Method for the Compound Annotation of Conjugates in Nontargeted Metabolomics Using Accurate Mass Spectrometry, Multistage Product Ion Spectra and Compound Database Searching

Abstract

Owing to biotransformation, xenobiotics are o en found in conjugated form in biological samples such as urine and plasma. Liquid chromatography coupled with accurate mass spectrometry with multistage collision-induced dissociation provides spectral information concerning these metabolites in complex materials. Unfortunately, compound databases typically do not contain a su cient number of records for such conjugates. We report here on the development of a novel protocol, referred to as ChemProphet, to annotate compounds, including conjugates, using compound databases such as PubChem and ChemSpider.e annotation of conjugates involves three steps: 1. Recognition of the type and number of conjugates in the sample; 2. Compound search and annotation of the deconjugated form; and 3. In silico evaluation of the candidate conjugate. ChemProphet assigns a spectrum to each candidate by automatically exploring the substructures corresponding to the observed product ion spectrum. When nished, it annotates the candidates assigning a rank for each candidate based on the calculated score that ranks its relative likelihood. We assessed our protocol by annotating a benchmark dataset by including the product ion spectra for 102 compounds, annotating the commercially available standard for quercetin 3-glucuronide, and by conducting a model experiment using urine from mice that had been administered a green tea extract. e results show that by using the ChemProphet approach, it is possible to annotate not only the deconjugated molecules but also the conjugated molecules using an automatic interpretation method based on deconjugation that involves multistage collision-induced dissociation and in silico calculated conjugation.Please cite this article as: Mass Spectrom (Tokyo) 2015; 4(1): A0036

Updates in metabolomics tools and resources: 2014–2015

“…CFM‐ID is the freely available web server based on the CFM approach aiding in the interpretation of MS/MS for the purpose of automated metabolite identification by facilitating annotation of the peaks in a spectrum for a known chemical structure, prediction of spectra for a given chemical structure, and putative metabolite identification . Another tool, ChemProphet, can be used to annotate compounds using databases such as PubChem and ChemSpider for LC‐HRMS with multistage, CID–provided spectral information on conjugated metabolites . The annotation of conjugates involves recognition of the type and number of conjugates, compound search and annotation of the deconjugated form, and in silico evaluation of the candidate conjugate, where spectra are assigned to each candidate by automatically exploring the substructures corresponding to the observed product ion spectrum.…”

In silico deconjugation of glucuronide conjugates enhances tandem mass spectra library annotation of human samples

“…Some conjugates produce a specific neutral loss (NL) in tandem mass spectrometry [13], which can be utilized as an analytical tool to detect those species [6]. Neutral loss scans have already been applied for detecting glucuronides and sulfates [14][15][16] as well as mercapturic acids [17,18] in biological samples.…”