PFΔScreen - an open-source tool for automated PFAS feature prioritization in non-target HRMS data

Per- and polyfluoroalkyl substances (PFAS) are a huge group of anthropogenic chemicals with unique properties that are used in countless products and applications. Due to the high stability of their C-F bonds, PFAS or their transformation products (TPs) are persistent in the environment, leading to ubiquitous detection in various samples worldwide. Since PFAS are industrial chemicals, the availability of authentic PFAS reference standards is limited, making non-target screening (NTS) approaches based on high-resolution mass spectrometry (HRMS) necessary for a more comprehensive characterization. NTS usually is a time-consuming process, since only a small fraction of the detected chemicals can be identified. Therefore, efficient prioritization of relevant HRMS signals is one of the most crucial steps. We developed PFΔScreen, a Python-based open-source tool with a simple graphical user interface (GUI) to perform efficient feature prioritization using several PFAS-specific techniques such as the highly promising MD/C-m/C approach, Kendrick mass defect analysis, diagnostic fragments (MS2), fragment mass differences (MS2), and suspect screening. Feature detection from vendor-independent MS raw data (mzML, data-dependent acquisition) is performed via pyOpenMS (or custom feature lists) with subsequent calculations for prioritization and identification of PFAS in both HPLC- and GC-HRMS data. The PFΔScreen workflow is presented on four PFAS-contaminated agricultural soil samples from south-western Germany. Over 15 classes of PFAS (more than 80 single compounds with several isomers) could be identified, including four novel classes, potentially TPs of the precursors fluorotelomer mercapto alkyl phosphates (FTMAPs). PFΔScreen can be used within the Python environment and is easily automatically installable and executable on Windows. Its source code is freely available on GitHub ( https://github.com/JonZwe/PFAScreen ).

Improvement of Ionization Efficiency and Application of Structural Analysis for MALDI-TOFMS by Derivatization of Polyacrylic Acid

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) is a suitable method for polymer analysis. MALDI is a soft ionization technique that can generate mainly singly charged ions. Therefore, the polymer's molecular weight distribution is easy to analyze, facilitating the calculation of the number average molecular weight and weight average molecular weight and polydispersity. However, there are polymers that are difficult to detect by MALDI-TOFMS. For example, polyacrylic acid includes carboxylic acid in the main chain, which is difficult to measure due to its low ionization efficiency. As a solution, the ionization efficiency was improved by methylation. In this technical report, we introduce a method to utilize derivatization to determine the degree of polymerization by accurate mass spectrometry (MS). Furthermore, the structures of both ends of the polymers were estimated by tandem time-of-flight MS.

PFAS Analysis with Ultrahigh Resolution 21T FT-ICR MS: Suspect and Nontargeted Screening with Unrivaled Mass Resolving Power and Accuracy

Per- and polyfluoroalkyl substances (PFASs) are a large family of thousands of chemicals, many of which have been identified using nontargeted time-of-flight and Orbitrap mass spectrometry methods. Comprehensive characterization of complex PFAS mixtures is critical to assess their environmental transport, transformation, exposure, and uptake. Because 21 tesla (T) Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) offers the highest available mass resolving power and sub-ppm mass errors across a wide molecular weight range, we developed a nontargeted 21 T FT-ICR MS method to screen for PFASs in an aqueous film-forming foam (AFFF) using suspect screening, a targeted formula database (C, H, Cl, F, N, O, P, S; ≤865 Da), isotopologues, and Kendrick-analogous mass difference networks (KAMDNs). False-positive PFAS identifications in a natural organic matter (NOM) sample, which served as the negative control, suggested that a minimum length of 3 should be imposed when annotating CF₂-homologous series with positive mass defects. We putatively identified 163 known PFASs during suspect screening, as well as 134 novel PFASs during nontargeted screening, including a suspected polyethoxylated perfluoroalkane sulfonamide series. This study shows that 21 T FT-ICR MS analysis can provide unique insights into complex PFAS composition and expand our understanding of PFAS chemistries in impacted matrices.

