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Robert Winkler - Processing Metabolomics and Proteomics Data with Open Software: A Practical Guide (ISSN)

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Robert Winkler Processing Metabolomics and Proteomics Data with Open Software: A Practical Guide (ISSN)
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Metabolomics and proteomics allow deep insights into the chemistry and physiological processes of biological systems. These omics methods rely heavily on mass spectrometry, however, building valid models from raw mass spectrometry data is challenging, and the field of data analysis and integration is evolving rapidly. This book will enable researchers, practitioners and students from different backgrounds to analyze metabolomics and proteomics mass spectrometry data. The book contains tutorials, code examples and datasets that facilitate the training and the development of the readers own programs and workflows.

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Contents Contents Processing Metabolomics and Proteomics Data with Open - photo 1
Contents

Contents

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

Processing Metabolomics and Proteomics Data with Open Software

A Practical Guide

Edited by
Robert Winkler
CINVESTAV Unidad Irapuato, Mexico
Email:
New Developments in Mass Spectrometry No 8 Print ISBN 978-1-78801-721-3 PDF - photo 2

New Developments in Mass Spectrometry No. 8

Print ISBN: 978-1-78801-721-3

PDF ISBN: 978-1-78801-988-0

EPUB ISBN: 978-1-78801-990-3

Print ISSN: 2045-7545

Electronic ISSN: 2045-7553

A catalogue record for this book is available from the British Library

The Royal Society of Chemistry 2020

All rights reserved

Apart from fair dealing for the purposes of research for non-commercial purposes or for private study, criticism or review, as permitted under the Copyright, Designs and Patents Act 1988 and the Copyright and Related Rights Regulations 2003, this publication may not be reproduced, stored or transmitted, in any form or by any means, without the prior permission in writing of The Royal Society of Chemistry or the copyright owner, or in the case of reproduction in accordance with the terms of licences issued by the Copyright Licensing Agency in the UK, or in accordance with the terms of the licences issued by the appropriate Reproduction Rights Organization outside the UK. Enquiries concerning reproduction outside the terms stated here should be sent to The Royal Society of Chemistry at the address printed on this page.

Whilst this material has been produced with all due care, The Royal Society of Chemistry cannot be held responsible or liable for its accuracy and completeness, nor for any consequences arising from any errors or the use of the information contained in this publication. The publication of advertisements does not constitute any endorsement by The Royal Society of Chemistry or Authors of any products advertised. The views and opinions advanced by contributors do not necessarily reflect those of The Royal Society of Chemistry which shall not be liable for any resulting loss or damage arising as a result of reliance upon this material.

The Royal Society of Chemistry is a charity, registered in England and Wales, Number 207890, and a company incorporated in England by Royal Charter (Registered No. RC000524), registered office: Burlington House, Piccadilly, London W1J 0BA, UK, Telephone: +44 (0) 20 7437 8656.

For further information see our web site at www.rsc.org

Printed in the United Kingdom by CPI Group (UK) Ltd, Croydon, CR0 4YY, UK

New Developments in Mass Spectrometry
Editor-in-chief:
Frank Sobott, University of Leeds, UK
Series editors:
Juan F. GarciaReyes, Universidad de Jan, Spain
Marek Domin, Boston College, USA
Titles in the Series:
1: Quantitative Proteomics
2: Ambient Ionization Mass Spectrometry
3: Sector Field Mass Spectrometry for Elemental and Isotopic Analysis
4: Tandem Mass Spectrometry of Lipids: Molecular Analysis of Complex Lipids
5: Proteome Informatics
6: Capillary ElectrophoresisMass Spectrometry for Metabolomics
7: Lipidomics: Current and Emerging Techniques
8: Processing Metabolomics and Proteomics Data with Open Software: A Practical Guide
How to obtain future titles on publication:
A standing order plan is available for this series. A standing order will bring delivery of each new volume immediately on publication.
For further information please contact:
Book Sales Department, Royal Society of Chemistry, Thomas Graham House, Science Park, Milton Road, Cambridge, CB4 0WF, UK
Telephone: +44 (0)1223 420066, Fax: +44 (0)1223 420247
E-mail:
Visit our website at www.rsc.org/books

Preface

The development of data analysis software accompanies technological advances in mass spectrometry. Naturally, academic laboratories are often the first to implement new ideas and algorithms into scientific software. The public release of code has led to the community-driven creation, testing, and improvement of applications, and the compilation of complete data-analysis platforms. The definition of open data formats has facilitated the exchange of data between researchers and the analysis of data by a variety of diverse programs.
Open software for the analysis of mass spectrometry data has reached a maturity that makes it suitable for professional use by analytical chemists in academia and industry. Further, exciting new tools, such as data mining by machine learning/artificial intelligence and DevOpsagile software development/testing/deliveryare accelerating developments in all fields of computer science.
However, documentation for the multiple existing programs and their optimal use is scattered in package manuals, read-mes, and online forums. This information fragmentation complicates the efficient use of open-source software, especially for students, scientists, and professionals who analyse mass spectrometry data occasionally or for first-time users.
In my laboratory, we develop analytical platforms for mass spectrometry, including hardware, software, and databases. Consequently, programming is an essential part of our daily work. Furthermore, we regularly provide mass spectrometry primers to new lab members and offer optional courses in our postgraduate programs. Many of our collaborators are more interested in biological questions than technical details, but also want to understand their data or reanalyse their results. As a result, we identified the need for a book that provides the very basics, facilitates an understanding of the technology, and that also covers practical aspects of mass spectrometry data analysis.
Consequently, when Marek Domin asked me to edit a book about metabolomics for the Royal Society of Chemistry, I suggested that the scope be widened to mass spectrometry (MS) data analysis using open-source software. We discussed possible contents with the Editorial Board of the Royal Society of Chemistry and agreed on a book that strongly focuses on MS data analysis with open source software and statistical methods, but also covers the most prominent MS-based omics methods, namely metabolomics and proteomics.
The primary target audience of this book is the students and scientists who are experiencing mass spectrometry for the first time, as well as MS professionals who currently work with commercial data processing software and want to explore new ways of interpreting their results. Furthermore, (bio)informaticians working on omics datasets or MS software development can profit from the book since the book presents diverse modules, toolkits, and strategies for workflow design and data mining.
A central feature of this book is the inclusion of example data and workflows, which provides the reader with the opportunity to reproduce the presented protocols. The demo data are downloadable from public repositories free of charge and serve as useful practice material for hands-on courses or as templates for the development of individual workflows.
The book comprises three parts. Part A describes general concepts and holds five main chapters:
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