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Metabolomics

, 14:48 | Cite as

Van Krevelen diagram visualization of high resolution-mass spectrometry metabolomics data with OpenVanKrevelen

  • Stephen A. Brockman
  • Eric V. Roden
  • Adrian D. Hegeman
Short Communication
First Online:
Received:
Accepted:

Abstract

Introduction

Van Krevelen (VK) diagrams provide a promising but uncommon solution to a number of challenges associated with the visualization of metabolomics data. VK diagrams are created by plotting H:C ratios against O:C ratios of the compounds in a chemical mixture.

Objectives

The aim of this manuscript is to present an open-source software tool and reference map that we have developed to make VK diagrams for visualization of metabolomics data.

Methods

Software was created with a prompt-driven command line user interface and was written using Python 2.7. We empirically derived an accompanying map by plotting where compounds from seven biomolecule types fall within the VK plot space.

Results

We’ve created an easy to use, open source software tool named OpenVanKrevelen for making a range of VK diagrams that is available on GitHub: https://github.com/HegemanLab/VanKrevelenLocal. The empirical mapping approach has produced several improvements from previously published maps.

Conclusions

OpenVanKrevelen provides the metabolomics community with access to a new tool for visualization of complex metabolomics datasets.

Keywords

Metabolomics Mass-spectrometry Van Krevelen 

Abbreviations

HRMS

High-resolution mass spectrometry

VK

Van Krevelen

H

Hydrogen

O

Oxygen

N

Nitrogen

LC-MS

Liquid-chromatography mass-spectrometry

Q-TOF

Quadrupole time-of-flight mass spectrometer

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Notes

Acknowledgements

The authors thank Dana M. Freund, Kate A. Sammons, Katrina Freund Saxhaug, Nadia R. Handler and Jayanti Suresh for helpful feedback and/or advice on ease of use. We also thank Geoffrey A. Dubrow for providing test data, and the Biological Magnetic Resonance Bank for providing the database and useful feedback. We are grateful for funding provided by the National Science Foundation Plant Genome Research Program Grants IOS-0923960 and IOS-1238812 and National Science Foundation grant DBI-1458524. We thank the Minnesota Agriculture Experiment Station and the University of Minnesota, College of Food, Agricultural and Natural Resource Sciences at the University of Minnesota–Twin Cites for support.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

No human participants or animals were involved in this study.

Supplementary material

11306_2018_1343_MOESM1_ESM.pdf (348 kb)
Supplementary material 1. Online Resource 1 A van Krevelen heat map visualization of the same high-resolution liquid-chromatography mass-spectrometry data used in Fig. 2. The heatmap only displays the areas of highest feature density and does not convey the same depth of information as a van Krevelen scatter plot. However sometimes a simpler plot is desirable and for this and other reasons van Krevelen heatmaps are still quite useful. In this case the heatmap accurately portrays flavonoid compounds as the most abundant metabolites in the sample. This function of EasyVanKrevelen allows users to create reference maps of their own, for classes of compounds we did not include in the provided map or other applications. The data used were collected using a 25 min reversed phase gradient and a Q Exactive high resolution mass spectrometer (Thermo-Fisher Scientific, Germany) (PDF 347 KB)
11306_2018_1343_MOESM2_ESM.csv (1 kb)
Supplementary material 2. Online Resource 2 Because a suitable database could not be found the nucleic acids section of the empirical map was plotted using a manually compiled lists of compounds. This list has been provided as a .CSV file. The .CSV file contains a manually curated list of nucleic acids and derivatives known to be important in many major biological processes (CSV 0 KB)
11306_2018_1343_MOESM3_ESM.csv (3 kb)
Supplementary material 3. Online Resource 3 Because a suitable database could not be found the amino acids and peptides section of the empirical map was plotted using a manually compiled lists of compounds. This list has been provided as a .CSV file. The .CSV file contains a list of proteinogenic, non-proteinogenic amino acids, and their derivatives (CSV 2 KB)

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© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Microbial and Plant Genomics Institute and the Departments of Horticultural Science and Plant and Microbial BiologyUniversity of Minnesota, Twin CitiesSt. PaulUSA

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