A novel approach to calculating the kinetically derived maximum dose

The kinetically derived maximal dose (KMD) provides a toxicologically relevant upper range for the determination of chemical safety. Here, we describe a new way of calculating the KMD that is based on sound Bayesian, theoretical, biochemical, and toxicokinetic principles, that avoids the problems of relying upon the area under the curve (AUC) approach that has often been used. Our new, mathematically rigorous approach is based on converting toxicokinetic data to the overall, or system-wide, Michaelis–Menten curve (which is the slope function for the toxicokinetic data) using Bayesian methods and using the “kneedle” algorithm to find the “knee” or “elbow”—the point at which there is diminishing returns in the velocity of the Michaelis–Menten curve (or acceleration of the toxicokinetic curve). Our work fundamentally reshapes the KMD methodology, placing it within the well-established Michaelis–Menten theoretical framework by defining the KMD as the point where the kinetic rate approximates the Michaelis–Menten asymptote at higher concentrations. By putting the KMD within the Michaelis–Menten framework, we leverage existing biochemical and pharmacological concepts such as “saturation” to establish the region where the KMD is likely to exist. The advantage of defining KMD as a region, rather than as an inflection point along the curve, is that a region reflects uncertainty and clarifies that there is no single point where the curve is expected to “break;” rather, there is a region where the curve begins to taper off as it approaches the asymptote (V_max in the Michaelis–Menten equation).

Opportunities and challenges related to saturation of toxicokinetic processes: Implications for risk assessment

Top dose selection for repeated dose animal studies has generally focused on identification of apical endpoints, use of the limit dose, or determination of a maximum tolerated dose (MTD). The intent is to optimize the ability of toxicity tests performed in a small number of animals to detect effects for hazard identification. An alternative approach, the kinetically derived maximum dose (KMD), has been proposed as a mechanism to integrate toxicokinetic (TK) data into the dose selection process. The approach refers to the dose above which the systemic exposures depart from being proportional to external doses. This non-linear external-internal dose relationship arises from saturation or limitation of TK process(es), such as absorption or metabolism. The importance of TK information is widely acknowledged when assessing human health risks arising from exposures to environmental chemicals, as TK determines the amount of chemical at potential sites of toxicological responses. However, there have been differing opinions and interpretations within the scientific and regulatory communities related to the validity and application of the KMD concept. A multi-stakeholder working group, led by the Health and Environmental Sciences Institute (HESI), was formed to provide an opportunity for impacted stakeholders to address commonly raised scientific and technical issues related to this topic and, more specifically, a weight of evidence approach is recommended to inform design and dose selection for repeated dose animal studies. Commonly raised challenges related to the use of TK data for dose selection are discussed, recommendations are provided, and illustrative case examples are provided to address these challenges or refute misconceptions.

Afidopyropen: Challenges and impact of a toxicokinetic study designed to identify a point of inflection from dose-proportionality

Afidopyropen is an insecticide that acts as a transient receptor potential vanilloid subtype (TRPV) channel modulator in chordotonal organs of target insects and has been assessed for a wide range of toxicity endpoints including chronic toxicity and carcinogenicity in rats and mice. The current study evaluates the toxicokinetic properties of afidopyropen and its plasma metabolites in rats at dose levels where the pharmacokinetics (PK) are linear and nonlinear in an attempt to identify a point of inflection. Based on the results of this study and depending on the analysis method used, the kinetically derived maximum dose (KMD) is estimated to be between 2.5 and 12.5 mg/kg bw/d with linearity observed at doses below 2.5 mg/kg bw/d. A defined point of inflection could not be determined. These data demonstrate that consideration of PK is critical for improving the dose-selection in toxicity studies as well as to enhance human relevance of the interpretation of animal toxicity studies. The study also demonstrates the technical difficulty in obtaining a defined point of inflection from in vivo PK data.

Peer review of a cancer weight of evidence assessment based on updated toxicokinetics, genotoxicity, and carcinogenicity data for 1,3-dichloropropene using a blinded, virtual panel of experts

A cancer weight of evidence (WOE) analysis based on updated toxicokinetics, genotoxicity, and carcinogenicity data for 1,3-dichloropropene was peer reviewed by a panel of experts. Historically, 1,3-dichloropropene has been classified in the U.S. as "likely to be carcinogenic to humans" via oral and inhalation exposure routes based upon the results of rodent cancer bioassays conducted in the 1980s. Contemporary studies led the authors of the WOE analysis to conclude that the currently manufactured form of 1,3-dichloropropene is not mutagenic and not carcinogenic below certain doses, pointing to a threshold-based approach for cancer risk assessment. SciPinion conducted a peer review of the WOE analysis using methods for assembling and managing blinded expert panels that maximize expertise while minimizing potential selection/participation bias. The process was implemented through a web-based application that poses a series of questions soliciting the experts' scientific opinions and observations about specific topics. The goal of the peer review was to have experts provide conclusions about the WOE for carcinogenicity classification of 1,3-dichloropropene, identify potential data gaps, and evaluate the validity of a threshold-based risk assessment for 1,3-dichloropropene. Based on a robust peer review of the current scientific information, a cancer WOE classification of "not likely to be carcinogenic to humans" is best supported for 1,3-dichloropropene. This conclusion is reached with a high degree of consensus (consensus score = 0.92) across expert panel members.

