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Processing Metabolomics and Proteomics Data with Open Software: A Practical Guide Editor: Robert Winkler


About this book

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.


Book content

  • Section A – General Part: Introduction
  • MS Data Operations and Workflows
  • Metabolomics
  • Proteomics
  • Statistics, Data Mining and Modelling
  • Section B - Open MS Programs, Toolkits and Workflow Platforms: Resources of Mass Spectrometry Software
  • OpenMS/KNIME
  • MZmine
  • Metabolomic Data Analysis with XCMS/R and XCMS Online
  • Metabolomic Data Analysis with MetaboAnalyst
  • MetaboSearch
  • Ceu Mass Mediator
  • metaX
  • Trans-Proteomic Pipeline
  • Quantitative Proteomics Data Analysis with PANDA/MaxQuant
  • R
  • Python in Proteomics
  • Java/MSDK
  • Installation-free MS Data Processing with MASSyPup64
  • BioDocker
  • Section C - Concluding Remarks and Perspectives

The print version of this book is planned for release on 27 March 2020. Information about this book is subject to change without notice.

Pre-order hardback £179.00 *
* Exclusive of taxes
This book contains 400 pages.

Publication details

Copyright year: 2020
Print ISBN: 978-1-78801-721-3
ePub eISBN: 978-1-78801-990-3