Expanded coverage of non-targeted LC-HRMS using atmospheric pressure chemical ionization: a case study with ENTACT mixtures

Communicating with Stakeholders to Identify High-Impact Research Directions for Non-Targeted Analysis

Non-targeted analysis (NTA) using high-resolution mass spectrometry without defined chemical targets has the potential to expand and improve chemical monitoring in many fields. Despite rapid advancements within the research community, NTA methods and data remain underutilized by many potential beneficiaries. To better understand barriers toward widespread adoption, the Best Practices for Non-Targeted Analysis (BP4NTA) working group conducted focus group meetings and follow-up surveys with scientists (n = 61) from various sectors (e.g., drinking water utilities, epidemiologists, n = 9) where NTA is expected to provide future value. Meeting participants included producers and end-users of NTA data with a wide range of familiarity with NTA methods and outputs. Discussions focused on identifying specific barriers that limit adoption and on setting NTA product development priorities. Stated priorities fell into four major categories: 1) education and training materials; 2) QA/QC frameworks and study design guidance; 3) accessible compound databases and libraries; and 4) NTA data linkages with chemical fate and toxicity information. Based on participant feedback, this manuscript proposes research directions, such as standardization of training materials, that BP4NTA and other institutions can pursue to expand NTA use in various application scenarios and decision contexts.

Progress, applications, and challenges in high-throughput effect-directed analysis for toxicity driver identification - is it time for HT-EDA?

The rapid increase in the production and global use of chemicals and their mixtures has raised concerns about their potential impact on human and environmental health. With advances in analytical techniques, in particular, high-resolution mass spectrometry (HRMS), thousands of compounds and transformation products with potential adverse effects can now be detected in environmental samples. However, identifying and prioritizing the toxicity drivers among these compounds remain a significant challenge. Effect-directed analysis (EDA) emerged as an important tool to address this challenge, combining biotesting, sample fractionation, and chemical analysis to unravel toxicity drivers in complex mixtures. Traditional EDA workflows are labor-intensive and time-consuming, hindering large-scale applications. The concept of high-throughput (HT) EDA has recently gained traction as a means of accelerating these workflows. Key features of HT-EDA include the combination of microfractionation and downscaled bioassays, automation of sample preparation and biotesting, and efficient data processing workflows supported by novel computational tools. In addition to microplate-based fractionation, high-performance thin-layer chromatography (HPTLC) offers an interesting alternative to HPLC in HT-EDA. This review provides an updated perspective on the state-of-the-art in HT-EDA, and novel methods/tools that can be incorporated into HT-EDA workflows. It also discusses recent studies on HT-EDA, HT bioassays, and computational prioritization tools, along with considerations regarding HPTLC. By identifying current gaps in HT-EDA and proposing new approaches to overcome them, this review aims to bring HT-EDA a step closer to monitoring applications.

Investigating the chemical space coverage of multiple chromatographic and ionization methods using non-targeted analysis on surface and drinking water collected using passive sampling

Multiple non-targeted analysis tools were used to look for a broad range of possible chemical contaminants present in surface and drinking water using liquid chromatography separation and high-resolution mass spectrometry detection, including both quadrupole time of flight (Q-ToF) and Orbitrap instruments. Two chromatographic techniques were evaluated on an LC-Q-ToF with electrospray ionization in both positive and negative modes: (1) the traditionally used reverse phase C18 and (2) the hydrophilic interaction liquid chromatography (HILIC) aimed to capture more polar contaminants that may be present in water. Multiple ionization modes were evaluated with an LC-Orbitrap, including electrospray (ESI) and atmospheric pressure chemical ionization (APCI), also in both positive and negative modes. A suspect screening library of over 1300 possible environmental contaminants, including pesticides, pharmaceuticals, personal care products, illicit drugs/drugs of abuse, and various anthropogenic markers was made with experimentally collected data with the LC-Q-ToF with both column types, with 227 chemicals being retained by the HILIC column. The non-targeted methods using multiple chromatographic and ionization modes were applied to environmental water samples collected with polar organic chemical integrative samplers (POCIS), including surface water upstream and downstream from wastewater effluent discharge, and the downstream drinking water intake and treated drinking water for three distinct sampling events. For the LC-Q-ToF, 442 chemical features were detected on the C18 column and 91 with the HILIC column in the POCIS extracts, while 556 features were found on the Orbitrap workflow by ESI and 131 features detected by APCI. Over 100 chemicals were tentatively identified by suspect screening and database searching. The comprehensive and systematic evaluation of these methods serve as a step in characterizing the chemical space covered when utilizing different chromatography and ionization methods, or different instrument workflows on complex environmental mixtures.

