XCMS Online is a cloud version of the original XCMS technology (a bioinformatics software designed for statistical analysis of mass spectrometry data), created by the Siuzdak Lab at

Scripps Research Scripps Research, previously known as The Scripps Research Institute (TSRI), is a nonprofit American medical research facility that focuses on research and education in the biomedical sciences. Headquartered in San Diego, California, the institu ...

. XCMS introduced the concept of nonlinear retention time alignment that allowed for the statistical assessment of the detected peaks across LCMS and GCMS datasets. XCMS Online was designed to facilitate XCMS analyses through a cloud portal and as a more straightforward (non command driven) way to analyze, visualize and share untargeted metabolomic data. Further to this, the combination of XCMS and METLIN allows for the identification of known molecules using METLIN's tandem mass spectrometry data, and enables the identification of unknown (uncharacterized molecules) via similarity searching of tandem mass spectrometry data. XCMS Online has also become a systems biology tool for integrating different omic data sets. As of January 2021, th
XCMSOnline
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METLIN The METLIN Metabolite and Chemical Entity Database is the largest repository of experimental tandem mass spectrometry and neutral loss data acquired from standards. The tandem mass spectrometry data on over 870,000 molecular standards (as of Augu ...

platform has over 44,000 registered users. XCMS Online works by comparing groups of raw or preprocessed metabolomic data to discover metabolites using methods such as nonlinear retention time alignment and feature detection & matching. Once analysis is complete the data can be viewed several different ways including via bubble plots, heat maps, chromatograms, and box plots. In addition, XCMS Online is integrated with

, a large metabolite database. The following file formats are supported for direct upload to the site.

History

In 2005, the Siuzdak Lab created an open-source tool named XCMS in the programming language R. Noticing the need for a more accessible, graphical data processing tool they created the cloud-based XCMS Online in 2012. The ability for users to stream data directly from instruments while being acquired was added in 2014. Also in that year a commercial version named XCMS Plus (owned by Mass Consortium Corporation) was released and, in 2015, SCIEX became a reseller. In 2017 it was shown that XCMS Online could be used in a

systems biology Systems biology is the computational modeling, computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological syst ...

workflow. One year later, in the absence of a publicly available alternative, a version of XCMS Online was released with the ability to perform

multiple reaction monitoring Selected reaction monitoring (SRM), also called Multiple reaction monitoring, (MRM), is a method used in tandem mass spectrometry in which an ion of a particular mass is selected in the first stage of a tandem mass spectrometer and an ion produc ...

(MRM).

References

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External links

XCMS Online
Bioinformatics software Mass spectrometry software