley & Sons ISBN: 0471231886 Category : Science Languages : en Pages : 321
Book Description
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
Author: Sacha Baginsky Publisher: Springer Science & Business Media ISBN: 376437439X Category : Science Languages : en Pages : 362
Book Description
This volume aims to provide a timely view of the state-of-the-art in systems biology. The editors take the opportunity to define systems biology as they and the contributing authors see it, and this will lay the groundwork for future studies. The volume is well-suited to both students and researchers interested in the methods of systems biology. Although the focus is on plant systems biology, the proposed material could be suitably applied to any organism.
Author: Adrian Lewis Guthals Publisher: ISBN: 9781321891584 Category : Languages : en Pages : 108
Book Description
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.
Author: John R. Chapman Publisher: Springer Science & Business Media ISBN: 1592590454 Category : Science Languages : en Pages : 539
Book Description
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.
Author: Peter James Publisher: Springer Science & Business Media ISBN: 9783540672562 Category : Science Languages : en Pages : 306
Book Description
Recent advances in large scale DNA sequencing technology have made it possible to sequence the entire genome of an organism. Attention is now turning to the analysis of the product of the genome, the proteome, which is the set of proteins being expressed by a cell. Mass spectrometry is the method of choice for the rapid large-scale identification of these proteomes and their modifications. This is the first book to extensively cover the applications of mass spectrometry to proteome research.
Author: Bryan John Smith Publisher: Springer Science & Business Media ISBN: 1592593429 Category : Science Languages : en Pages : 489
Book Description
Determination of the protein sequence is as important today as it was a half century ago, even though the techniques and purposes have changed over time. Mass spectrometry has continued its recent rapid development to find notable application in the characterization of small amounts of protein, for example, in the field of proteomics. The “traditional” chemical N-terminal sequencing is still of great value in quality assurance of the increasing number of biopharmaceuticals that are to be found in the clinic, checking processing events of recombinant proteins, and so on. It is joined in the armory of me- ods of protein analysis by such techniques as C-terminal sequencing and amino acid analysis. These methods are continually developing. The first edition of Protein Sequencing Protocols was a “snapshot” of methods in use in protein biochemistry laboratories at the time, and this, the second edition, is likewise. Methods have evolved in the intervening period, and the content of this book has similarly changed, the content of some chapters having been superceded and replaced by other approaches. Thus, in this edition, there is inclusion of approaches to validation of methods for quality assurance work, reflecting the current importance of biopharmaceuticals, and also a guide to further analysis of protein sequence information, acknowledging the importance of bioinformatics.
Author: Willy Vincent Bienvenut Publisher: Springer Science & Business Media ISBN: 9781402033186 Category : Medical Languages : en Pages : 324
Book Description
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: Oscar Alzate Publisher: CRC Press ISBN: 1420076264 Category : Medical Languages : en Pages : 356
Book Description
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
Author: Andrew J. Link Publisher: Springer Science & Business Media ISBN: 1592595847 Category : Science Languages : en Pages : 585
Book Description
With the completion of sequencing projects and the advancement of a- lytical tools for protein identification, proteomics—the study of the expressed part of the genome—has become a major region of the burgeoning field of functional genomics. High-resolution 2-D gels can reveal virtually all p- teins present in a cell or tissue at any given time, including posttranslationally modified proteins. Changes in the expression and structure of most cellular proteins caused by differentiation or external stimuli can be displayed and eventually identified using 2-D protein gels. 2-D Proteome Analysis Protocols covers all aspects of the use of 2-D protein electrophoresis for the analysis of biological problems. The contri- tors include many of the leaders in the fields of biochemistry and analytical chemistry who were instrumental in the development of high-resolution 2-D gels, immobilized pH gradients, computer analysis, and mass spectromet- based protein identification methodologies. This book is intended as a benchtop manual and guide both for novices to 2-D gels and for those aficionados who wish to try the newer techniques. Any group using protein biochemistry—especially in the fields of molecular biology, biochemistry, microbiology, and cell biology—should find this book eminently useful. 2-D Proteome Analysis Protocols takes the researcher through the c- plete process of working with 2-D protein gels from making the protein - tract to finally identifying the proteins of interest. It includes protocols for generating 2-D protein extracts from most of the standard model organisms, including bacteria, yeast, nematode, Drosophila, plants, mouse, and human.
Author: Michael Kinter
Author: Michael Kinter
Author: Sacha Baginsky
Author: Adrian Lewis Guthals
Author: John R. Chapman
Author: John Robert Yates
Author: Peter James
Author: Bryan John Smith
Author: Willy Vincent Bienvenut
Author: Oscar Alzate
Author: Andrew J. Link