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winkler r processing metabolomics proteomics data 2020

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Textbook in PDF format 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. General Section Introduction Mass Spectrometry Data Operations and Workflows Metabolomics Proteomics Statistics, Data Mining and Modeling Open MS Programs, Toolkits and Workflow Platforms 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 Conclusion Concluding Remarks and Perspectives

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Winkler R. Processing Metabolomics and Proteomics Data...2020.pdf 36.2 MB

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winkler r processing metabolomics proteomics data 2020

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