Proteomic analysis of the lake trout (Salvelinus namaycush) heart and blood: The beginning of a comprehensive lake trout protein database.

Lake trout (Salvelinus namaycush) are a top-predator species in the Laurentian Great Lakes that are often used as bioindicators of chemical stressors in the ecosystem. Although many studies are done using these fish to determine concentrations of stressors like legacy persistent, bioaccumulative and toxic chemicals, there are currently no proteomic studies on the biological effects these stressors have on the ecosystem. This lack of proteomic studies on Great Lakes lake trout is because there is currently no complete, comprehensive protein database for this species. Here, we employed proteomics approaches to develop a lake trout protein database that could aid in future research on this fish, in particular exposomics and adductomics. The current study utilized heart tissue and blood from two lake trout. Our previous work using lake trout liver revealed 4194 potential protein hits in the NCBI databases and 3811 potential protein hits in the UniProtKB databases. In the current study, using the NCBI databases we identified 838 proteins for the heart and 580 proteins for the blood tissues in the biological replicate 1 (BR1) and 1180 potential protein hits for the heart and 561 potential protein hits for the blood in BR2. Similar results were obtained using the UniProtKB databases. This study builds on our previous work by continuing to build the first comprehensive lake trout protein database and provides insight into protein homology through evolutionary relationships. This data is available via the PRIDE partner repository with the dataset identifier PXD023970.

Suspect Screening and Nontargeted Analysis of Per- and Polyfluoroalkyl Substances in a Lake Ontario Food Web.

Per- and polyfluoroalkyl substances (PFAS) are globally distributed in the natural environment, and their persistent and bioaccumulative potential illicit public concern. The production of certain PFAS has been halted or controlled by regulation due to their adverse effect on the health of humans and wildlife. However, new PFAS are continuously developed as alternatives to legacy PFAS. Additionally, many precursors are unknown, and their metabolites have not been assessed. To better understand the PFAS profiles in the Lake Ontario (LO) aquatic food web, a quadrupole time-of-flight mass spectrometer (QToF) coupled to ultrahigh-performance liquid chromatography (UPLC) was used to generate high-resolution mass spectra (HRMS) from sample extracts. The HRMS data files were analyzed using an isotopic profile deconvoluted chromatogram (IPDC) algorithm to isolate PFAS profiles in aquatic organisms. Fourteen legacy PFAAs (C5-C14) and 15 known precursors were detected in the LO food web. In addition, over 400 unknown PFAS features that appear to biomagnify in the LO food web were found. Profundal benthic organisms, deepwater sculpin(Myoxocephalus thompsonii), and Mysis were found to have more known precursors than other species in the food web, suggesting that there is a large reservoir of fluorinated substances in the benthic zone.

Nontargeted Discovery of Novel Contaminants in the Great Lakes Region: A Comparison of Fish Fillets and Fish Consumers.

Sport fish fillets and human sera (fish consumers) were collected in the Lake Superior and Lake Michigan basin and screened for novel contaminants using the isotopic profile deconvoluted chromatogram (IPDC) algorithm. The IPDC algorithm was extended beyond traditional Cl/Br filters to detect additional potential bioaccumulative and toxic (PBT) such as perfluoroalkyl substances (PFAS). The IPDC algorithm screened for approximately 13.5 million theoretical molecular formulas. Additional algorithm modules were developed to detect data independent MS/MS fragmentation products and a retention time index calculator using a series of 13C-labeled perfluoroalkyl carboxylic acids (13C-PFCAs). Ten potential compound classes were isolated including six untargeted PFAS, six homologue groups of polyfluorinated carboxylic acids, polyfluorinated telomer alcohols (PoFTOHs), two hydroxylated polychlorobiphenyls, pesticides, herbicides, antifungals, pharmaceuticals, artificial sweeteners, and personal care products with minimal postprocessing efforts. The algorithm isolated 48 ubiquitous PoFTOHs in both fish fillet and serum of fish consumers suggesting a region wide distribution of this class of compounds. The 3, 4, and 7 fluorine substituted PoFTOH were the most abundant congeners in both biological matrices.

Characterization of Halogenated Organic Compounds in Pelagic Sharks and Sea Turtles Using a Nontargeted Approach.

