Mass-Suite: a novel open-source python package for high-resolution mass spectrometry data analysis.

Mass-Suite (MSS) is a Python-based, open-source software package designed to analyze high-resolution mass spectrometry (HRMS)-based non-targeted analysis (NTA) data, particularly for water quality assessment and other environmental applications. MSS provides flexible, user-defined workflows for HRMS data processing and analysis, including both basic functions (e.g., feature extraction, data reduction, feature annotation, data visualization, and statistical analyses) and advanced exploratory data mining and predictive modeling capabilities that are not provided by currently available open-source software (e.g., unsupervised clustering analyses, a machine learning-based source tracking and apportionment tool). As a key advance, most core MSS functions are supported by machine learning algorithms (e.g., clustering algorithms and predictive modeling algorithms) to facilitate function accuracy and/or efficiency. MSS reliability was validated with mixed chemical standards of known composition, with 99.5% feature extraction accuracy and ~ 52% overlap of extracted features relative to other open-source software tools. Example user cases of laboratory data evaluation are provided to illustrate MSS functionalities and demonstrate reliability. MSS expands available HRMS data analysis workflows for water quality evaluation and environmental forensics, and is readily integrated with existing capabilities. As an open-source package, we anticipate further development of improved data analysis capabilities in collaboration with interested users.

Chemical characteristics, leaching, and stability of the ubiquitous tire rubber-derived toxicant 6PPD-quinone.

We here report chemical characteristics relevant to the fate and transport of the recently discovered environmental toxicant 6PPD-quinone (2-((4-methylpentan-2-yl)amino)-5-(phenylamino)cyclohexa-2,5-diene-1,4-dione or "6PPDQ"). 6PPDQ is a transformation product of the tire rubber antioxidant 6PPD that is ubiquitous in roadway environments, including atmospheric particulate matter, soils, runoff, and receiving waters, after dispersal from tire rubber use and wear on roadways. The aqueous solubility and octanol-water partitioning coefficient (i.e. log KOW) for 6PPDQ were measured to be 38 ± 10 µg L-1 and 4.30 ± 0.02, respectively. Within the context of analytical measurement and laboratory processing, sorption to various laboratory materials was evaluated, indicating that glass was largely inert but loss of 6PPDQ to other materials was common. Aqueous leaching simulations from tire tread wear particles (TWPs) indicated short term release of ∼5.2 µg 6PPDQ per gram TWP over 6 h under flow-through conditions. Aqueous stability tests observed a slight-to-moderate loss of 6PPDQ over 47 days (26 ± 3% loss) for pH 5, 7 and 9. These measured physicochemical properties suggest that 6PPDQ is generally poorly soluble but fairly stable over short time periods in simple aqueous systems. 6PPDQ can also leach readily from TWPs for subsequent environmental transport, posing high potential for adverse effects in local aquatic environments.

Transformation Products of Tire Rubber Antioxidant 6PPD in Heterogeneous Gas-Phase Ozonation: Identification and Environmental Occurrence.

6PPD, a tire rubber antioxidant, poses substantial ecological risks because it can form a highly toxic quinone transformation product (TP), 6PPD-quinone (6PPDQ), during exposure to gas-phase ozone. Important data gaps exist regarding the structures, reaction mechanisms, and environmental occurrence of TPs from 6PPD ozonation. To address these data gaps, gas-phase ozonation of 6PPD was conducted over 24-168 h and ozonation TPs were characterized using high-resolution mass spectrometry. The probable structures were proposed for 23 TPs with 5 subsequently standard-verified. Consistent with prior findings, 6PPDQ (C18H22N2O2) was one of the major TPs in 6PPD ozonation (∼1 to 19% yield). Notably, 6PPDQ was not observed during ozonation of 6QDI (N-(1,3-dimethylbutyl)-N'-phenyl-p-quinonediimine), indicating that 6PPDQ formation does not proceed through 6QDI or associated 6QDI TPs. Other major 6PPD TPs included multiple C18H22N2O and C18H22N2O2 isomers, with presumptive N-oxide, N,N'-dioxide, and orthoquinone structures. Standard-verified TPs were quantified in roadway-impacted environmental samples, with total concentrations of 130 ± 3.2 µg/g in methanol extracts of tire tread wear particles (TWPs), 34 ± 4 µg/g-TWP in aqueous TWP leachates, 2700 ± 1500 ng/L in roadway runoff, and 1900 ± 1200 ng/L in roadway-impacted creeks. These data demonstrate that 6PPD TPs are likely an important and ubiquitous class of contaminants in roadway-impacted environments.