High-Resolution Mass Spectrometry for Human Exposomics: Expanding Chemical Space Coverage

In the modern "omics" era, measurement of the human exposome is a critical missing link between genetic drivers and disease outcomes. High-resolution mass spectrometry (HRMS), routinely used in proteomics and metabolomics, has emerged as a leading technology to broadly profile chemical exposure agents and related biomolecules for accurate mass measurement, high sensitivity, rapid data acquisition, and increased resolution of chemical space. Non-targeted approaches are increasingly accessible, supporting a shift from conventional hypothesis-driven, quantitation-centric targeted analyses toward data-driven, hypothesis-generating chemical exposome-wide profiling. However, HRMS-based exposomics encounters unique challenges. New analytical and computational infrastructures are needed to expand the analysis coverage through streamlined, scalable, and harmonized workflows and data pipelines that permit longitudinal chemical exposome tracking, retrospective validation, and multi-omics integration for meaningful health-oriented inferences. In this article, we survey the literature on state-of-the-art HRMS-based technologies, review current analytical workflows and informatic pipelines, and provide an up-to-date reference on exposomic approaches for chemists, toxicologists, epidemiologists, care providers, and stakeholders in health sciences and medicine. We propose efforts to benchmark fit-for-purpose platforms for expanding coverage of chemical space, including gas/liquid chromatography-HRMS (GC-HRMS and LC-HRMS), and discuss opportunities, challenges, and strategies to advance the burgeoning field of the exposome.

Critical Assessment of the Chemical Space Covered by LC-HRMS Non-Targeted Analysis

Non-targeted analysis (NTA) has emerged as a valuable approach for the comprehensive monitoring of chemicals of emerging concern (CECs) in the exposome. The NTA approach can theoretically identify compounds with diverse physicochemical properties and sources. Even though they are generic and have a wide scope, non-targeted analysis methods have been shown to have limitations in terms of their coverage of the chemical space, as the number of identified chemicals in each sample is very low (e.g., ≤5%). Investigating the chemical space that is covered by each NTA assay is crucial for understanding the limitations and challenges associated with the workflow, from the experimental methods to the data acquisition and data processing techniques. In this review, we examined recent NTA studies published between 2017 and 2023 that employed liquid chromatography-high-resolution mass spectrometry. The parameters used in each study were documented, and the reported chemicals at confidence levels 1 and 2 were retrieved. The chosen experimental setups and the quality of the reporting were critically evaluated and discussed. Our findings reveal that only around 2% of the estimated chemical space was covered by the NTA studies investigated for this review. Little to no trend was found between the experimental setup and the observed coverage due to the generic and wide scope of the NTA studies. The limited coverage of the chemical space by the reviewed NTA studies highlights the necessity for a more comprehensive approach in the experimental and data processing setups in order to enable the exploration of a broader range of chemical space, with the ultimate goal of protecting human and environmental health. Recommendations for further exploring a wider range of the chemical space are given.

Cracked and shucked: GC-APCI-IMS-HRMS facilitates identification of unknown halogenated organic chemicals in French marine bivalves

High resolution mass spectrometry (HRMS)-based non-target analysis coupled with ion mobility spectrometry (IMS) is gaining momentum due to its ability to provide complementary information which can be useful in the identification of unknown organic chemicals in support of efforts in unraveling the complexity of the chemical exposome. The chemical exposome in the marine environment, though not as well studied as its freshwater counterparts, is not foreign to chemical diversity specially when it comes to potentially bioaccumulative and bioactive polyhalogenated organic contaminants and natural products. In this work we present in detail how we utilized IMS-HRMS coupled with gas chromatographic separation and atmospheric pressure chemical ionization (APCI) to annotate polyhalogenated organic chemicals in French bivalves collected from 25 sites along the French coasts. We describe how we used open cheminformatic tools to exploit isotopologue patterns, isotope ratios, Kendrick mass defect (Cl scale), and collisional cross section (CCS), in order to annotate 157 halogenated features (level 1: 54, level 2: 47, level 3: 50, and level 4: 6). Grouping the features into 11 compound classes was facilitated by a KMD vs CCS plot which showed co-clustering of potentially structurally-related compounds. The features were semi-quantified to gain insight into the distribution of these halogenated features along the French coast, ultimately allowing us to differentiate between sites that are more anthropologically impacted versus sites that are potentially biodiverse.

