@article{rainey_watson_asef_foster_baker_fernandez_2022, title={CCS Predictor 2.0: An Open-Source Jupyter Notebook Tool for Filtering Out False Positives in Metabolomics}, volume={12}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.2c03491}, abstractNote={Metabolite annotation continues to be the widely accepted bottleneck in nontargeted metabolomics workflows. Annotation of metabolites typically relies on a combination of high-resolution mass spectrometry (MS) with parent and tandem measurements, isotope cluster evaluations, and Kendrick mass defect (KMD) analysis. Chromatographic retention time matching with standards is often used at the later stages of the process, which can also be followed by metabolite isolation and structure confirmation utilizing nuclear magnetic resonance (NMR) spectroscopy. The measurement of gas-phase collision cross-section (CCS) values by ion mobility (IM) spectrometry also adds an important dimension to this workflow by generating an additional molecular parameter that can be used for filtering unlikely structures. The millisecond timescale of IM spectrometry allows the rapid measurement of CCS values and allows easy pairing with existing MS workflows. Here, we report on a highly accurate machine learning algorithm (CCSP 2.0) in an open-source Jupyter Notebook format to predict CCS values based on linear support vector regression models. This tool allows customization of the training set to the needs of the user, enabling the production of models for new adducts or previously unexplored molecular classes. CCSP produces predictions with accuracy equal to or greater than existing machine learning approaches such as CCSbase, DeepCCS, and AllCCS, while being better aligned with FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. Another unique aspect of CCSP 2.0 is its inclusion of a large library of 1613 molecular descriptors via the Mordred Python package, further encoding the fine aspects of isomeric molecular structures. CCS prediction accuracy was tested using CCS values in the McLean CCS Compendium with median relative errors of 1.25, 1.73, and 1.87% for the 170 [M – H]−, 155 [M + H]+, and 138 [M + Na]+ adducts tested. For superclass-matched data sets, CCS predictions via CCSP allowed filtering of 36.1% of incorrect structures while retaining a total of 100% of the correct annotations using a ΔCCS threshold of 2.8% and a mass error of 10 ppm.}, journal={ANALYTICAL CHEMISTRY}, author={Rainey, Markace A. and Watson, Chandler A. and Asef, Carter K. and Foster, Makayla R. and Baker, Erin S. and Fernandez, Facundo M.}, year={2022}, month={Dec} }
 @article{foster_rainey_watson_dodds_kirkwood_fernandez_baker_2022, title={Uncovering PFAS and Other Xenobiotics in the Dark Metabolome Using Ion Mobility Spectrometry, Mass Defect Analysis, and Machine Learning}, volume={56}, ISSN={["1520-5851"]}, DOI={10.1021/acs.est.2c00201}, abstractNote={The identification of xenobiotics in nontargeted metabolomic analyses is a vital step in understanding human exposure. Xenobiotic metabolism, transformation, excretion, and coexistence with other endogenous molecules, however, greatly complicate the interpretation of features detected in nontargeted studies. While mass spectrometry (MS)-based platforms are commonly used in metabolomic measurements, deconvoluting endogenous metabolites from xenobiotics is also often challenged by the lack of xenobiotic parent and metabolite standards as well as the numerous isomers possible for each small molecule m/z feature. Here, we evaluate a xenobiotic structural annotation workflow using ion mobility spectrometry coupled with MS (IMS-MS), mass defect filtering, and machine learning to uncover potential xenobiotic classes and species in large metabolomic feature lists. Xenobiotic classes examined included those of known high toxicities, including per- and polyfluoroalkyl substances (PFAS), polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and pesticides. Specifically, when the workflow was applied to identify PFAS in the NIST SRM 1957 and 909c human serum samples, it greatly reduced the hundreds of detected liquid chromatography (LC)-IMS-MS features by utilizing both mass defect filtering and m/z versus IMS collision cross sections relationships. These potential PFAS features were then compared to the EPA CompTox entries, and while some matched within specific m/z tolerances, there were still many unknowns illustrating the importance of nontargeted studies for detecting new molecules with known chemical characteristics. Additionally, this workflow can also be utilized to evaluate other xenobiotics and enable more confident annotations from nontargeted studies.}, number={12}, journal={ENVIRONMENTAL SCIENCE & TECHNOLOGY}, author={Foster, MaKayla and Rainey, Markace and Watson, Chandler and Dodds, James N. and Kirkwood, Kaylie I and Fernandez, Facundo M. and Baker, Erin S.}, year={2022}, month={Jun}, pages={9133–9143} }