Halogenated organic compounds (HOCs) in marine species collected from the Atlantic Ocean [3 shortfin mako (Isurus oxyrinchus) and 1 porbeagle (Lamna nasus)], and 12 sea turtles collected from the Pacific Ocean [3 loggerhead (Caretta caretta), 3 green (Chelonia mydas), 3 olive ridley (Lepidochelys olivacea), and 3 hawksbill (Eretmochelys imbricata)] were analyzed with a nontargeted analytical method using two-dimensional gas chromatography coupled to high-resolution time-of-flight mass spectrometry. Sharks and sea turtles had distinct HOC profiles. Halogenated methoxyphenols (halo-MeOPs) were the most abundant compound class identified in sea turtle livers, while polychlorinated biphenyls (PCBs) were the most abundant in shark livers. In addition to legacy contaminants and halo-MeOPs, a total of 110 nontargeted/novel HOCs (NHOCs) were observed in the shark livers. Shortfin mako collected from the northern Gulf of Mexico contained the largest number (89) and most diverse structural classes of NHOCs. Among all NHOCs, a group of compounds with the elemental composition C14H12-nCln (n = 5-8) exhibited the highest concentrations, followed by chlorocarbazoles and tris(chlorophenyl) methanes (TCPMs). Using nontargeted workflows, a variety of known and unknown HOCs were observed, which demonstrate the need to develop more complete chemical profiles in the marine environment.

Decadal Differences in Emerging Halogenated Contaminant Profiles in Great Lakes Top Predator Fish.

Legacy halogenated contaminants have been monitored in the Great Lakes for decades, but there are many additional unknown halogenated contaminants potentially affecting the Great Lakes ecosystem. To address this concern, lake trout (Salvelinus namaycush) were collected in 2005/2006 and 2015/2016 from each lake and screened for previously unidentified compounds. The isotopic profile deconvoluted chromatogram algorithm was used to isolate unknown halogenated components using high-resolution mass spectrometry data files generated by an atmospheric pressure gas chromatography-quadrupole time-of-flight mass spectrometer operated in positive and negative modes. The temporal and spatial differences in the newly detected features were used to isolate new potential contaminants. Decadal differences in the unknown halogenated compounds (or features) were compared with the total polychlorinated biphenyl concentration trends. Greater than 2000 unknown halogenated features were detected. As expected, Lake Superior contained the lowest number of unknown halogenated features, whereas Lake Ontario contained the highest. Unknown features tended to have fewer Cl and/or Br atoms compared to traditional legacy contaminant features typically monitored. Diverse patterns of unknown halogenated compounds between lakes suggested that there continues to be unidentified sources of halogenated contaminants in the Great Lakes missed by current monitoring programs.

Nontargeted Screening of Halogenated Organic Compounds in Fish Fillet Tissues from the Great Lakes.

Fish have been used for decades as bioindicators for assessing toxic contaminants in the Great Lakes ecosystem. Routine environmental monitoring programs target predetermined compounds that do not reflect the complete exposure of chemicals to biota and do not provide the complete halogenated fingerprint of the biota. In the current work, a nontargeted screening method was developed using a two-dimensional gas chromatograph coupled to a high-resolution time-of-flight mass spectrometer and was applied to 149 edible fish fillets from different species in the Great Lakes to characterize a more robust set of halogenated organic compounds across species and among lakes. Lake Ontario had the largest number of novel halogenated organic compounds (NHOCs). Seven NHOCs were observed in species from all lakes, indicating that this regional signature was not species-dependent. Hierarchical cluster analysis showed identical NHOC profiles between bottom dwelling and pelagic species. The NHOCs were grouped into seven clusters with similar structures and potentially similar environmental behaviors. Seven of the 29 NHOCs likely containing methoxy or ethoxy groups on a benzene or benzene-methanol backbone were clustered into one group with similar retention times. Five NHOCs were clustered with legacy contaminants that likely have similar structures or are their degradation products.

Concentrations and Long-Term Temporal Trends of Hexabromocyclododecanes (HBCDD) in Lake Trout and Walleye from the Great Lakes.

Hexabromocyclododecane (HBCDD) is a hazardous, persistent, bioaccumlative brominated flame retardant. To investigate how its use has affected the Great Lakes, total HBCDD (∑HBCDD) concentrations and temporal trends in homogenized whole fish samples from the Great Lakes region (1978 to 2016) were determined. ∑HBCDD concentrations (ng/g ww) for each lake are Erie (0.49-2.60), Ontario (3.12-8.90), Michigan (3.91-9.01), Superior (5.69-13.1), and Huron (5.57-13.7). Early years (1978 to 1992) showed no significant trend. However, recent trends (2004 to 2016) suggest concentrations are increasing in Lakes Erie and Ontario, decreasing in Lakes Superior and Michigan, and not changing in Lake Huron. Decreasing trends for Lakes Superior and Michigan are likely the result of decreased usage of the compound globally, regionally, and locally. For the other lakes, increasing or zero trends are consistent with food web changes due to invasive species and climate change, which has caused more intense storms and less ice cover leading to increased sediment resuspension.

