1
|
Hupatz H, Rahu I, Wang WC, Peets P, Palm EH, Kruve A. Critical review on in silico methods for structural annotation of chemicals detected with LC/HRMS non-targeted screening. Anal Bioanal Chem 2024:10.1007/s00216-024-05471-x. [PMID: 39138659 DOI: 10.1007/s00216-024-05471-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/15/2024]
Abstract
Non-targeted screening with liquid chromatography coupled to high-resolution mass spectrometry (LC/HRMS) is increasingly leveraging in silico methods, including machine learning, to obtain candidate structures for structural annotation of LC/HRMS features and their further prioritization. Candidate structures are commonly retrieved based on the tandem mass spectral information either from spectral or structural databases; however, the vast majority of the detected LC/HRMS features remain unannotated, constituting what we refer to as a part of the unknown chemical space. Recently, the exploration of this chemical space has become accessible through generative models. Furthermore, the evaluation of the candidate structures benefits from the complementary empirical analytical information such as retention time, collision cross section values, and ionization type. In this critical review, we provide an overview of the current approaches for retrieving and prioritizing candidate structures. These approaches come with their own set of advantages and limitations, as we showcase in the example of structural annotation of ten known and ten unknown LC/HRMS features. We emphasize that these limitations stem from both experimental and computational considerations. Finally, we highlight three key considerations for the future development of in silico methods.
Collapse
Affiliation(s)
- Henrik Hupatz
- Department of Materials and Environmental Chemistry, Stockholm University, Svante Arrhenius Väg 16, 114 18, Stockholm, Sweden
- Stockholm University Center for Circular and Sustainable Systems (SUCCeSS), Stockholm University, 106 91, Stockholm, Sweden
| | - Ida Rahu
- Department of Materials and Environmental Chemistry, Stockholm University, Svante Arrhenius Väg 16, 114 18, Stockholm, Sweden.
| | - Wei-Chieh Wang
- Department of Materials and Environmental Chemistry, Stockholm University, Svante Arrhenius Väg 16, 114 18, Stockholm, Sweden
| | - Pilleriin Peets
- Institute of Biodiversity, Faculty of Biological Science, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Emma H Palm
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367, Belvaux, Luxembourg
| | - Anneli Kruve
- Department of Materials and Environmental Chemistry, Stockholm University, Svante Arrhenius Väg 16, 114 18, Stockholm, Sweden.
- Stockholm University Center for Circular and Sustainable Systems (SUCCeSS), Stockholm University, 106 91, Stockholm, Sweden.
- Department of Environmental Science, Stockholm University, Svante Arrhenius Väg 8, 114 18, Stockholm, Sweden.
| |
Collapse
|
2
|
Vink MA, Alarcan J, Martens J, Buma WJ, Braeuning A, Berden G, Oomens J. Structural Elucidation of Agrochemical Metabolic Transformation Products Based on Infrared Ion Spectroscopy to Improve In Silico Toxicity Assessment. Chem Res Toxicol 2024; 37:81-97. [PMID: 38118149 PMCID: PMC10792670 DOI: 10.1021/acs.chemrestox.3c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023]
Abstract
Toxicological assessments of newly developed agrochemical agents consider chemical modifications and their metabolic and biotransformation products. To carry out an in silico hazard assessment, understanding the type of chemical modification and its location on the original compound can greatly enhance the reliability of the evaluation. Here, we present and apply a method based on liquid chromatography-mass spectrometry (LC-MS) enhanced with infrared ion spectroscopy (IRIS) to better delineate the molecular structures of transformation products before in silico toxicology evaluation. IRIS facilitates the recording of IR spectra directly in the mass spectrometer for features selected by retention time and mass-to-charge ratio. By utilizing quantum-chemically predicted IR spectra for candidate molecular structures, one can either derive the actual structure or significantly reduce the number of (isomeric) candidate structures. This approach can assist in making informed decisions. We apply this method to a plant growth stimulant, digeraniol sinapoyl malate (DGSM), that is currently under development. Incubation of the compound in Caco-2 and HepaRG cell lines in multiwell plates and analysis by LC-MS reveals oxidation, glucuronidation, and sulfonation metabolic products, whose structures were elucidated by IRIS and used as input for an in silico toxicology assessment. The toxicity of isomeric metabolites predicted by in silico tools was also assessed, which revealed that assigning the right metabolite structure is an important step in the overall toxicity assessment of the agrochemical. We believe this identification approach can be advantageous when specific isomers are significantly more hazardous than others and can help better understand metabolic pathways.
Collapse
Affiliation(s)
- Matthias
J. A. Vink
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jimmy Alarcan
- Department
of Food Safety, German Federal Institute
for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Jonathan Martens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Wybren Jan Buma
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
- van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science
Park 904, 1098 XH Amsterdam, The Netherlands
| | - Albert Braeuning
- Department
of Food Safety, German Federal Institute
for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Giel Berden
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
- van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science
Park 904, 1098 XH Amsterdam, The Netherlands
| |
Collapse
|