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Metabolites. 2019 Apr 30;9(5). pii: E85. doi: 10.3390/metabo9050085.

DynaStI: A Dynamic Retention Time Database for Steroidomics.

Author information

1
School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1206 Geneva, Switzerland. Santiago.Codesido@unige.ch.
2
School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1206 Geneva, Switzerland. marco.randazzo@supsi.ch.
3
Dalle Molle Institute for Artificial Intelligence, 6928 Manno, Switzerland. marco.randazzo@supsi.ch.
4
Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. fabio.lehmann87@gmail.com.
5
School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1206 Geneva, Switzerland. Victor.Gonzalez@unige.ch.
6
Swiss Center for Applied Human Toxicology, 4055 Basel, Switzerland. Victor.Gonzalez@unige.ch.
7
School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1206 Geneva, Switzerland. Arnaud.Garcia@unige.ch.
8
Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. ioannis.xenarios@unil.ch.
9
Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland. ioannis.xenarios@unil.ch.
10
Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. robin.liechti@sib.swiss.
11
Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. Alan.Bridge@sib.swiss.
12
School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1206 Geneva, Switzerland. Julien.Boccard@unige.ch.
13
Swiss Center for Applied Human Toxicology, 4055 Basel, Switzerland. Julien.Boccard@unige.ch.
14
School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1206 Geneva, Switzerland. Serge.Rudaz@unige.ch.
15
Swiss Center for Applied Human Toxicology, 4055 Basel, Switzerland. Serge.Rudaz@unige.ch.

Abstract

: Steroidomics studies face the challenge of separating analytical compounds with very similar structures (i.e., isomers). Liquid chromatography (LC) is commonly used to this end, but the shared core structure of this family of compounds compromises effective separations among the numerous chemical analytes with comparable physico-chemical properties. Careful tuning of the mobile phase gradient and an appropriate choice of the stationary phase can be used to overcome this problem, in turn modifying the retention times in different ways for each compound. In the usual workflow, this approach is suboptimal for the annotation of features based on retention times since it requires characterizing a library of known compounds for every fine-tuned configuration. We introduce a software solution, DynaStI, that is capable of annotating liquid chromatography-mass spectrometry (LC-MS) features by dynamically generating the retention times from a database containing intrinsic properties of a library of metabolites. DynaStI uses the well-established linear solvent strength (LSS) model for reversed-phase LC. Given a list of LC-MS features and some characteristics of the LC setup, this software computes the corresponding retention times for the internal database and then annotates the features using the exact masses with predicted retention times at the working conditions. DynaStI (https://dynasti.vital-it.ch) is able to automatically calibrate its predictions to compensate for deviations in the input parameters. The database also includes identification and structural information for each annotation, such as IUPAC name, CAS number, SMILES string, metabolic pathways, and links to external metabolomic or lipidomic databases.

KEYWORDS:

database; metabolomics; prediction; steroidomics

PMID:
31052310
DOI:
10.3390/metabo9050085
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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

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