Overview

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.

Full Product Details

Author:   Robert Winkler (CINVESTAV Unidad Irapuato, Mexico) ,  Magnus Palmblad ,  Hannes Roest ,  Tomas Pluskal
Publisher:   Royal Society of Chemistry
Imprint:   Royal Society of Chemistry
Volume:   Volume 8
Dimensions:   Width: 15.60cm , Height: 2.70cm , Length: 23.40cm
Weight:   0.806kg
ISBN:  

9781788017213

ISBN 10:   1788017218
Pages:   448
Publication Date:   19 March 2020
Audience:   Professional and scholarly ,  Professional & Vocational
Format:   Hardback
Publisher's Status:   Active
Availability:   In Print  
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Table of Contents

Introduction; Mass Spectrometry Data Operations and Workflows; Metabolomics; Proteomics; Statistics, Data Mining and Modeling; OpenMS and KNIME for Mass Spectrometry Data Processing; Metabolomics Data Analysis Using MZmine; Pre-processing and Analysis of Metabolomics Data with XCMS/R and XCMS Online; Statistical Evaluation and Integration of Multi-omics Data with MetaboAnalyst; Modular metaX Pipeline for Processing Untargeted Metabolomics Data; Metabolite Annotation With CEU Mass Mediator; Metabolite Annotation Using In Silico Generated Compounds: MINE and BioTransformer; Trans-Proteomic Pipeline for the Identification, Validation, and Quantification of Proteins; Quantitative Proteomics Data Analysis with PANDA, LFAQ and PANDA-view; Proteomic Workflows with R/R Markdown; Python in Proteomics; Mass Spectrometry Development Kit (MSDK): a Java Library for Mass Spectrometry Data Processing; MASSyPup64: Linux Live System for Mass Spectrometry Data Processing; Cross-platform Software Development and Distribution with Bioconda and BioContainers; Concluding Remarks and Perspectives

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