Read Books Online and Download eBooks, EPub, PDF, Mobi, Kindle, Text Full Free.
Enrichment And Identification Of Disulfide Bonded Peptides By Tandem Mass Spectrometry
Download Enrichment And Identification Of Disulfide Bonded Peptides By Tandem Mass Spectrometry full books in PDF, epub, and Kindle. Read online Enrichment And Identification Of Disulfide Bonded Peptides By Tandem Mass Spectrometry ebook anywhere anytime directly on your device. Fast Download speed and no annoying ads. We cannot guarantee that every ebooks is available!
Book Synopsis Enrichment and Identification of Disulfide Bonded Peptides by Tandem Mass Spectrometry by : Pooja Rajeshbhai Ramanuj
Download or read book Enrichment and Identification of Disulfide Bonded Peptides by Tandem Mass Spectrometry written by Pooja Rajeshbhai Ramanuj and published by . This book was released on 2017 with total page 64 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are Comprised of different amino acids which can undergo various modifications known as post-translational modifications (PTMs). Amino acid's side chains are the most common sites for the PTMs. Cysteine side chain can undergo several PTMs and one very common one is disulfide bond formation. Disulfide bond aids in maintaining protein tertiary structures, its identification is an inevitable aspect in studying protein functions. Furthermore, disulfide bonds are potential targets to develop new protein therapeutics for life-threatening diseases such as cancer. Literature surveys revealed several methods to identify disulfide bonds, which require either high quality sample or are highly laborious. Moreover, unexpected folding patterns in protein structure limits the use of data software in disulfide identification. In this study, a straightforward and novel method was developed for confident identification of cysteine residues involved in disulfide bond formation. In order to develop a robust strategy for mapping disulfide bonds in proteins, we developed a chemical strategy. First, we reduced the disulfide bonds to two -SH and subsequently reacted with a reagent called 2, 3- dibromomaleimide (DBM). The maleimide reacted with sulfhydryl bond of cysteine amino acid and substituted the disulfide bonds. Cysteine sulfur was converted to sulfoxide by mild oxidation to make this bond low energy tandem mass spectrometry cleavable. Due to cleavage, this produced two different peptides peaks in the mass spectra so disulfide-bonded peptides can be sequenced as linear modified peptides using tandem mass spectrometry. Furthermore, to enrich the disulfide bonds, we added a biotin group in the dibromomaleimide. Biotin is a small molecule, which has strong interaction with a protein avidin. After reduction of disulfide bonds in peptides, we used a similar dibromomaleimide reagent with a biotin group incorporated in it. After that peptide were enriched using avidin immobilized agarose or magnetic beads. After washing the non-binders, the disulfide-bonded peptide was eluted from the beads and peptide sequence was analyzed using liquid chromatography and tandem mass spectrometry. We tested our approach with standard disulfide containing peptides, somatostatin and a protein lysozyme. Efficient labeling was observed in standard peptides and we have identified several disulfide bond scrambling in lysozyme.In comparison to conventional approaches, our method has three major advantages: (I) reduced sample complexity (II) precise mapping of disulfide bonds (III) faster and easy MS data analysis. Although, there are certain challenges involving oxidation study using biotin dibromomaleimide (BDBM), this method highly enhances the confidence identification of disulfide bonds. We believe this strategy could be an efficient way to enrich and analyze disulfide bonds in proteins.
Book Synopsis Novel Data Analysis Methods and Algorithms for Identification of Peptides and Proteins by Use of Tandem Mass Spectrometry by : Hua Xu
Download or read book Novel Data Analysis Methods and Algorithms for Identification of Peptides and Proteins by Use of Tandem Mass Spectrometry written by Hua Xu and published by . This book was released on 2007 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: Tandem mass spectrometry is one of the most important tools for protein analysis. This thesis is focused on the development of new methods and algorithms for tandem mass spectrometry data analysis. A database search engine, MassMatrix, has also been developed that incorporates these methods and algorithms. The program is publicly available both on the web server at www.massmatrix.net and as a deliverable software package for personal computers. Three different scoring algorithms have been developed to identify and characterize proteins and peptides by use of tandem mass spectrometry data. The first one is targeted at the next generation of tandem mass spectrometers that are capable of high mass accuracy and resolution. Two scores calculated by the algorithm are sensitive to high mass accuracy due to the fact that this new algorithm explicitly incorporates mass accuracy into scoring potential peptide and protein matches for tandem mass spectra. The algorithm is further improved by employing Monte Carlo Simulations to calculate ion abundance based scores without any assumptions or simplifications. For high mass accuracy data, MassMatrix provides improvements in sensitivity over other database search programs. The second scoring algorithm based on peptide sequence tags inferred from tandem mass spectra further improves the performance of MassMatrix for low mass accuracy tandem mass spectrometry data. The third algorithm is the first automated data analysis method that uses peptide retention times in liquid chromatography to evaluate potential peptide matches for tandem mass spectrometry data. The algorithm predicts reverse phase liquid chromatography retention times of peptides by their hydrophobicities and compares the predicted retention times with the observed ones to evaluate the peptide matches. In order to handle low quality data, a new method has also been developed to reduce noise in tandem mass spectra and screen poor quality spectra. In addition, a data analysis method for identification of disulfide bonds in proteins and peptides by tandem mass spectrometry data has been developed and incorporated in MassMatrix. By this new approach, proteins and peptides with disulfide bonds can be directly identified in tandem mass spectrometry with high confidence without any chemical reduction and/or other derivatization.