Approaches for assessing performance of high-resolution mass spectrometry-based non-targeted analysis methods.

Non-targeted analysis (NTA) using high-resolution mass spectrometry has enabled the detection and identification of unknown and unexpected compounds of interest in a wide range of sample matrices. Despite these benefits of NTA methods, standardized procedures do not yet exist for assessing performance, limiting stakeholders' abilities to suitably interpret and utilize NTA results. Herein, we first summarize existing performance assessment metrics for targeted analyses to provide context and clarify terminology that may be shared between targeted and NTA methods (e.g., terms such as accuracy, precision, sensitivity, and selectivity). We then discuss promising approaches for assessing NTA method performance, listing strengths and key caveats for each approach, and highlighting areas in need of further development. To structure the discussion, we define three types of NTA study objectives: sample classification, chemical identification, and chemical quantitation. Qualitative study performance (i.e., focusing on sample classification and/or chemical identification) can be assessed using the traditional confusion matrix, with some challenges and limitations. Quantitative study performance can be assessed using estimation procedures developed for targeted methods with consideration for additional sources of uncontrolled experimental error. This article is intended to stimulate discussion and further efforts to develop and improve procedures for assessing NTA method performance. Ultimately, improved performance assessments will enable accurate communication and effective utilization of NTA results by stakeholders.

Characterizing the Chemical Profile of Biological Decline in Stormwater-Impacted Urban Watersheds.

Chemical contamination is an increasingly important conservation issue in urban runoff-impacted watersheds. Regulatory and restoration efforts typically evaluate limited conventional parameters and pollutants. However, complex urban chemical mixtures contain hundreds to thousands of organic contaminants that remain unidentified, unregulated, and poorly understood. This study aimed to develop broadly representative metrics of water quality impairment corresponding to previously documented biological degradation along gradients of human impacts. Stream samples (n = 65, baseflow/rainfall conditions, 2017-2018) were collected from 15 regional watersheds (Puget Sound, WA, USA) across an urbanization gradient defined by landscape characteristics. Surface water chemical composition characterized via non-targeted high-resolution mass spectrometry (7068 detections) was highly correlated with landscape-based urbanization gradient (p < 0.01) and season (p < 0.01). Landscape-scale changes in chemical composition closely aligned with two anchors of biological decline: coho salmon (Oncorhynchus kisutch) mortality risk (p < 0.001) and loss of stream macroinvertebrate diversity and abundance (p < 0.001). We isolated and identified 32 indicators for urban runoff impacts and corresponding receiving water ecological health, including well-known anthropogenic contaminants (e.g., caffeine, organophosphates, vehicle-derived chemicals), two related environmental transformation products, and a novel (methoxymethyl)melamine compound. Outcomes support data-directed selection of next-generation water quality indicators for prioritization and evaluation of watershed management efforts intended to protect aquatic ecosystems.

Assessing Reliability of Non-targeted High-Resolution Mass Spectrometry Fingerprints for Quantitative Source Apportionment in Complex Matrices.