Proteomic Analysis of the Lake Trout (Salvelinus namaycush) Liver Identifies Proteins from Evolutionarily Close and -Distant Fish Relatives.

Lake trout are used as bioindicators for toxics exposure in the Great Lakes ecosystem. Here the first lake trout (Salvelinus namaycush) liver proteomics study is performed and searched against specific databases: (NCBI and UniProtKB) Salvelinus, Salmonidae, Actinopterygii, and Oncorhynchus mykiss, and the more distant relative, Danio rerio. In the biological replicate 1 (BR1), technical replicate 1 (TR1), (BR1TR1), a large number of lake trout liver proteins are not in the Salvelinus protein database, suggesting that lake trout liver proteins have homology to some proteins from the Salmonidae family and Actinopterygii class, and to Oncorhynchus mykiss and Danio rerio, two more highly studied fish. In the NCBI search, 4194 proteins are identified: 3069 proteins in Actinopterygii, 1617 in Salmonidae, 68 in Salvelinus, 568 in Oncorhynchus mykiss, and 946 in Danio rerio protein databases. Similar results are observed in the UniProtKB searches of BR1RT1, as well as in a technical replicate (BR1TR2), and then in a second biological replicate experiment, with two technical replicates (BR2TR1 and BR2TR2). This study opens the possibility of identifying evolutionary relationships (i.e., adaptive mutations) between various groups (i.e., zebrafish, rainbow trout, Salmonidae, Salvelinus and lake trout) through evolutionary proteomics. Data are available via the PRIDE Q2 (PXD011924).

Automated Isotopic Profile Deconvolution for High Resolution Mass Spectrometric Data (APGC-QToF) from Biological Matrices.

An isotopic profile matching algorithm, the isotopic profile deconvoluted chromatogram (IPDC), was developed to screen for a wide variety of organic compounds in high-resolution mass spectrometry (HRMS) data acquired from instruments with resolution power as low as 22 000 fwhm. The algorithm initiates the screening process by generating a series of C/Br/Cl/S isotopic patterns consistent with the profiles of approximately 3 million molecular formulas for compounds with potentially persistent, bioaccumulative, and toxic (PBT) properties. To evaluate this algorithm, HRMS data were screened using these seed profiles to isolate relevant chlorinated and/or brominated compounds. Data reduction techniques included mass defect filtering and retention time prediction from estimated boiling points predicted using molecular formulas and reasonable elemental conformations. A machine learning classifier was also developed using spectrometric and chromatographic variables to minimize false positives. A scoring system was developed to rank candidate molecular formulas for an isotopic feature. The IPDC algorithm was applied to a Lake Michigan lake trout extract analyzed by atmospheric pressure gas chromatography-quadrupole time-of-flight (APGC-QToF) mass spectrometry in positive and negative modes. The IPDC algorithm detected isotopic features associated with legacy contaminants and a series of unknown halogenated features. The IPDC algorithm resolved 313 and 855 halogenated features in positive and negative modes, respectively, in Lake Michigan lake trout.

Spatial and Temporal Trends (2004-2016) of Selected Alternative Flame Retardants in Fish of the Laurentian Great Lakes.

Following the phase-out of polybrominated diphenyl ether (PBDE) and hexabromocyclododecane (HBCDD) flame retardants (FRs) from North American markets, the use of alternative FRs has increased. In this study the occurrence and spatiotemporal distributions of 18 dechlorane analogues (collectively referred to as DECs) and 20 alternative brominated FRs (referred to as ABFRs, i.e., brominated FRs other than PBDEs and HBCDD) were investigated in top predator fish megacomposites (i.e., a composite of all 50 fish) collected yearly from each of the Great Lakes from 2004 to 2016. Frequently detected substances include dechlorane 602, 603, 604 Component B, anti- and syn-dechlorane plus, and chlordene plus, as well as several brominated benzene FRs (i.e., hexabromobenzene, pentabromotoluene, and tetrabromo- o-chlorotoluene). Concentrations of ΣDECs and ΣABFRs ranged from 0.33-31.9 ng/g lipid weight (lw) (0.01-8.3 ng/g wet weight or ww) and 0.91-54.7 ng/g lw (0.09-7.1 ng/g ww), respectively. Flame retardant contamination exhibited chemical-specific spatial variations across the five lakes. Concentrations of ΣABFRs in Lake Erie fish were generally lower than those from other lakes. By contrast, fish ΣDEC concentrations were highest in Lake Ontario and the composition of dechlorane analogues differed significantly between Lake Ontario and the other lakes, indicating likely point-source influences. Temporal analyses revealed declining trends of ΣDECs and ΣABFRs in most lakes except Lake Erie, with age corrected trend slopes of -13.5% to -8.8% and -20.1% to -7.0% per year, respectively.