Nontarget Analysis of Polluted Surface Waters in Bangladesh Using Open Science Workflows

Nontarget mass spectrometry has great potential to reveal patterns of water contamination globally through community science, but few studies are conducted in low-income countries, nor with open-source workflows, and few datasets are FAIR (Findable, Accessible, Interoperable, Reusable). Water was collected from urban and rural rivers around Dhaka, Bangladesh, and analyzed by liquid chromatography high-resolution mass spectrometry in four ionization modes (electrospray ionization ±, atmospheric pressure chemical ionization ±) with data-independent MS2 acquisition. The acquisition strategy was complementary: 19,427 and 7365 features were unique to ESI and APCI, respectively. The complexity of water pollution was revealed by >26,000 unique molecular features resolved by MS-DIAL, among which >20,000 correlated with urban sources in Dhaka. A major wastewater treatment plant was not a dominant pollution source, consistent with major contributions from uncontrolled urban drainage, a result that encourages development of further wastewater infrastructures. Matching of deconvoluted MS2 spectra to public libraries resulted in 62 confident annotations (i.e., Level 1-2a) and allowed semiquantification of 42 analytes including pharmaceuticals, pesticides, and personal care products. In silico structure prediction for the top 100 unknown molecular features associated with an urban source allowed 15 additional chemicals of anthropogenic origin to be annotated (i.e., Level 3). The authentic MS2 spectra were uploaded to MassBank Europe, mass spectral data were openly shared on the MassIVE repository, a tool (i.e., MASST) that could be used for community science environmental surveillance was demonstrated, and current limitations were discussed.

Chemical and biological assessments of environmental mixtures: A review of current trends, advances, and future perspectives

Considering the chemical complexity and toxicity data gaps of environmental mixtures, most studies evaluate the chemical risk individually. However, humans are usually exposed to a cocktail of chemicals in real life. Mixture health assessment remains to be a research area having significant knowledge gaps. Characterization of chemical composition and bioactivity/toxicity are the two critical aspects of mixture health assessments. This review seeks to introduce the recent progress and tools for the chemical and biological characterization of environmental mixtures. The state-of-the-art techniques include the sampling, extraction, rapid detection methods, and the in vitro, in vivo, and in silico approaches to generate the toxicity data of an environmental mixture. Application of these novel methods, or new approach methodologies (NAMs), has increased the throughput of generating chemical and toxicity data for mixtures and thus refined the mixture health assessment. Combined with computational methods, the chemical and biological information would shed light on identifying the bioactive/toxic components in an environmental mixture.

Differential Organic Contaminant Ionization Source Detection and Identification in Environmental Waters by Nontargeted Analysis

The development of nontargeted analysis (NTA) methods to assess environmental contaminants of emerging concern, which are not commonly monitored, is paramount, especially when no previous knowledge on the identity of the pollution source is available. We compared complementary ionization techniques, namely electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI), in the detection and identification of organic contaminants in tap and surface waters from South Florida. Furthermore, the performance of a simple rationalized NTA method was assessed by analyzing 10 complex mixtures as part of the US Environmental Protection Agency's Non-targeted Analysis Collaborative Trial interlaboratory study, where limitations of the NTA approach have been identified (e.g., number of employed databases, false positives). Different water bodies displayed unique chemical features that can be used as chemical fingerprints for source tracking and discrimination. The APCI technique detected at least threefold as many chemical features as ESI in environmental water samples, corroborating the fact that APCI is more energetic and can ionize certain classes of compounds that are traditionally difficult to ionize by liquid chromatography-mass spectrometry. Kendrick mass defect plots and Van Krevelen diagrams were applied to elucidate unique patterns and theoretical chemical space regions of anthropogenic organic compounds belonging to homologous series or similar classes covered by ESI and APCI. Overall, APCI and ESI were established as complementary, expanding the detected NTA chemical space which would otherwise be underestimated by a single ionization source operated in a single polarity setting. Environ Toxicol Chem 2022;41:1154-1164. © 2021 SETAC.

Chemical Characterization and Non-targeted Analysis of Medical Device Extracts: A Review of Current Approaches, Gaps, and Emerging Practices