Effective management of contaminated sites requires differentiating and deconvoluting contaminant source impacts in complex environmental systems. The existing source apportionment approaches that use targeted analyses of preselected indicator chemicals are limited whenever target analytes are below the detection limits or derived from multiple sources. However, non-targeted analyses that leverage high-resolution mass spectrometry (HRMS) yield rich datasets that deeply characterize sample-specific chemical compositions, providing additional potential end-members for source differentiation and apportionment. Previous work demonstrated that HRMS fingerprints can define sample uniqueness and support accurate, quantitative source concentration estimates. Here, using two aqueous film-forming foams as representative complex sources, we assessed the qualitative fidelity and quantitative accuracy of HRMS source fingerprints in increasingly complex background matrices. Across all matrices, HRMS-derived source concentration estimates were 0.81 ± 0.11-fold and 0.64 ± 0.24-fold of actual in samples impacted solely by analytical matrix effects (MEs) or by sample processing recovery and analytical MEs, respectively. Isotopic internal standards were not easily paired to individual unidentified non-target features, but bulk internal standard-based abundance corrections improved apportionment accuracy in higher matrix samples (to 0.90 ± 0.12-fold of actual) and/or informed concentration estimate relative errors. HRMS fingerprint mining could identify, based on the dilution behavior, effective individual chemical end-members across 16 homologous series. Although method development is needed, the results further demonstrate the potential applications of non-targeted HRMS data for source apportionment and other quantitative outcomes.

An Introduction to the Benchmarking and Publications for Non-Targeted Analysis Working Group.

Non-targeted analysis (NTA) encompasses a rapidly evolving set of mass spectrometry techniques aimed at characterizing the chemical composition of complex samples, identifying unknown compounds, and/or classifying samples, without prior knowledge regarding the chemical content of the samples. Recent advances in NTA are the result of improved and more accessible instrumentation for data generation and analysis tools for data evaluation and interpretation. As researchers continue to develop NTA approaches in various scientific fields, there is a growing need to identify, disseminate, and adopt community-wide method reporting guidelines. In 2018, NTA researchers formed the Benchmarking and Publications for Non-Targeted Analysis Working Group (BP4NTA) to address this need. Consisting of participants from around the world and representing fields ranging from environmental science and food chemistry to 'omics and toxicology, BP4NTA provides resources addressing a variety of challenges associated with NTA. Thus far, BP4NTA group members have aimed to establish a consensus on NTA-related terms and concepts and to create consistency in reporting practices by providing resources on a public Web site, including consensus definitions, reference content, and lists of available tools. Moving forward, BP4NTA will provide a setting for NTA researchers to continue discussing emerging challenges and contribute to additional harmonization efforts.

Nontargeted Analysis Study Reporting Tool: A Framework to Improve Research Transparency and Reproducibility.

Non-targeted analysis (NTA) workflows using mass spectrometry are gaining popularity in many disciplines, but universally accepted reporting standards are nonexistent. Current guidance addresses limited elements of NTA reporting-most notably, identification confidence-and is insufficient to ensure scientific transparency and reproducibility given the complexity of these methods. This lack of reporting standards hinders researchers' development of thorough study protocols and reviewers' ability to efficiently assess grant and manuscript submissions. To overcome these challenges, we developed the NTA Study Reporting Tool (SRT), an easy-to-use, interdisciplinary framework for comprehensive NTA methods and results reporting. Eleven NTA practitioners reviewed eight published articles covering environmental, food, and health-based exposomic applications with the SRT. Overall, our analysis demonstrated that the SRT provides a valid structure to guide study design and manuscript writing, as well as to evaluate NTA reporting quality. Scores self-assigned by authors fell within the range of peer-reviewer scores, indicating that SRT use for self-evaluation will strengthen reporting practices. The results also highlighted NTA reporting areas that need immediate improvement, such as analytical sequence and quality assurance/quality control information. Although scores intentionally do not correspond to data/results quality, widespread implementation of the SRT could improve study design and standardize reporting practices, ultimately leading to broader use and acceptance of NTA data.

Treading Water: Tire Wear Particle Leachate Recreates an Urban Runoff Mortality Syndrome in Coho but Not Chum Salmon.

