Title: A View from Above: Cloud Plots to Visualize Global Metabolomic Data

Abstract

Global metabolomics describes the comprehensive analysis of small molecules in a biological system without bias. With mass spectrometry-based methods, global metabolomic data sets typically comprise thousands of peaks, each of which is associated with a mass-to-charge ratio, retention time, fold change, p-value, and relative intensity. Although several visualization schemes have been used for metabolomic data, most commonly used representations exclude important data dimensions and therefore limit interpretation of global data sets. Given that metabolite identification through tandem mass spectrometry data acquisition is a time-limiting step of the untargeted metabolomic workflow, simultaneous visualization of these parameters from large sets of data could facilitate compound identification and data interpretation. Here, we present such a visualization scheme of global metabolomic data using a so-called “cloud plot” to represent multidimensional data from septic mice. While much attention has been dedicated to lipid compounds as potential biomarkers for sepsis, the cloud plot shows that alterations in hydrophilic metabolites may provide an early signature of the disease prior to the onset of clinical symptoms. The cloud plot is an effective representation of global mass spectrometry-based metabolomic data, and we describe how to extract it as standard output from our XCMS metabolomic software.

Authors:

Patti, Gary J. ^[1]; Tautenhahn, Ralf ^[2]; Rinehart, Duane ^[2]; Cho, Kevin ^[1]; Shriver, Leah P. ^[3]; Manchester, Marianne ^[4]; Nikolskiy, Igor ^[1]; Johnson, Caroline H. ^[2]; Mahieu, Nathaniel G. ^[1]; Siuzdak, Gary ^[2]

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+ Show Author Affiliations

1. Washington Univ., St. Louis, MO (United States). Departments of Chemistry, Genetics, and Medicine
2. The Scripps Research Inst., La Jolla, CA (United States). Departments of Chemistry, Molecular Biology, and Center for Metabolomics
3. Univ. of Akron, OH (United States). Departments of Chemistry and Biology; Univ. of California, San Diego, CA (United States). Skaggs School of Pharmacy and Pharmaceutical Sciences
4. Univ. of California, San Diego, CA (United States). Skaggs School of Pharmacy and Pharmaceutical Sciences

Publication Date:

Mon Dec 03 00:00:00 EST 2012

Research Org.:

Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:

USDOE Office of Science (SC)

OSTI Identifier:

1788445

Grant/Contract Number:  

AC02-05CH11231

Resource Type:

Accepted Manuscript

Journal Name:

Analytical Chemistry

Additional Journal Information:

Journal Volume: 85; Journal Issue: 2; Journal ID: ISSN 0003-2700

Publisher:

American Chemical Society (ACS)

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; 47 OTHER INSTRUMENTATION; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Lipids; Metabolomics; Metabolism; Biological databases; Rodent models