Extraction efficiency and quantification of dissolved metabolites in targeted marine metabolomics

Winifred M Johnson,Melissa C Kido Soule,Elizabeth B Kujawinski

doi:10.1002/lom3.10181

Abstract

AbstractThe field of metabolomics seeks to characterize the suite of small molecules that comprise the end‐products of cellular regulation. Metabolomics has been used in biomedical applications as well as environmental studies that explore ecological and biogeochemical questions. We have developed a targeted metabolomics method using electrospray ionization–liquid chromatography tandem mass spectrometry to analyze metabolites dissolved in seawater. Preparation of samples from the marine environment presents challenges because dilute metabolites must be concentrated and desalted. We present the extraction efficiencies of 89 metabolites in our targeted method using solid phase extraction (SPE). In addition, we calculate the limits of detection and quantification for the metabolites in the method and compare the instrument response factors in five different matrices ranging from deionized water to spent medium from cultured marine microbes. High background organic matter content reduces the instrument response factor for only a small group of metabolites, yet enhances the extraction efficiency for other metabolites on the SPE cartridge used here, a modified styrene‐divinylbenzene polymer called PPL. Aromatic or larger uncharged compounds, in particular, are reproducibly well retained on the PPL polymer. This method is suitable for the detection of dissolved metabolites in marine samples, with limits of detection ranging from < 1 pM to ∼ 2 nM dependent on the dual impacts of seawater matrix on extraction efficiency and on instrument response factors.

Highlights

The field of metabolomics seeks to characterize the suite of small molecules that comprise the endproducts of cellular regulation
Taurocholic acid, with a retention time of 17 min, is only significantly reduced in the M. pusilla (Mp) matrix, while malic acid, with a retention time of 1.9 min, has decreased ionization efficiencies in both R. pomeroyi (Rpom) and Mp. These are notable observations because do these metabolites have different polarities and functional groups, but they are ionized in distinct matrix environments due to their different retention times. These results suggest that changes in response factor are linked to dissolved organic carbon (DOC) content but are molecule specific
The eLODs for many metabolites in the VSW and Rpom matrices are similar to the calculated limit of detection (LOD) in MQ, there seem to be more metabolites with elevated eLODs and greater uncertainty in the Rpom matrix compared to the VSW matrix (Table 2)

Summary

Introduction

The field of metabolomics seeks to characterize the suite of small molecules that comprise the endproducts of cellular regulation. We calculate the limits of detection and quantification for the metabolites in the method and compare the instrument response factors in five different matrices ranging from deionized water to spent medium from cultured marine microbes. High background organic matter content reduces the instrument response factor for only a small group of metabolites, yet enhances the extraction efficiency for other metabolites on the SPE cartridge used here, a modified styrene-divinylbenzene polymer called PPL. Aromatic or larger uncharged compounds, in particular, are reproducibly well retained on the PPL polymer. This method is suitable for the detection of dissolved metabolites in marine samples, with limits of detection ranging from < 1 pM to 2 nM dependent on the dual impacts of seawater matrix on extraction efficiency and on instrument response factor

Methods

Findings

Discussion

Conclusion