Processing Metabolomics and Proteomics Data with Open Software
A Practical Guide
Robert Winkler, Marek Domin, Robert Winkler
- 430 pagine
- English
- ePUB (disponibile sull'app)
- Disponibile su iOS e Android
Processing Metabolomics and Proteomics Data with Open Software
A Practical Guide
Robert Winkler, Marek Domin, Robert Winkler
Informazioni sul libro
Metabolomics and proteomics allow deep insights into the chemistry and physiology of biological systems. This book expounds open-source programs, platforms and programming tools for analysing metabolomics and proteomics mass spectrometry data. In contrast to commercial software, open-source software is created by the academic community, which facilitates the direct interaction between users and developers and accelerates the implementation of new concepts and ideas. The first section of the book covers the basics of mass spectrometry, experimental strategies, data operations, the open-source philosophy, metabolomics, proteomics and statistics/ data mining. In the second section, active programmers and users describe available software packages. Included tutorials, datasets and code examples can be used for training and for building custom workflows. Finally, every reader is invited to participate in the open science movement.
Domande frequenti
Informazioni
Open MS Programs, Toolkits and Workflow Platforms
d Department for Computer Science, Applied Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
e Biomolecular Interactions, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
f Institute for Translational Bioinformatics, University Hospital Tübingen, Hoppe-Seyler-Str. 9, 72076 Tübingen, Germany
g Institute for Biomedical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
h Quantitative Biology Center, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
i Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania, 9th Floor, Smilow Center for Translational Research 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
j Department for Computer Science, Algorithmic Bioinformatics, Freie Universität Berlin, Takustr. 9, 14195 Berlin, Germany
k STORM Therapeutics Limited, Moneta Building, Babraham Research Campus, Cambridge CB22 3AT, UK
*E-mail: [email protected]
Computational mass spectrometry is plagued by a multitude of issues, including a heterogeneous software environment, complex workflows and proprietary tools. OpenMS addresses these challenges by providing robust open-source software for users and an open, well-designed software environment for developers. OpenMS is an open-source software C++ library for LC-MS data management and analyses using modern C++11. It offers an infrastructure for rapid development of mass spectrometry related software. OpenMS is free software available under the three clause BSD license. It comes with a variety of pre-built and ready-to-use tools for high-throughput Proteomics and Metabolomics data analysis (TOPPTools), covering most MS and LC-MS data processing and mining tasks, as well as visualization (TOPPView). OpenMS offers automated analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, TMT, SRM, SWATH. It provides built-in algorithms for de novo identification and database search, as well as adapters to other tools like X!Tandem, Mascot, OMSSA, SIRIUS. It supports easy integration of OpenMS built tools into workflow engines like KNIME, Galaxy, WS-Pgrade, and TOPPAS. OpenMS supports the Proteomics Standard Initiative (PSI) formats for MS data including mzML, mzXML, mzIdentXML, pepXML. With pyOpenMS, OpenMS offers Python bindings to a large part of the OpenMS API to enable rapid algorithm development.