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 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.
Highlights
Recent times have seen an overhaul of our understanding of fundamental biochemistry owing to ever-improving analytical techniques
The error inherent to the prediction most likely outweighs that coming from measurement, owing to the high reproducibility of the chromatographic process in reverse-phase liquid chromatography (RPLC)
We have introduced and documented DynaStI, a dynamic retention time databa annotation interface for Liquid chromatography (LC)–MS datasets in untargeted steroidomics
Summary
Recent times have seen an overhaul of our understanding of fundamental biochemistry owing to ever-improving analytical techniques. The ability to perform high-resolution, multidimensional separations has allowed the field to move from compound-specific measurements to wide untargeted analyses that can in turn be fed to powerful statistical tools [1]. These advances have been useful for metabolomics, where the space of possible compounds ranges widely with respect to mass, size, and chemical properties. Compounds can be separated in a first dimension by LC, relying on the chemical interactions between the compounds and the column used in the separation. Afterwards, high-resolution MS is able to resolve masses up to the nuclear mass defect, unequivocally determining which atoms are present in a compound
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