Tire tread wear particles (TWP) are increasingly recognized as a global pollutant of surface waters, but their impact on biota in receiving waters is rarely addressed. In the developed U.S. Pacific Northwest, acute mortality of adult coho salmon (Oncorhynchus kisutch) follows rain events and is correlated with roadway density. Roadway runoff experimentally triggers behavioral symptoms and associated changes in blood indicative of cardiorespiratory distress prior to death. Closely related chum salmon (O. keta) lack an equivalent response. Acute mortality of juvenile coho was recently experimentally linked to a transformation product of a tire-derived chemical. We evaluated whether TWP leachate is sufficient to trigger the acute mortality syndrome in adult coho salmon. We characterized the acute response of adult coho and chum salmon to TWP leachate (survival, behavior, blood physiology) and compared it with that caused by roadway runoff. TWP leachate was acutely lethal to coho at concentrations similar to roadway runoff, with the same behaviors and blood parameters impacted. As with runoff, chum salmon appeared insensitive to TWP leachate at concentrations lethal to coho. Our results confirm that environmentally relevant TWP exposures cause acute mortalities of a keystone aquatic species.

A ubiquitous tire rubber-derived chemical induces acute mortality in coho salmon.

In U.S. Pacific Northwest coho salmon (Oncorhynchus kisutch), stormwater exposure annually causes unexplained acute mortality when adult salmon migrate to urban creeks to reproduce. By investigating this phenomenon, we identified a highly toxic quinone transformation product of N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD), a globally ubiquitous tire rubber antioxidant. Retrospective analysis of representative roadway runoff and stormwater-affected creeks of the U.S. West Coast indicated widespread occurrence of 6PPD-quinone (<0.3 to 19 micrograms per liter) at toxic concentrations (median lethal concentration of 0.8 ± 0.16 micrograms per liter). These results reveal unanticipated risks of 6PPD antioxidants to an aquatic species and imply toxicological relevance for dissipated tire rubber residues.

More Than a First Flush: Urban Creek Storm Hydrographs Demonstrate Broad Contaminant Pollutographs.

Stormwater runoff clearly impacts water quality and ecological health of urban receiving waters. Subsequent management efforts are often guided by conceptual models of contaminant "first flushes", defined by disproportionate concentrations or mass loads early in the storm hydrograph. However, studies examining the dynamics of contaminant transport and receiving water hydrology have primarily focused on "traditional" stormwater contaminants and point sources, with less evaluation of chemically complex nonpoint pollution sources. Accordingly, we conducted baseflow and storm sampling in Miller Creek, a representative small, urban watershed in the Puget Sound region (WA, USA). We comprehensively characterized organic contaminant profiles and dynamics via targeted quantification of 35 stormwater-derived chemicals, complementary nontarget HRMS analyses, and surrogate chemical metrics of ecological health. For quantified analytes, total daily baseflow loads were 0.8-3.4 g/day and storm event loads were ∼80-320 g/storm (∼48 h interval), with nine contaminants detected during storms at >500 ng/L. Notably, urban creek "pollutographs" were much broader than relatively sharp storm hydrographs and exhibited transport-limited (rather than mass-limited) source dynamics, with immediate water quality degradation during low-intensity precipitation and continued mobilization of contaminant mass across the entire hydrograph. Study outcomes support prioritization of source identification and focused stormwater management efforts to improve water quality and promote ecosystem function in small urban receiving waters.

Developing Unique Nontarget High-Resolution Mass Spectrometry Signatures to Track Contaminant Sources in Urban Waters.