 @article{valdiviezo_aly_luo_cordova_casillas_foster_baker_rusyn_2022, title={Analysis of per- and polyfluoroalkyl substances in Houston Ship Channel and Galveston Bay following a large-scale industrial fire using ion-mobility-spectrometry-mass spectrometry}, volume={115}, ISSN={["1878-7320"]}, DOI={10.1016/j.jes.2021.08.004}, abstractNote={Per- and polyfluoroalkyl substances (PFAS) are persistent organic pollutants of concern because of their ubiquitous presence in surface and ground water; analytical methods that can be used for rapid comprehensive exposure assessment and fingerprinting of PFAS are needed. Following the fires at the Intercontinental Terminals Company (ITC) in Deer Park, TX in 2019, large quantities of PFAS-containing firefighting foams were deployed. The release of these substances into the Houston Ship Channel/Galveston Bay (HSC/GB) prompted concerns over the extent and level of PFAS contamination. A targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based study of temporal and spatial patterns of PFAS associated with this incident revealed presence of 7 species; their levels gradually decreased over a 6-month period. Because the targeted LC-MS/MS analysis was focused on about 30 PFAS molecules, it may have missed other PFAS compounds present in firefighting foams. Therefore, we utilized untargeted LC-ion mobility spectrometry-mass spectrometry (LC-IMS-MS)-based analytical approach for a more comprehensive characterization of PFAS in these water samples. We analyzed 31 samples from 9 sites in the HSC/GB that were collected over 5 months after the incident. Our data showed that additional 19 PFAS were detected in surface water of HSC/GB, most of them decreased gradually after the incident. PFAS features detected by LC-MS/MS correlated well in abundance with LC-IMS-MS data; however, LC-IMS-MS identified a number of additional PFAS, many known to be components of firefighting foams. These findings therefore illustrate that untargeted LC-IMS-MS improved our understanding of PFAS presence in complex environmental samples.}, journal={JOURNAL OF ENVIRONMENTAL SCIENCES}, author={Valdiviezo, Alan and Aly, Noor A. and Luo, Yu-Syuan and Cordova, Alexandra and Casillas, Gaston and Foster, MaKayla and Baker, Erin S. and Rusyn, Ivan}, year={2022}, month={May}, pages={350–362} }
 @article{aly_dodds_luo_grimm_foster_rusyn_baker_2021, title={Utilizing ion mobility spectrometry-mass spectrometry for the characterization and detection of persistent organic pollutants and their metabolites}, volume={10}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-021-03686-w}, abstractNote={Persistent organic pollutants (POPs) are xenobiotic chemicals of global concern due to their long-range transport capabilities, persistence, ability to bioaccumulate, and potential to have negative effects on human health and the environment. Identifying POPs in both the environment and human body is therefore essential for assessing potential health risks, but their diverse range of chemical classes challenge analytical techniques. Currently, platforms coupling chromatography approaches with mass spectrometry (MS) are the most common analytical methods employed to evaluate both parent POPs and their respective metabolites and/or degradants in samples ranging from d rinking water to biofluids. Unfortunately, different types of analyses are commonly needed to assess both the parent and metabolite/degradant POPs from the various chemical classes. The multiple time-consuming analyses necessary thus present a number of technical and logistical challenges when rapid evaluations are needed and sample volumes are limited. To address these challenges, we characterized 64 compounds including parent per- and polyfluoroalkyl substances (PFAS), pesticides, polychlorinated biphenyls (PCBs), industrial chemicals, and pharmaceuticals and personal care products (PPCPs), in addition to their metabolites and/or degradants, using ion mobility spectrometry coupled with MS (IMS-MS) as a potential rapid screening technique. Different ionization sources including electrospray ionization (ESI) and atmospheric pressure photoionization (APPI) were employed to determine optimal ionization for each chemical. Collectively, this study advances the field of exposure assessment by structurally characterizing the 64 important environmental pollutants, assessing their best ionization sources, and evaluating their rapid screening potential with IMS-MS.}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Aly, Noor A. and Dodds, James N. and Luo, Yu-Syuan and Grimm, Fabian A. and Foster, MaKayla and Rusyn, Ivan and Baker, Erin S.}, year={2021}, month={Oct} }
 @misc{dodds_alexander_kirkwood_foster_hopkins_knappe_baker_2021, title={From Pesticides to Per- and Polyfluoroalkyl Substances: An Evaluation of Recent Targeted and Untargeted Mass Spectrometry Methods for Xenobiotics}, volume={93}, ISSN={["1520-6882"]}, url={https://doi.org/10.1021/acs.analchem.0c04359}, DOI={10.1021/acs.analchem.0c04359}, abstractNote={Environmental analysis of xenobiotics is a challenging yet necessary undertaking to characterize pollution levels, assess the effectiveness of remediation interventions, and prevent adverse environmental and health outcomes. Xenobiotics are concerning from an environmental perspective due to their chemical persistence, toxicity to humans and wildlife, and prolific use in agricultural and industrial applications.1 Many xenobiotics are persistent organic pollutants (POPs), and the number of POPs listed in the Stockholm Convention is}, number={1}, journal={ANALYTICAL CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Dodds, James N. and Alexander, Nancy Lee M. and Kirkwood, Kaylie I and Foster, MaKayla R. and Hopkins, Zachary R. and Knappe, Detlef R. U. and Baker, Erin S.}, year={2021}, month={Jan}, pages={641–656} }