Legacy Polybrominated Diphenyl Ethers (PBDEs) Trends in Top Predator Fish of the Laurentian Great Lakes (GL) from 1979 to 2016: Will Concentrations Continue to Decrease?

Polybrominated diphenyl ethers (PBDEs) were widely used as fire retardants and have been detected throughout the Great Lakes (GL) ecosystem. The concentration trends (after fish age normalization) of PBDEs in top predator fish (lake trout and walleye) of the GLs were determined from 1979 to 2016, which includes most of the period when PBDEs were manufactured and used in this region. The fish samples were collected by two national (U.S. and Canada) long-term monitoring and surveillance programs. Trends in total concentrations (age-normalized) of the five major PBDE congeners (BDE-47, 99, 100, 153, and 154) found in fish across all five lakes have varied over time. Significant increases were observed from 1990 to 2000 (16.3% per year). Rapidly decreasing concentrations (-19.5% per year) were found from 2000 to 2007. Since 2007, the decreasing trend has become smaller (less than -5.5% per year) and relatively unchanged from 2011 to 2015. BDE-47, the congener with the highest concentrations in lake trout, has decreased continuously (ranging from -6.7% to -16.2% per year) in all lakes except Lake Erie. This decrease can be associated with the voluntary and regulatory phase out of production and/or usage of PBDEs since 2000. However, it has been offset by recent (since 2007) increasing trends of the other four higher brominated BDE congeners, especially BDE-100 and 154. Production and usage of commercial penta- and octa- BDE mixtures containing primarily the five major PBDE congeners was discontinued in 2004 in the U.S.A. and 2008 in Canada. These results indicate increasing fish uptake and bioaccumulation of higher brominated BDE congeners may be related to the transformation of BDE-209 to lower brominated BDE compounds in the GL environment or food web. Considering the abundance of BDE-209 in existing products and sediment in GL region, the duration of the unchanging total PBDE concentration trend in GL fish could be longer than expected.

Non-targeted Screening in Environmental Monitoring Programs.

Contaminant monitoring programs have been tasked with understanding the fate and transport of toxic chemicals in the environment. Mass spectrometry based methods have traditionally been developed to maximize sensitivity and accuracy of a select set of target compounds. As mass spectrometry methods have advanced, so has the breadth of questions proposed by environmental chemists. Incorporating these methods in chemical monitoring programs provides large data sets to explore the effects of complex mixtures on environmental systems.

Developing Well-Annotated Species-Specific Protein Databases Using Comparative Proteogenomics.

Proteomics is a mass spectrometry-based discipline that aims to analyze proteomes and their functions. Many proteomic studies require well-developed protein databases for reference. However, most proteomes are not well-annotated, aside from model organisms. Techniques like six-frame translation, ab initio gene prediction, and EST databases can aid in maximizing the amount of proteins identified in proteomics experiments, however, each of these has its downfalls. Proteogenomics is a term used to describe the union of proteomics, genomics and transcriptomics to assist in the identification of peptides which would help build better annotated proteome databases. Here, current proteomic and proteogenomic methods will be reviewed, and an example of a comparative proteomics method using lake trout liver samples will be described.

Bioaccumulation and Spatiotemporal Trends of Polyhalogenated Carbazoles in Great Lakes Fish from 2004 to 2016.

