Data Mining in Proteomics: From Standards to Applications

ISBN-13: 9781493958030 / Angielski / Miękka / 2016 / 461 str.

Michael Hamacher; Martin Eisenacher; Christian Stephan

Opis

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.

Recenzje

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)

Spis treści

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

Blurb

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™ 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.