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 Wiley-Interscience. This book was released on 2005-04-12 with total page 320 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
Book Synopsis Mass Spectrometry of Peptides by : Dominic M. Desiderio
Download or read book Mass Spectrometry of Peptides written by Dominic M. Desiderio and published by CRC Press. This book was released on 1990-11-14 with total page 438 pages. Available in PDF, EPUB and Kindle. Book excerpt: The purpose of this book is to collect into one volume the research done on the mass spectrometry of peptides. It balances a range of topics including theory, instrumentation, analytical techniques, and biological applications. The scope of the work contains three major sections: ionization methods, instrumental developments, and analysis of peptides. It describes 252Cf plasma desorption and laser-induced multiphoton ionization methodology. This exciting resource covers many new areas, including continuous flow FAB, quantification of human neuropeptides, and peptide mapping. It also discusses Q-FTMS, cross-links, and metal ions.
Book Synopsis Identification and Quantification of Oxidative Modification of Peptides and Proteins by Mass Spectrometry by : Lijie Men
Download or read book Identification and Quantification of Oxidative Modification of Peptides and Proteins by Mass Spectrometry written by Lijie Men and published by . This book was released on 2007 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Expanding the Toolbox of Tandem Mass Spectrometry with Algorithms to Identify Mass Spectra from More Than One Peptide by : Jian Wang
Download or read book Expanding the Toolbox of Tandem Mass Spectrometry with Algorithms to Identify Mass Spectra from More Than One Peptide written by Jian Wang and published by . This book was released on 2013 with total page 124 pages. Available in PDF, EPUB and Kindle. Book excerpt: In high-throughput proteomics the development of computational methods and novel experimental strategies often rely on each other. In several areas, mass spectrometry methods for data acquisition are ahead of computational methods to interpret the resulting tandem mass (MS/MS) spectra. While there are numerous situations where two or more peptides are co-fragmented in the same MS/MS spectrum, nearly all mainstream computational approaches still make the ubiquitous assumption that each MS/MS spectrum comes from only one peptide. In this thesis we addressed problems in three emerging areas where computational tools that relax the above assumption are crucial for the success application of these approaches on a large-scale. In the first chapter we describe algorithms for the identification of mixture spectra that are from more than one co-eluting peptide precursors. The ability to interpret mixture spectra not only improves peptide identification in traditional data-dependent-acquisition (DDA) workflows but is also crucial for the success application of emerging data-independent-acquisition (DIA) techniques that have the potential to greatly improve the throughput of peptide identification. In chapter two, we address the problem of identification of peptides with complex post-translational modification (PTM). Detection of PTMs is important to understand the functional dynamics of proteins. Complex PTMs resulted from the conjugation of another macromolecule onto the substrate protein. The resultant modified peptides not only generate spectrum that contains a mixture of fragment ions from both the PTM and the substrate peptide but they also display substantially different fragmentation patterns as compared to conventional, unmodified peptides. We describe a hybrid experimental and computational approach to build search tools that capture the specific fragmentation patterns of modified peptides. Finally in chapter three we address the problem of identification of linked peptides. Linked peptides are two peptides that are covalently linked together. The generation and identification of linked peptides has recently been demonstrated to be a versatile tool to study protein-protein interactions and protein structures, however the identification of linked peptides face many challenges. We integrate lessons learned in the previous chapters to build an efficient and sensitive tool to identify linked peptides from MS/MS spectra.
Book Synopsis New Methods in Peptide Mapping for the Characterization of Proteins by : William S. Hancock
Download or read book New Methods in Peptide Mapping for the Characterization of Proteins written by William S. Hancock and published by CRC Press. This book was released on 1995-10-23 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text is devoted to the characterization of recombinant DNA-derived proteins by peptide mapping. It describes new technological procedures including capillary electrophoresis, analysis of glycopeptides and the use of electrospray and matrix-assisted laser desorption mass spectrometry. The book presents practical procedures for preparing a protein sample, the enzyme digestion, choice of separation method and procedures for the structural analysis of the separated species. Many figures of peptide maps illustrate typical results. Tables of summary information about digestion, separation conditions, and analyses of important protein samples are also presented.