Polyhalogenated carbazoles (PHCZs) were recently discovered in Great Lakes sediment and other aquatic systems. However, knowledge about their bioaccumulation and potential risks to fish and wildlife remains very limited. The present study investigated PHCZs in Great Lakes lake trout ( Salvelinus namaycush) and walleye ( Sander vitreus; Lake Erie only) composites collected between 2004 and 2016. Median concentrations of ∑PHCZs by lake ranged from 54.7 to 154 ng/g lipid weight or lw (6.8-28.0 ng/g wet weight). Dominant congeners included 3,6-dichlorocarbazole, 1,3,6-tribromocarbazole, and 1,3,6,8-tetrachlorocarbazole. The highest ∑PHCZs concentrations were found in Lakes Michigan and Ontario fish, followed by Lake Huron, whereas Lakes Erie and Superior fish contained the lowest concentrations. Congener profiles of PHCZs also exhibited spatial variations. After age normalization to minimize fish age influence on bioaccumulation rates, fish ∑PHCZs' concentrations declined significantly over time in all lakes except Lake Erie, with slopes ranging from -10.24% to -3.85% per year. The median toxic equivalent (TEQ) of PHCZs due to their dioxin-like activity was determined to range from 8.7 to 25.7 pg/g lw in Great Lakes fish. This study provides the first insight into the bioaccumulation and spatiotemporal trends of PHCZs in Great Lakes and suggests the need for further research on this group of chemicals.

Comprehensive Analysis of the Great Lakes Top Predator Fish for Novel Halogenated Organic Contaminants by GC×GC-HR-ToF Mass Spectrometry.

The U.S. Environmental Protection Agency's Great Lakes Fish Monitoring and Surveillance Program (GLFMSP) has traced the fate and transport of anthropogenic chemicals in the Great Lakes region for decades. Isolating and identifying halogenated species in fish is a major challenge due to the complexity of the biological matrix. A nontargeted screening methodology was developed and applied to lake trout using a 2-dimensional gas chromatograph coupled to a high resolution time-of-flight mass spectrometer (GC×GC-HR-ToF MS). Halogenated chemicals were identified using a combination of authentic standards and library spectral matching, with molecular formula estimations provided by exact mass spectral interpretation. In addition to the halogenated chemicals currently being targeted by the GLFMSP, more than 60 nontargeted halogenated species were identified. Most appear to be metabolites or breakdown products of larger halogenated organics. The most abundant compound class was halomethoxyphenols accounting for more than 60% of the total concentration of halogenated compounds in top predator fish from all five Great Lakes illustrating the need and utility of nontargeted halogenated screening of aquatic systems using this platform.

Age-Corrected Trends and Toxic Equivalence of PCDD/F and CP-PCBs in Lake Trout and Walleye from the Great Lakes: 2004-2014.

Our research reports polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), and coplanar polychlorinated biphenyls (CP-PCBs) concentrations and age-corrected trends for lake trout and walleye in the Great Lakes over the 2004-2014 period. We determined that age-contaminant corrections are required to accurately report contaminant trends due to significant lake trout age structure changes. The age-trend model (ATM) described here uses a lake-specific age-contaminant regression to mitigate the effect of a fluctuating lake trout age structure to directly improve the log-linear regression model. ATM results indicate that half-life (t1/2) and percent decreases for PCDD/Fs, CP-PCBs, and toxic equivalence (TEQ) (average -56 to 70%) were fairly uniform and consistent across the Great Lakes over the 2004-2014 period. The vast majority of TEQ associated with all Great Lakes lake trout and walleye samples is due to the nonortho CP-PCBs (average = 79%) as compared with PCDD/Fs (average = 21%). On average, CP-PCB_126 individually accounted for over 95% of the total CP-PCB TEQ. A retrospective analysis (1977-2014) of 2378-TCDF and 2378-TCDD raw concentrations in Lake Ontario lake trout revealed decreases of 94% and 96%, respectively. Tissue residue guidelines for wildlife protection based on lake trout and walleye total TEQ were uniformly exceeded in all the Great Lakes.

Comprehensive Emerging Chemical Discovery: Novel Polyfluorinated Compounds in Lake Michigan Trout.

A versatile screening algorithm capable of efficiently searching liquid chromatographic/mass spectrometric data for unknown compounds has been developed using a combination of open source and generic computing software packages. The script was used to search for select novel polyfluorinated contaminants in Great Lakes fish. However, the framework is applicable whenever full-scan, high-resolution mass spectral and chromatographic data are collected. Target compound classes are defined and a matrix of candidates is generated that includes mass spectral profiles and likely fragmentation pathways. The initial calibration was performed using a standard solution of known linear perfluoroalkyl acids. Once validated, Lake Michigan trout data files were analyzed for polyfluoroalkyl acids using the algorithm referencing 3570 possible compounds including C4-C10 perfluoro- and polyfluoroalkyl, polyfluorochloroalkyl acids and sulfonates, and potential ether forms. The results suggest the presence of 30 polyfluorinated chemical formulas which have not been previously reported in the literature. The identified candidates included mono- to hexafluoroalkyl carboxylic acids, mono- and trifluoroalkyl carboxylic acid ethers, and novel polyfluoroalkyl sulfonates. Candidate species identified in lake trout were qualified using theoretical isotopic profile matching, characteristic fragmentation patterns based on known linear perfluoroalkyl acid (PFAA) fragmentation, and retention time reproducibility among replicate extractions and injections. In addition, the relative retention times of multiple species within a compound class were compared based on theoretical octanol-water partition coefficients.