The developers of medical devices evaluate the biocompatibility of their device prior to FDA's review and subsequent introduction to the market. Chemical characterization, described in ISO 10993-18:2020, can generate information for toxicological risk assessment and is an alternative approach for addressing some biocompatibility end points (e.g., systemic toxicity, genotoxicity, carcinogenicity, reproductive/developmental toxicity) that can reduce the time and cost of testing and the need for animal testing. Additionally, chemical characterization can be used to determine whether modifications to the materials and manufacturing processes alter the chemistry of a patient-contacting device to an extent that could impact device safety. Extractables testing is one approach to chemical characterization that employs combinations of non-targeted analysis, non-targeted screening, and/or targeted analysis to establish the identities and quantities of the various chemical constituents that can be released from a device. Due to the difficulty in obtaining a priori information on all the constituents in finished devices, information generation strategies in the form of analytical chemistry testing are often used. Identified and quantified extractables are then assessed using toxicological risk assessment approaches to determine if reported quantities are sufficiently low to overcome the need for further chemical analysis, biological evaluation of select end points, or risk control. For extractables studies to be useful as a screening tool, comprehensive and reliable non-targeted methods are needed. Although non-targeted methods have been adopted by many laboratories, they are laboratory-specific and require expensive analytical instruments and advanced technical expertise to perform. In this Perspective, we describe the elements of extractables studies and provide an overview of the current practices, identified gaps, and emerging practices that may be adopted on a wider scale in the future. This Perspective is outlined according to the steps of an extractables study: information gathering, extraction, extract sample processing, system selection, qualification, quantification, and identification.

Occurrence and Distribution of Pharmaceuticals and Their Transformation Products in Luxembourgish Surface Waters

Pharmaceuticals and their transformation products (TPs) are continuously released into the aquatic environment via anthropogenic activity. To expand knowledge on the presence of pharmaceuticals and their known TPs in Luxembourgish rivers, 92 samples collected during routine monitoring events between 2019 and 2020 were investigated using nontarget analysis. Water samples were concentrated using solid-phase extraction and then analyzed using liquid chromatography coupled to a high-resolution mass spectrometer. Suspect screening was performed using several open source computational tools and resources including Shinyscreen (https://git-r3lab.uni.lu/eci/shinyscreen/), MetFrag (https://msbi.ipb-halle.de/MetFrag/), PubChemLite (https://zenodo.org/record/4432124), and MassBank (https://massbank.eu/MassBank/). A total of 94 pharmaceuticals, 88 confirmed at a level 1 confidence (86 of which could be quantified, two compounds too low to be quantified) and six identified at level 2a, were found to be present in Luxembourg rivers. Pharmaceutical TPs (12) were also found at a level 2a confidence. The pharmaceuticals were present at median concentrations up to 214 ng/L, with caffeine having a median concentration of 1424 ng/L. Antihypertensive drugs (15), psychoactive drugs (15), and antimicrobials (eight) were the most detected groups of pharmaceuticals. A spatiotemporal analysis of the data revealed areas with higher concentrations of the pharmaceuticals, as well as differences in pharmaceutical concentrations between 2019 and 2020. The results of this work will help guide activities for improving water management in the country and set baseline data for continuous monitoring and screening efforts, as well as for further open data and software developments.

Pharmacokinetic study of Ninjin'yoeito: Absorption and brain distribution of Ninjin'yoeito ingredients in mice

ETHNOPHARMACOLOGICAL RELEVANCE

Ninjin'yoeito (NYT), a Japanese traditional Kampo medicine, has been reported to exert various clinical benefits such as relief from fatigue, malaise, anorexia, frailty, sarcopenia, and cognitive dysfunction. Recently, some review articles described the pharmacological effects of NYT and additionally indicated the possibility that multiple ingredients in NYT contribute to these effects. However, pharmacokinetic data on the ingredients are essential in addition to data on their pharmacological activities to accurately determine the active ingredients in NYT.

AIM OF THE STUDY

This study assessed the in vivo pharmacokinetics of NYT using mice.

MATERIALS AND METHODS

Target liquid chromatography-mass spectrometry (LC-MS) and wide target LC-MS or LC-tandem MS of NYT ingredients in plasma and the brain after oral administration of NYT were performed. Imaging MS was performed to investigate the detailed brain distributions of NYT ingredients.

RESULTS

The concentrations of 13 ingredients in plasma and schizandrin in the brain were quantified via target LC-MS, and the wide target analysis illustrated that several ingredients are absorbed into blood and transported into the brain. Imaging MS revealed that schizandrin was homogenously dispersed in the NYT-treated mouse brain.

CONCLUSION

These results should be useful for clarifying the active ingredients of NYT and their mechanisms of actions.

