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See detailDevelopment and Application of Liquid Chromatographic Retention Time Indices in HRMS-Based Suspect and Nontarget Screening
Aalizadeh, Reza; Alygizakis, Nikiforos A.; Schymanski, Emma UL et al

in Analytical Chemistry (2021), 93(33), 11601--11611

There is an increasing need for comparable and harmonized retention times (tR) in liquid chromatography (LC) among different laboratories, to provide supplementary evidence for the identity of compounds ... [more ▼]

There is an increasing need for comparable and harmonized retention times (tR) in liquid chromatography (LC) among different laboratories, to provide supplementary evidence for the identity of compounds in high-resolution mass spectrometry (HRMS)-based suspect and nontarget screening investigations. In this study, a rigorously tested, flexible, and less system-dependent unified retention time index (RTI) approach for LC is presented, based on the calibration of the elution pattern. Two sets of 18 calibrants were selected for each of ESI+ and ESI-based on the maximum overlap with the retention times and chemical similarity indices from a total set of 2123 compounds. The resulting calibration set, with RTI set to range between 1 and 1000, was proposed as the most appropriate RTI system after rigorous evaluation, coordinated by the NORMAN network. The validation of the proposed RTI system was done externally on different instrumentation and LC conditions. The RTI can also be used to check the reproducibility and quality of LC conditions. Two quantitative structure−retention relationship (QSRR)-based models were built based on the developed RTI systems, which assist in the removal of false-positive annotations. The applicability domains of the QSRR models allowed completing the identification process with higher confidence for substances within the domain, while indicating those substances for which results should be treated with caution. The proposed RTI system was used to improve confidence in suspect and nontarget screening and increase the comparability between laboratories as demonstrated for two examples. All RTI-related calculations can be performed online at http://rti.chem.uoa.gr/. [less ▲]

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See detailUsing prepared mixtures of ToxCast chemicals to evaluate non-targeted analysis (NTA) method performance
Sobus, Jon R.; Grossman, Jarod N.; Chao, Alex et al

in Analytical and bioanalytical chemistry (2019), 411(4), 835-851

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See detail"MS-Ready" structures for non-targeted high-resolution mass spectrometry screening studies.
McEachran, Andrew D.; Mansouri, Kamel; Grulke, Chris et al

in Journal of cheminformatics (2018), 10(1), 45

Chemical database searching has become a fixture in many non-targeted identification workflows based on high-resolution mass spectrometry (HRMS). However, the form of a chemical structure observed in HRMS ... [more ▼]

Chemical database searching has become a fixture in many non-targeted identification workflows based on high-resolution mass spectrometry (HRMS). However, the form of a chemical structure observed in HRMS does not always match the form stored in a database (e.g., the neutral form versus a salt; one component of a mixture rather than the mixture form used in a consumer product). Linking the form of a structure observed via HRMS to its related form(s) within a database will enable the return of all relevant variants of a structure, as well as the related metadata, in a single query. A Konstanz Information Miner (KNIME) workflow has been developed to produce structural representations observed using HRMS ("MS-Ready structures") and links them to those stored in a database. These MS-Ready structures, and associated mappings to the full chemical representations, are surfaced via the US EPA's Chemistry Dashboard ( https://comptox.epa.gov/dashboard/ ). This article describes the workflow for the generation and linking of ~ 700,000 MS-Ready structures (derived from ~ 760,000 original structures) as well as download, search and export capabilities to serve structure identification using HRMS. The importance of this form of structural representation for HRMS is demonstrated with several examples, including integration with the in silico fragmentation software application MetFrag. The structures, search, download and export functionality are all available through the CompTox Chemistry Dashboard, while the MetFrag implementation can be viewed at https://msbi.ipb-halle.de/MetFragBeta/ . [less ▲]

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