A targeted/non-targeted screening method for perfluoroalkyl carboxylic acids and sulfonates in whole fish using quadrupole time-of-flight mass spectrometry and MS(e).

A new method for measuring perfluoroalkyl contaminants (PFCs) in biological matrices has been developed. An ultra-high pressure liquid chromatograph equipped with a quadrupole time-of-flight mass spectrometer (UPLC-QToF) was optimized using a continuous precursor/product ion monitoring mode. Unlike traditional targeted studies that isolate precursor/product ion pairs, the current method alternates between two ionization energy channels to continuously capture standard electrospray ionization (low energy) and collision induced dissociation (high energy) spectra. The result is the indiscriminant acquisition of paired low and high energy spectra for all constituents eluting from the chromatographic system. This technique was evaluated for the routine analysis of perfluoroalkyl species. Using this technique, linear perfluoroalkyl carboxylic acids (C4 to C14) and perfluoroalkyl sulfonates (C4, C6, C8 and C10) exhibited a linear range spanning over three orders of magnitude and were detectable at levels less than 1 pg on column with a root mean squared signal to noise ratio of 5 to 20. Lake trout (Salvelinus namaycush) and National Institutes of Standards and Technology Standard Reference Material 1946 were used to evaluate matrix effects and the accuracy of this method when applied to a whole fish extract. The current method was also evaluated as a diagnostic tool to identify unknown PFCs using experimental fragmentation patterns, mass defect filtering and Kendrick plots.

Comparison of PoraPak Rxn RP and XAD-2 adsorbents for monitoring dissolved hydrophobic organic contaminants.

Accurate determination of the levels of dissolved hydrophobic organic contaminants (HOCs) is an important step in estimating the dynamics of their inputs and losses in aqueous systems. This study explores an alternative method for efficiently sampling dissolved HOCs while mitigating a number of sampling artifacts associated with traditional methods. The adsorption characteristics of a new polymeric resin, PoraPak Rxn RP (PPR), were assessed using sorption isotherm experiments and fixed bed adsorption studies. The adsorption capacities and breakthrough times for four model contaminants (phenol, p-nitrophenol, naphthalene, and 2,4,6-tribromophenol) were proportional to the contaminant's hydrophobicity. The ability of PPR to isolate dissolved polychlorinated biphenyls (PCBs) in real samples was compared with that of XAD-2, a well-known macroporous polymer that suffers from high background contamination. The results indicated that the PPR resin can be effectively used for monitoring HOCs, with low ∑PCB levels in blanks, decreasing solvent use, and reducing extraction times.

Short- and medium-chain chlorinated paraffins in surface sediment from Lake Ontario.

Concentrations of short- and medium-chain chlorinated paraffins (SCCPs and MCCPs) were analyzed and investigated in surficial sediment collected in 2018 from ten different nearshore sites in Lake Ontario and the St. Lawrence River influenced by inputs from varying urban and historical land uses. Sites were grouped into two categories of tributary and lake according to their location. Results show that tributary sites had higher concentrations of total chlorinated paraffin (CP) than lake sites. Humber Bay, a lake site, had the highest total CP concentration (55,000 ng/gTOC) followed by Humber River, a tributary site (50,000 ng/gTOC). The lowest concentrations were found in eastern Lake Ontario and Lake St. Francis in the St. Lawrence River (540 ng/gTOC). Higher concentrations of chlorinated paraffins (CPs) were found where runoff and wastewater inputs from urban areas, current industrial activities, and population were the greatest. Levels of MCCPs were higher than SCCPs at all sites but one, Lake St. Francis. Among the SCCPs, C13 and among the MCCPs C14 were the dominant chain length alkanes, with C14 being the highest among both groups. The SCCPs and MCCPs profiles suggest that they can be used to distinguish between sites impacted by local sources vs. sites impacted by short-/long-range transport of these chemicals.