A Comprehensive Non-targeted Analysis Study of the Prenatal Exposome

Recent technological advances in mass spectrometry have enabled us to screen biological samples for a very broad spectrum of chemical compounds allowing us to more comprehensively characterize the human exposome in critical periods of development. The goal of this study was three-fold: (1) to analyze 590 matched maternal and cord blood samples (total 295 pairs) using non-targeted analysis (NTA); (2) to examine the differences in chemical abundance between maternal and cord blood samples; and (3) to examine the associations between exogenous chemicals and endogenous metabolites. We analyzed all samples with high-resolution mass spectrometry using liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-QTOF/MS) in both positive and negative electrospray ionization modes (ESI+ and ESI-) and in soft ionization (MS) and fragmentation (MS/MS) modes for prioritized features. We confirmed 19 unique compounds with analytical standards, we tentatively identified 73 compounds with MS/MS spectra matching, and we annotated 98 compounds using an annotation algorithm. We observed 103 significant associations in maternal and 128 in cord samples between compounds annotated as endogenous and compounds annotated as exogenous. An example of these relationships was an association between three poly and perfluoroalkyl substances (PFASs) and endogenous fatty acids in both the maternal and cord samples indicating potential interactions between PFASs and fatty acid regulating proteins.

Suspect and non-target screening: the last frontier in environmental analysis

Suspect and non-target screening (SNTS) techniques are arising as new analytical strategies useful to disentangle the environmental occurrence of the thousands of exogenous chemicals present in our ecosystems. The unbiased discovery of the wide number of substances present over environmental analysis needs to find a consensus with powerful technical and computational requirements, as well as with the time-consuming unequivocal identification of discovered analytes. Within these boundaries, the potential applications of SNTS include the studies of environmental pollution in aquatic, atmospheric, solid and biological samples, the assessment of new compounds, transformation products and metabolites, contaminant prioritization, bioremediation or soil/water treatment evaluation, and retrospective data analysis, among many others. In this review, we evaluate the state of the art of SNTS techniques going over the normalized workflow from sampling and sample treatment to instrumental analysis, data processing and a brief review of the more recent applications of SNTS in environmental occurrence and exposure to xenobiotics. The main issues related to harmonization and knowledge gaps are critically evaluated and the challenges of their implementation are assessed in order to ensure a proper use of these promising techniques in the near future.

Using the US EPA CompTox Chemicals Dashboard to interpret targeted and non-targeted GC-MS analyses from human breath and other biological media

The U.S. EPA CompTox Chemicals Dashboard is a freely available web-based application providing access to chemistry, toxicity, and exposure data for ∼900 000 chemicals. Data, search functionality, and prediction models within the Dashboard can help identify chemicals found in environmental analyses and human biomonitoring. It was designed to deliver data generated to support computational toxicology to reduce chemical testing on animals and provide access to new approach methodologies including prediction models. The inclusion of mass and formula-based searches, together with relevant ranking approaches, allows for the identification and prioritization of exogenous (environmental) chemicals from high resolution mass spectrometry in need of further evaluation. The Dashboard includes chemicals that can be detected by liquid chromatography, gas chromatography-mass spectrometry (GC-MS) and direct-MS analyses, and chemical lists have been added that highlight breath-borne volatile and semi-volatile organic compounds. The Dashboard can be searched using various chemical identifiers (e.g. chemical synonyms, CASRN and InChIKeys), chemical formula, MS-ready formulae monoisotopic mass, consumer product categories and assays/genes associated with high-throughput screening data. An integrated search at a chemical level performs searches against PubMed to identify relevant published literature. This article describes specific procedures using the Dashboard as a first-stop tool for exploring both targeted and non-targeted results from GC-MS analyses of chemicals found in breath, exhaled breath condensate, and associated aerosols.

patRoon: open source software platform for environmental mass spectrometry based non-target screening

Mass spectrometry based non-target analysis is increasingly adopted in environmental sciences to screen and identify numerous chemicals simultaneously in highly complex samples. However, current data processing software either lack functionality for environmental sciences, solve only part of the workflow, are not openly available and/or are restricted in input data formats. In this paper we present patRoon, a new R based open-source software platform, which provides comprehensive, fully tailored and straightforward non-target analysis workflows. This platform makes the use, evaluation and mixing of well-tested algorithms seamless by harmonizing various common (primarily open) software tools under a consistent interface. In addition, patRoon offers various functionality and strategies to simplify and perform automated processing of complex (environmental) data effectively. patRoon implements several effective optimization strategies to significantly reduce computational times. The ability of patRoon to perform time-efficient and automated non-target data annotation of environmental samples is demonstrated with a simple and reproducible workflow using open-access data of spiked samples from a drinking water treatment plant study. In addition, the ability to easily use, combine and evaluate different algorithms was demonstrated for three commonly used feature finding algorithms. This article, combined with already published works, demonstrate that patRoon helps make comprehensive (environmental) non-target analysis readily accessible to a wider community of researchers.