Book Synopsis Algorithms for Peptide Identification by Tandem Mass Spectrometry by : Franz Roos
Download or read book Algorithms for Peptide Identification by Tandem Mass Spectrometry written by Franz Roos and published by . This book was released on 2006 with total page 144 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Characterization of the Triphenylphosphonium Derivative of Peptides by Fast Atom Bombardment-tandem Mass Spectrometry, and Investigations of the Mechanisms of Fragmentation of Peptides by : David Scott Wagner
Download or read book Characterization of the Triphenylphosphonium Derivative of Peptides by Fast Atom Bombardment-tandem Mass Spectrometry, and Investigations of the Mechanisms of Fragmentation of Peptides written by David Scott Wagner and published by . This book was released on 1992 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Peptide Identification by Tandem Mass Spectrometry: a Tag-oriented Open-modification Search Method by :
Download or read book Peptide Identification by Tandem Mass Spectrometry: a Tag-oriented Open-modification Search Method written by and published by . This book was released on with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Dans la majorité des projets de recherche en protéomique, il faut, à un moment ou un autre, déterminer l'identité des protéines présentes dans l'échantillon biologique étudié. Généralement, la méthode utilisée est la corrélation de spectres obtenus par spectrométrie de masse avec des séquences protéiques répertoriées dans des banques de données. Nous avons développé une méthode pour identifier des protéines portant des modifications non attendues. Lorsque les spectres contiennent suffisamment d'information, il est possible de spécifier la position et la nature des modifications présentes.
Book Synopsis Characterization of Immunologically Relevant Peptides by Tandem Mass Spectrometry by : Gina Michelle King
Download or read book Characterization of Immunologically Relevant Peptides by Tandem Mass Spectrometry written by Gina Michelle King and published by . This book was released on 1997 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Effective Strategies for Improving Peptide Identification with Tandem Mass Spectrometry by : Han, Xi
Download or read book Effective Strategies for Improving Peptide Identification with Tandem Mass Spectrometry written by Han, Xi and published by . This book was released on 2011 with total page 69 pages. Available in PDF, EPUB and Kindle. Book excerpt: Tandem mass spectrometry (MS/MS) has been routinely used to identify peptides from protein mixtures in the field of proteomics. However, only about 30% to 40% of current MS/MS spectra can be identified, while many of them remain unassigned, even though they are of reasonable quality. The ubiquitous presence of post-translational modifications (PTMs) is one of the reasons for current low spectral identification rate. In order to identify post-translationally modified peptides, most existing software requires the specification of a few possible modifications. However, such knowledge of possible modifications is not always available. In this thesis, we describe a new algorithm for identifying modified peptides without requiring users to specify the possible modifications before the search routine; instead, all modifications from the Unimod database are considered. Meanwhile, several new techniques are employed to avoid the exponential growth of the search space, as well as to control the false discoveries due to this unrestricted search approach. A software tool, PeaksPTM, has been developed and it has already achieved a stronger performance than competitive tools for unrestricted identification of post-translationally modified peptides. Another important reason for the failure of the search tools is the inaccurate mass or charge state measurement of the precursor peptide ion. In this thesis, we study the precursor mono-isotopic mass and charge determination problem, and propose an algorithm to correct precursor ion mass error by assessing the isotopic features in its parent MS spectrum. The algorithm has been tested on two annotated data sets and achieved almost 100 percent accuracy. Furthermore, we have studied a more complicated problem, the MS/MS preprocessing problem, and propose a spectrum deconvolution algorithm. Experiments were provided to compare its performance with other existing software.
Book Synopsis Algorithms for Peptide Identification Via Tandem Mass Spectrometry by : Thomas Tschager
Download or read book Algorithms for Peptide Identification Via Tandem Mass Spectrometry written by Thomas Tschager and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Identification of Proteins by Tandem Mass Spectrometry Using Improved Peptide Fragmentation Models by : Frédéric Schütz
Download or read book Identification of Proteins by Tandem Mass Spectrometry Using Improved Peptide Fragmentation Models written by Frédéric Schütz and published by . This book was released on 2004 with total page 180 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Peptidomics written by Michael Schrader and published by Humana. This book was released on 2019-06-04 with total page 423 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume describes protocols for basic state-of-the-art approaches in the field of peptidomics. Most of these approaches are independent of the instruments used for analysis and can easily be adapted for equipment that is available in a typical proteomics facility. Chapters detail many of the basic techniques used to detect and identify peptides, methods for the relative quantitation of peptides between samples using isotopic labels or label-free approaches, and biological species as well as sample types. Written in the highly successful format of the Methods in Molecular Biology series, each chapter includes an introduction to the topic, a list of the necessary materials and reagents, reproducible step-by-step laboratory protocols, and tips on troubleshooting common problems and avoiding pitfalls. Authoritative and practical, Peptidomics: Methods and Strategies provides useful guidance for studies in the rapidly growing field of peptidomics.
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.