Diffuse pollution in urban receiving waters often adversely impacts both humans and ecosystems. Identifying such pollution sources is challenging and limits the effectiveness of management actions intended to reduce risk. Here, we evaluated the use of nontarget analysis via high-resolution mass spectrometry (HRMS) to develop chemical fingerprints/signatures for source tracking. Specifically, we applied nontarget HRMS to characterize and differentiate two urban chemical sources: roadway runoff and wastewater influent. We isolated 112 and 598 nontarget compounds (both known and unidentified chemicals) that co-occurred in all roadway runoff and wastewater influent samples, respectively, and were unique relative to other sampled sources. For example, methamphetamine, often considered wastewater derived, was detected in all samples, implying that individual wastewater indicators may lack sufficient specificity in urban receiving waters impacted by multiple sources. Hierarchical cluster analysis differentiated source types, and normalized abundance profiling prioritized nontarget compounds with consistent relative abundance patterns across field sites for a given source. Hexa(methoxymethyl)melamine, 1,3-diphenylguanidine, and polyethylene glycols co-occurred in roadway runoff across geographic areas and traffic intensities, supporting continued development of a universal roadway runoff fingerprint based on ubiquitous compounds. This study provides a proof-of-concept for isolating nontarget source fingerprints to track diffuse contamination in urban receiving waters.

Suspect and Nontarget Screening for Contaminants of Emerging Concern in an Urban Estuary.

This study used suspect and nontarget screening with high-resolution mass spectrometry to characterize the occurrence of contaminants of emerging concern (CECs) in the nearshore marine environment of Puget Sound (WA). In total, 87 non-polymeric CECs were identified; those confirmed with reference standards (45) included pharmaceuticals, herbicides, vehicle-related compounds, plasticizers, and flame retardants. Eight polyfluoroalkyl substances were detected; perfluorooctanesulfonic acid (PFOS) concentrations were as high as 72-140 ng/L at one location. Low levels of methamphetamine were detected in 41% of the samples. Transformation products of pesticides were tentatively identified, including two novel transformation products of tebuthiuron. While a hydrodynamic simulation, analytical results, and dilution calculations demonstrated the prevalence of wastewater effluent to nearshore marine environments, the identity and abundance of selected CECs revealed the additional contributions from stormwater and localized urban and industrial sources. For the confirmed CECs, risk quotients were calculated based on concentrations and predicted toxicities, and eight CECs had risk quotients >1. Dilution in the marine estuarine environment lowered the risks of most wastewater-derived CECs, but dilution alone is insufficient to mitigate risks of localized inputs. These findings highlighted the necessity of suspect and nontarget screening and revealed the importance of localized contamination sources in urban marine environments.

Quantification of organic contaminants in urban stormwater by isotope dilution and liquid chromatography-tandem mass spectrometry.

Pollutants transported in urban stormwater runoff induce pervasive water quality degradation in receiving waters. To accurately characterize stormwater quality and treatment system performance across the range of possible contaminant characteristics, comprehensive multi-residue analytical methods are necessary. Here, we developed a solid-phase extraction (SPE) and high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method to quantify representative stormwater-derived organic contaminants across multiple chemical classes, including vehicle-related chemicals, corrosion inhibitors, industrial chemicals, pesticides, pharmaceuticals and personal care products, and antioxidants. Extraction conditions, isotope-labeled internal standards, and LC-MS/MS parameters were optimized to enhance recovery, minimize matrix effects, and maximize selectivity and sensitivity. The developed method was sensitive (method quantification limits < 10 ng/L for > 80% of selected analytes) and accurate (mean relative recoveries in the range of 70-130%, with relative standard deviations < 25% for 77% of the analytes) for most of the analytes. The method was used to analyze samples collected from nine urban watersheds during a storm event; 62% of the 39 analytes were detected at least once at concentrations up to 540 ng/L (1,3-diphenylguanidine). Spatial trends in detection and concentration were observed for vehicle-related and industrial chemicals that correlated with vehicle traffic. Total concentrations of pesticides suggested that residential uses could be more important sources than agriculture. This study illustrates the pervasive occurrence of a wide variety of stormwater-derived chemicals in urban receiving waters and highlights the need to better understand their environmental fate and ecological implications. Graphical abstract.

Application of Nontarget High Resolution Mass Spectrometry Data to Quantitative Source Apportionment.