The Relationship Between Internal and External Dose: Some General Results Based on a Generic Compartmental Model

Statements on how the internal-to-external-dose (IED) relationship looks like are often based on qualitative toxicokinetic arguments. For example, the recently proposed kinetically derived maximum dose (KMD) states that the IED relationship must have an inflection point, due to saturation of underlying processes like metabolism or absorption. However, such statements lack a solid quantitative foundation. Therefore, we derived expressions for the IED relationship for a number of scenarios based on a generic compartmental model involving saturation. The scenarios included repeated or single dose, and saturable metabolism or saturable absorption. For some of these scenarios, an explicit expression for the IED relationship can be derived, for others only implicit expressions can be established, which need to be evaluated numerically. The results show that saturable processes will lead to an IED relationship that is nonlinear over the whole dose range, ie, it can be approximated by a linear relationship at the lower end, whereas the approximation will become gradually poorer with increasing doses. The finding that saturation does not lead to an inflection point in the IED relationship, as assumed in the KMD, implies that the KMD is not a valid approach for selecting the top dose in toxicological studies. An additional use of our results is that the derived explicit expressions of the IED relationship can be fitted to IED data, and, possibly, for extrapolation outside the observed dose range.

Development of a certified genomic DNA reference material for detection and quantification of genetically modified rice KMD

Qualitative and quantitative detection of genetically modified products is inseparable from the application of reference materials (RMs). In this study, a batch of genomic DNA (gDNA) certified reference materials (CRMs) was developed using genetically modified rice Kemingdao (KMD) homozygotes as the raw material. The gDNA CRMs in this batch showed good homogeneity; the minimum sample intake was determined to be 2 μL. The stability study showed that transportation by cold chain is preferable, no significant degradation trend was observed during a 12-month period when storing the gDNA CRMs at 4 °C and - 20 °C, and the number of freeze-thaw cycles cannot exceed 10. The property values of the copy number ratio of transgene and endogenous gene and the copy number concentration for gDNA CRMs were determined by a collaborative characterization of eight laboratories using the duplex KMD/PLD droplet digital PCR (ddPCR) assays. The uncertainty components of characterization, potential between-unit heterogeneity, and potential degradation during long-term storage were combined to estimate the expanded uncertainty of the certified value with a coverage factor k of 2.0. The certified value of copy number ratio for KMD gDNA CRM is 0.99 ± 0.05, and that of copy number concentration is (1.76 ± 0.10) × 10⁵ copies/μL. Compared to the gDNA CRMs in availability, this batch of KMD gDNA CRMs is assigned accurate property values and can be directly used for qualitative and quantitative detection of GMOs as well as evaluation of the parameters of analytical methods with no need of further DNA concentration measurement. Graphical abstract.

Use of toxicokinetic data for afidopyropen to determine the dose levels in developmental toxicity studies

Afidopyropen is an insecticide that acts as a TRPV channel modulator in chordotonal organs of target insects and has been assessed for a wide range of toxicity endpoints including developmental toxicity in rats and rabbits. The GLP developmental toxicity study in rabbits did not produce evidence of maternal or fetal toxicity at the highest dose tested (32 mg/kg/day) but pharmacokinetics (PK) in pregnant rabbits in this study exhibited onset of PK nonlinearity from 5 mg/kg/day on, as measured by plasma C_max and AUC. The NOAEL (32 mg/kg/day) is 9000X higher than maximum expected human dietary exposures to afidopyropen; the dose range where nonlinear PK were observed (5-15 mg/kg/day) is 1400-4200X higher. As nonlinearity occurred between 5 and 15 mg/kg/day, 32 mg/kg/day is concluded to be a sufficiently high dose (kinetically derived maximum dose) for a prenatal developmental toxicity study. As recognized by regulatory dose-selection guidance, onset of saturated PK is evidence of excessive biological stress to test animals rendering any effects at such doses of questionable relevance for human risk assessment. These data demonstrate that consideration of PK is critical for improving the dose-selection in developmental toxicity studies to enhance human relevance of animal toxicity studies.

