What question did this study set out to answer?

The study aims to evaluate the effectiveness of mass accuracy and isotopic abundance in correctly identifying molecular formulas in metabolomic research.

April 28, 2006Open Access

Metabolomic database annotations via query of elemental compositions: Mass accuracy is insufficient even at less than 1 ppm

Key Points

The study aims to evaluate the effectiveness of mass accuracy and isotopic abundance in correctly identifying molecular formulas in metabolomic research.
Analyzed data involving mass spectrometers with various accuracy levels (<1 ppm to 3 ppm).
Applied orthogonal filters using isotopic abundance information to assess candidate elimination.
Conducted comparisons across multiple chemical databases for effective molecular formula query.
High mass accuracy (<1 ppm) alone fails to adequately narrow down candidates, leading to excessive false positives.
The inclusion of isotopic abundance patterns successfully removes over 95% of incorrect candidates.
Effective strategies reduced thousands of possible formulas to a small, accurate subset.

Abstract

BACKGROUND: Metabolomic studies are targeted at identifying and quantifying all metabolites in a given biological context. Among the tools used for metabolomic research, mass spectrometry is one of the most powerful tools. However, metabolomics by mass spectrometry always reveals a high number of unknown compounds which complicate in depth mechanistic or biochemical understanding. In principle, mass spectrometry can be utilized within strategies of de novo structure elucidation of small molecules, starting with the computation of the elemental composition of an unknown metabolite using accurate masses with errors 95% of false candidates. This orthogonal filter can condense several thousand candidates down to only a small number of molecular formulas. Example calculations for 10, 5, 3, 1 and 0.1 ppm mass accuracy are given. Corresponding software scripts can be downloaded from http://fiehnlab.ucdavis.edu. A comparison of eight chemical databases revealed that PubChem and the Dictionary of Natural Products can be recommended for automatic queries using molecular formulae. CONCLUSION: More than 1.6 million molecular formulae in the range 0-500 Da were generated in an exhaustive manner under strict observation of mathematical and chemical rules. Assuming that ion species are fully resolved (either by chromatography or by high resolution mass spectrometry), we conclude that a mass spectrometer capable of 3 ppm mass accuracy and 2% error for isotopic abundance patterns outperforms mass spectrometers with less than 1 ppm mass accuracy or even hypothetical mass spectrometers with 0.1 ppm mass accuracy that do not include isotope information in the calculation of molecular formulae.

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