High resolution mass spectrometry (HRMS) analyses provide expansive chemical characterizations of environmental samples. To date, most research efforts have developed tools to expedite labor- and time-intensive contaminant identification efforts. However, even without chemical identity, the richness of nontarget HRMS data sets represents a significant opportunity to chemically differentiate samples and delineate source contributions. To develop this potential, we evaluated the use of unidentified HRMS detections to define sample uniqueness and provide additional statistical resolution for quantitative source apportionment, overcoming a critical limitation of existing approaches based on targeted contaminants. By creating a series of sample mixtures that mimic pollution sources in a representative watershed, we assessed the fidelity of HRMS source fingerprints during dilution and mixing. This approach isolated 8-447 nontarget compounds per sample for source apportionment and yielded accurate source concentration estimates (between 0.82 and 1.4-fold of actual values), even in multisource systems with <1% source contributions. Furthermore, we mined the nontarget data to identify five source-specific chemical end-members amenable to apportionment. While additional development studies are needed to fully evaluate the myriad factors affecting method accuracy and capabilities, this study provides a conceptual foundation for novel applications of nontarget HRMS data to confidently distinguish and quantify source impacts in complex systems.

Evaluating emerging organic contaminant removal in an engineered hyporheic zone using high resolution mass spectrometry.

The hyporheic zone (HZ), located at the interface of surface and groundwater, is a natural bioreactor for attenuation of chemical contaminants. Engineered HZs can be incorporated into stream restoration projects to enhance hyporheic exchange, with flowpaths optimized to promote biological habitat, water quantity, and water quality improvements. Designing HZs for in-stream treatment of stormwater, a significant source of flow and contaminant loads to urban creeks, requires assessment of both the hydrology and biogeochemical capacity for water quality improvement. Here, we applied tracer tests and high resolution mass spectrometry (HRMS) to characterize an engineered hyporheic zone unit process, called a hyporheic design element (HDE), in the Thornton Creek Watershed in Seattle, WA. Dye, NaCl, and bromide were used to hydrologically link downwelling and upwelling zones and estimate the hydraulic retention time (HRT) of hyporheic flowpaths. We then compared water quality improvements across hydrologically-linked surface and hyporheic flowpaths (3-5 m length; ∼30 min to >3 h) during baseflow and stormflow conditions. We evaluated fate outcomes for 83 identified contaminants during stormflow, including those correlated with an urban runoff mortality syndrome in coho salmon. Non-target HRMS analysis was used to assess holistic water quality improvements and evaluate attenuation mechanisms. The data indicated substantial water quality improvement in hyporheic flowpaths relative to surface flow and improved contaminant removal with longer hyporheic HRT (for ∼1900 non-target compounds detected during stormflow, <17% were attenuated >50% via surface flow vs. 59% and 78% via short and long hyporheic residence times, respectively), and strong contributions of hydrophobic sorption towards observed contaminant attenuation.

Using High-Resolution Mass Spectrometry to Identify Organic Contaminants Linked to Urban Stormwater Mortality Syndrome in Coho Salmon.

Urban stormwater is a major threat to ecological health, causing a range of adverse, mostly sublethal effects. In western North America, urban runoff is acutely lethal to adult coho salmon ( Oncorhynchus kisutch) that spawn each fall in freshwater creeks. Although the mortality syndrome is correlated to urbanization and attributed to road runoff contaminant(s), the causal agent(s) remain unknown. We applied high-resolution mass spectrometry to isolate a coho mortality chemical signature: a list of nontarget and identified features that co-occurred in waters lethal to coho spawners (road runoff from controlled exposures and urban receiving waters from two field observations of symptomatic coho). Hierarchical cluster analysis indicated that tire wear particle (TWP) leachates were most chemically similar to the waters with observed toxicity, relative to other vehicle-derived sources. Prominent road runoff contaminants in the signature included two groups of nitrogen-containing compounds derived from TWP, polyethylene glycols, octylphenol ethoxylates, and polypropylene glycols. A (methoxymethyl)melamine compound family, previously unreported in North America, was detected in road runoff and urban creeks at concentrations up to ∼9 and ∼0.3 µg/L, respectively. The results indicate TWPs are an under-appreciated contaminant source in urban watersheds and should be prioritized for fate and toxicity assessment.