On the Kendrick Mass Defect Plots of Multiply Charged Polymer Ions: Splits, Misalignments, and How to Correct Them

The Kendrick mass defect (KMD) analysis of multiply charged polymeric distributions has recently revealed a surprising isotopic split in their KMD plots-namely a 1/z difference between KMDs of isotopes of an oligomer at charge state z. Relying on the KMD analysis of actual and simulated distributions of poly(ethylene oxide) (PEO), the isotopic split is mathematically accounted for and found to go with an isotopic misalignment in certain cases. It is demonstrated that the divisibility (resp. indivisibility) of the nominal mass of the repeating unit (R) by z is the condition for homolog ions to line up horizontally (resp. misaligned obliquely) in a KMD plot. Computing KMDs using a fractional base unit R/z eventually corrects the misalignments for the associated charge state while using the least common multiple of all the charge states as the divisor realigns all the points at once. The isotopic split itself can be removed by using either a new charge-dependent KMD plot compatible with any fractional base unit or the remainders of KM (RKM) recently developed for low-resolution data all found to be linked in a unified theory. These original applications of the fractional base units and the RKM plots are of importance theoretically to satisfy the basics of a mass defect analysis and practically for a correct data handling of single stage and tandem mass spectra of multiply charged homo- and copolymers. Graphical Abstract ᅟ.

Reproductive and developmental toxicity testing: Examination of the extended one-generation reproductive toxicity study guideline

An important aspect of safety assessment of chemicals (industrial and agricultural chemicals and pharmaceuticals) is determining their potential reproductive and developmental toxicity. A number of guidelines have outlined a series of separate reproductive and developmental toxicity studies from fertilization through adulthood and in some cases to second generation. The Extended One-Generation Reproductive Toxicity Study (EOGRTS) is the most recent and comprehensive guideline in this series. EOGRTS design makes toxicity testing progressive, comprehensive, and efficient by assessing key endpoints across multiple life-stages at relevant doses using a minimum number of animals, combining studies/evaluations and proposing tiered-testing approaches based on outcomes. EOGRTS determines toxicity during preconception, development of embryo/fetus and newborn, adolescence, and adults, with specific emphasis on the nervous, immunological, and endocrine systems, EOGRTS also assesses maternal and paternal toxicity. However, EOGRTS guideline is complex, criteria for selecting doses is unclear, and monitoring systemic dose during the course of the study for better interpretation and human relevance is not clear. This paper discusses potential simplification of EOGRTS, suggests procedures for relevant dose selection and monitors systemic dose at multiple life-stages for better interpretation of data and human relevance.

An F1-extended one-generation reproductive toxicity study in Crl:CD(SD) rats with 2,4-dichlorophenoxyacetic acid

2,4-Dichlorophenoxyacetic acid (2,4-D) was assessed for systemic toxicity, reproductive toxicity, developmental neurotoxicity (DNT), developmental immunotoxicity (DIT), and endocrine toxicity. CD rats (27/sex/dose) were exposed to 0, 100, 300, 600 (female), or 800 (male) ppm 2,4-D in diet. Nonlinear toxicokinetic behavior was shown at high doses; the renal clearance saturation threshold for 2,4-D was exceeded markedly in females and slightly exceeded in males. Exposure was 4 weeks premating, 7 weeks postmating for P1 males and through lactation for P1 females. F1 offspring were examined for survival and development, and at weaning, pups were divided in cohorts, by sex and dose, and by systemic toxicity (10), DNT (10), DIT (20), and reproductive toxicity (≥ 23). Remaining weanlings were evaluated for systemic toxicity and neuropathology (10–12). Body weight decreased during lactation in high-dose P1 females and in F1 pups. Kidney was the primary target organ, with slight degeneration of proximal convoluted tubules observed in high-dose P1 males and in high-dose F1 males and females. A slight intergenerational difference in kidney toxicity was attributed to increased intake of 2,4-D in F1 offspring. Decreased weanling testes weights and delayed preputial separation in F1 males were attributed to decreased body weights. Endocrine-related effects were limited to slight thyroid hormone changes and adaptive histopathology in high-dose GD 17 dams seen only at a nonlinear toxicokinetic dose. 2,4-D did not cause reproductive toxicity, DNT, or DIT. The “No Observed Adverse Effect Level” for systemic toxicity was 300 ppm in both males (16.6mg/kg/day) and females (20.6mg/kg/day), which is approximately 6700- to 93 000-fold higher than that reported for 2,4-D exposures in human biomonitoring studies.