Metabolomics Data Processing Using XCMS

Xavier Domingo-Almenara; Gary Siuzdak

doi:10.1007/978-1-0716-0239-3_2

Metabolomics Data Processing Using XCMS

Methods Mol Biol. 2020:2104:11-24. doi: 10.1007/978-1-0716-0239-3_2.

Authors

Xavier Domingo-Almenara¹, Gary Siuzdak^{2

3}

Affiliations

¹ Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA, USA. xavier.domingoa@eurecat.org.
² Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA, USA.
³ Department of Molecular and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.

PMID: 31953810
DOI: 10.1007/978-1-0716-0239-3_2

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.

Keywords: Data processing; Liquid chromatography; Mass spectrometry; Metabolomics; XCMS.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Algorithms
Chromatography, Liquid
Computational Biology / methods
Data Interpretation, Statistical*
Mass Spectrometry
Metabolomics* / methods
Online Systems
Software*
User-Computer Interface
Workflow

Abstract

Publication types

MeSH terms

Grants and funding