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Data Mining in Proteomics

  • Kartonierter Einband
  • 476 Seiten
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Data Mining in Proteomics presents new insights within the proteomics community, while taking into account the historical evolutio... Weiterlesen
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Beschreibung

Data Mining in Proteomics presents new insights within the proteomics community, while taking into account the historical evolution and international standardization projects. The text presents overviews of proteomics technologies, standard data formats, databases, and more.

Through the rapid development of proteomics methods and technologies, an enormous amount of data was created, leading to a wide-spread rethinking of strategy design and data interpretation. In Data Mining in Proteomics: From Standards to Applications, experts in the field present these new insights within the proteomics community, taking the historical evolution as well as the most important international standardization projects into account. Along with basic and sophisticated overviews of proteomics technologies, standard data formats, and databases, the volume features chapters on data interpretation strategies including statistics, spectra interpretation, and analysis environments as well as specialized tasks such as data annotation, peak picking, phosphoproteomics, spectrum libraries, LC/MS imaging, and splice isoforms. As a part of the highly successful Methods in Molecular Biology(TM) series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results.

Authoritative and cutting-edge, Data Mining in Proteomics: From Standards to Applications is a well-balanced compendium for beginners and experts, offering a broad scope of data mining topics but always focusing on the current state-of-the-art and beyond.

From the reviews:

The field of data mining in proteomics is currently extremely dynamic while encompassing a wide range of specialties, topics and implications, and so is this book. This is a very interesting compendium of theoretical, almost philosophical contributions next to requirements and tools with suggestions for their integration. Overall the book is a valuable aid for beginners and for experts as well; moreover, it provides some stimulating materials for discussion in an open perspective. (Molecular Biotechnology, February, 2012)



Inhalt

Part I: Data Generation and Result Finding

1. Instruments and Methods in Proteomics
Caroline May, Frederic Brosseron, Piotr Chartowski, Cornelia Schumbrutzki, Bodo Schoenebeck, and Katrin Marcus

2. In-Depth Protein Characterization by Mass Spectrometry
Daniel Chamrad, Gerhard Körting, and Martin Blüggel

3. Analysis of Phosphoproteomics Data
Christoph Schaab

Part II: Databases

4. The Origin and Early Reception of Sequence Databases
Joel B. Hagen

5. Laboratory Data and Sample Management for Proteomics
Jari Häkkinen and Fredrik Levander

6. PRIDE and 'Database on Demand' as Valuable Tools for Computational Proteomics
Juan Antonio Vizcaíno, Florian Reisinger, Richard Côté, and Lennart Martens

7. Analyzing Proteomics Identifications in the Context of Functional and Structural Protein Annotation: Integrating Annotation Using PICR, DAS, and BioMart
Philip Jones

8. Tranche Distributed Repository and ProteomeCommons.org
Bryan E. Smith, James A. Hill, Mark A. Gjukich, and Philip C. Andrews

Part III: Standards

9. Data Standardization by the HUPO-PSI: How Has the Community Benefitted?
Sandra Orchard and Henning Hermjakob

10. mzIdentML: An Open Community-Built Standard Format for the Results of Proteomics Spectrum Identification Algorithms
Martin Eisenacher

11. Spectra, Chromatograms, Metadata: mzML - The Standard Data Format for Mass Spectrometer Output
Michael Turewicz and Eric W. Deutsch

12. imzML: Imaging Mass Spectrometry Markup Language - A Common Data Format for Mass Spectrometry Imaging
Andreas Römpp, Thorsten Schramm, Alfons Hester, Ivo Klinkert, Jean-Pierre Both, Ron M.A. Heeren, Markus Stöckli, and Bernhard Spengler

13. Tandem Mass Spectrometry Spectral Libraries and Library Searching
Eric W. Deutsch

Part IV: Processing and Interpretation of Data

14. Inter-Lab Proteomics: Data Mining in Collaborative Projects on the Basis of the HUPO Brain Proteome Project s Pilot Studies
Michael Hamacher, Bernd Gröttrup, Martin Eisenacher, Katrion Marcus, Young Mok Park, Helmut E. Meyer, and Christian Stephan

15. Data Management and Data Integration in the HUPO Plasma Proteome Project
Gilbert S. Omenn

16. Statistics in Experimental Design, Preprocessing, and Analysis of Proteomics Data
Klaus Jung

17. The Evolution of Protein Interaction Networks
Andreas Schüler and Erich Bornberg-Bauer

18. Cytoscape: Software for Visualization and Analysis of Biological Networks
Michael Kohl, Sebastian Wiese, and Bettina Warscheid

19. Text Mining for Systems Modelling
Axel Kowald and Sebastian Schmeier

20. Identification of Alternatively Spliced Transcripts Using a Proteomic Informatics Approach
Rajasree Menon and Gilbert S. Omenn

21. Distributions of Ion Series in ETD and CID Spectra: Making a Comparison
Sarah R. Hart, King Wai Lau, Simon J. Gaskell, and Simon J. Hubbard

Part V: Tools

22. Evaluation of Peak Picking Algorithms for Protein Mass Spectrometry
Chris Bauer, Rainer Cramer, and Johannes Schuchhardt

23. OpenMS and TOPP: Open Source Software for LC-MS Data Analysis
Andreas Bertsch, Clemens Gröpl, Knut Reinert, and Oliver Kohlbacher

24. LC/MS Data Processing for Label-Free Quantitative Analysis
Patricia M. Palagi, Markus Müller, Daniel Walther, and Frédérique Lisacek

Part VI: Modelling and Systems Biology

25. Spectral Properties of Correlation Matrices: Towards Enhanced Spectral Clustering
Daniel Fulger and Enrico Scalas

26. Standards, Databases, and Modeling Tools in Systems Biology
Michael Kohl

27. Modelling of Cellular Processes: Methods, Data, and Requirements
Thomas Millat, Olaf Wolkenhauer, Ralf-Jörg Fischer, and Hubert Bahl

Produktinformationen

Titel: Data Mining in Proteomics
Untertitel: From Standards to Applications
Editor:
EAN: 9781493958030
ISBN: 1493958038
Format: Kartonierter Einband
Herausgeber: Humana Press
Anzahl Seiten: 476
Gewicht: 887g
Größe: H254mm x B178mm x T25mm
Jahr: 2016
Auflage: Softcover reprint of the original 1st ed. 2011

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