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Metabolomics Data Processing Using XCMS

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Computational Methods and Data Analysis for Metabolomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2104))

Abstract

XCMS is one of the most used software for liquid chromatography–mass spectrometry (LC-MS) data processing and it exists both as an R package and as a cloud-based platform known as XCMS Online. In this chapter, we first overview the nature of LC-MS data to contextualize the need for data processing software. Next, we describe the algorithms used by XCMS and the role that the different user-defined parameters play in the data processing. Finally, we describe the extended capabilities of XCMS Online.

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Acknowledgments

This research was partially funded by the US National Institutes of Health grants R35 GM130385, P30 MH062261, P01 DA026146 and U01 CA235493; and by Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA), a Scientific Focus Area Program at Lawrence Berkeley National Laboratory for the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, under contract number DE-AC02-05CH11231. This research benefited from the use of credits from the National Institutes of Health (NIH) Cloud Credits Model Pilot, a component of the NIH Big Data to Knowledge (BD2K) program.

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Authors and Affiliations

  1. Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA, USA

    Xavier Domingo-Almenara & Gary Siuzdak

  2. Department of Molecular and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA

    Gary Siuzdak

Authors
  1. Xavier Domingo-Almenara
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  2. Gary Siuzdak
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Corresponding author

Correspondence to Xavier Domingo-Almenara .

Editor information

Editors and Affiliations

  1. Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA

    Shuzhao Li

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Domingo-Almenara, X., Siuzdak, G. (2020). Metabolomics Data Processing Using XCMS. In: Li, S. (eds) Computational Methods and Data Analysis for Metabolomics. Methods in Molecular Biology, vol 2104. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0239-3_2

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  • DOI: https://doi.org/10.1007/978-1-0716-0239-3_2

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0238-6

  • Online ISBN: 978-1-0716-0239-3

  • eBook Packages: Springer Protocols

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