@article{ryan_kostelic_hsieh_powers_aspinwall_dodds_schiel_marty_baker_2023, title={Characterizing Adeno-Associated Virus Capsids with Both Denaturing and Intact Analysis Methods}, volume={34}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.3c00321}, abstractNote={Adeno-associated virus (AAV) capsids are among the leading gene delivery platforms used to treat a vast array of human diseases and conditions. AAVs exist in a variety of serotypes due to differences in viral protein (VP) sequences with distinct serotypes targeting specific cells and tissues. As the utility of AAVs in gene therapy increases, ensuring their specific composition is imperative for the correct targeting and gene delivery. From a quality control perspective, current analytical tools are limited in their selectivity for viral protein (VP) subunits due to their sequence similarities, instrumental difficulties in assessing the large molecular weights of intact capsids, and the uncertainty in distinguishing empty and filled capsids. To address these challenges, we combined two distinct analytical workflows that assess the intact capsids and VP subunits separately. First, a selective temporal overview of resonant ion (STORI)-based charge detection-mass spectrometry (CD-MS) was applied for characterization of the intact capsids. Liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) separations were then used for the capsid denaturing measurements. This multimethod combination was applied to three AAV serotypes (AAV2, AAV6, and AAV8) to evaluate their intact empty and filled capsid ratios and then examine the distinct VP sequences and modifications present.}, number={12}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Ryan, Jack P. and Kostelic, Marius M. and Hsieh, Chih-Chieh and Powers, Joshua and Aspinwall, Craig and Dodds, James N. and Schiel, John E. and Marty, Michael T. and Baker, Erin S.}, year={2023}, month={Nov}, pages={2811–2821} }
 @article{stewart_foley_dougherty_mcgill_gulati_gentry_hagey_dorrestein_theriot_dodds_et al._2023, title={Using Multidimensional Separations to Distinguish Isomeric Amino Acid-Bile Acid Conjugates and Assess Their Presence and Perturbations in Model Systems}, volume={95}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.3c03057}, abstractNote={Bile acids play key roles in nutrient uptake, inflammation, signaling, and microbiome composition. While previous bile acid analyses have primarily focused on profiling 5 canonical primary and secondary bile acids and their glycine and taurine amino acid-bile acid (AA-BA) conjugates, recent studies suggest that many other microbial conjugated bile acids (or MCBAs) exist. MCBAs are produced by the gut microbiota and serve as biomarkers, providing information about early disease onset and gut health. Here we analyzed 8 core bile acids synthetically conjugated with 22 proteinogenic and nonproteogenic amino acids totaling 176 MCBAs. Since many of the conjugates were isomeric and only 42 different m/z values resulted from the 176 MCBAs, a platform coupling liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) was used for their separation. Their molecular characteristics were then used to create an in-house extended bile acid library for a combined total of 182 unique compounds. Additionally, ∼250 rare bile acid extracts were also assessed to provide additional resources for bile acid profiling and identification. This library was then applied to healthy mice dosed with antibiotics and humans having fecal microbiota transplantation (FMT) to assess the MCBA presence and changes in the gut before and after each perturbation.}, number={41}, journal={ANALYTICAL CHEMISTRY}, author={Stewart, Allison K. and Foley, Matthew H. and Dougherty, Michael K. and Mcgill, Sarah K. and Gulati, Ajay S. and Gentry, Emily C. and Hagey, Lee R. and Dorrestein, Pieter C. and Theriot, Casey M. and Dodds, James N. and et al.}, year={2023}, month={Oct}, pages={15357–15366} }
 @article{roman-hubers_cordova_rohde_chiu_mcdonald_wright_dodds_baker_rusyn_2022, title={Characterization of compositional variability in petroleum substances}, volume={317}, ISSN={["1873-7153"]}, DOI={10.1016/j.fuel.2022.123547}, abstractNote={In the process of registration of substances of Unknown or Variable Composition, Complex Reaction Products or Biological Materials (UVCBs), information sufficient to enable substance identification must be provided. Substance identification for UVCBs formed through petroleum refining is particularly challenging due to their chemical complexity, as well as variability in refining process conditions and composition of the feedstocks. This study aimed to characterize compositional variability of petroleum UVCBs both within and across product categories. We utilized ion mobility spectrometry (IMS)-MS as a technique to evaluate detailed chemical composition of independent production cycle-derived samples of 6 petroleum products from 3 manufacturing categories (heavy aromatic, hydrotreated light paraffinic, and hydrotreated heavy paraffinic). Atmospheric pressure photoionization and drift tube IMS-MS were used to identify structurally related compounds and quantified between- and within-product variability. In addition, we determined both individual molecules and hydrocarbon blocks that were most variable in samples from different production cycles. We found that detailed chemical compositional data on petroleum UVCBs obtained from IMS-MS can provide the information necessary for hazard and risk characterization in terms of quantifying the variability of the products in a manufacturing category, as well as in subsequent production cycles of the same product.}, journal={FUEL}, author={Roman-Hubers, Alina T. and Cordova, Alexandra C. and Rohde, Arlean M. and Chiu, Weihsueh A. and McDonald, Thomas J. and Wright, Fred A. and Dodds, James N. and Baker, Erin S. and Rusyn, Ivan}, year={2022}, month={Jun} }
 @article{dodds_wang_patti_baker_2022, title={Combining Isotopologue Workflows and Simultaneous Multidimensional Separations to Detect, Identify, and Validate Metabolites in Untargeted Analyses}, volume={1}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.1c04430}, abstractNote={While the combination of liquid chromatography and tandem mass spectrometry (LC-MS/MS) is commonly used for feature annotation in untargeted omics experiments, ensuring these prioritized features originate from endogenous metabolism remains challenging. Isotopologue workflows, such as isotopic ratio outlier analysis (IROA), mass isotopomer ratio analysis of U-13C labeled extracts (MIRACLE), and credentialing incorporate isotopic labels directly into metabolic precursors, guaranteeing that all features of interest are unequivocal byproducts of cellular metabolism. Furthermore, comprehensive separation and annotation of small molecules continue to challenge the metabolomics field, particularly for isomeric systems. In this paper, we evaluate the analytical utility of incorporating ion mobility spectrometry (IMS) as an additional separation mechanism into standard LC-MS/MS isotopologue workflows. Since isotopically labeled molecules codrift in the IMS dimension with their 12C versions, LC-IMS-CID-MS provides four dimensions (LC, IMS, MS, and MS/MS) to directly investigate the metabolic activity of prioritized untargeted features. Here, we demonstrate this additional selectivity by showcasing how a preliminary data set of 30 endogeneous metabolites are putatively annotated from isotopically labeled Escherichia coli cultures when analyzed by LC-IMS-CID-MS. Metabolite annotations were based on several molecular descriptors, including accurate mass measurement, carbon number, annotated fragmentation spectra, and collision cross section (CCS), collectively illustrating the importance of incorporating IMS into isotopologue workflows. Overall, our results highlight the enhanced separation space and increased annotation confidence afforded by IMS for metabolic characterization and provide a unique perspective for future developments in isotopically labeled MS experiments.}, journal={ANALYTICAL CHEMISTRY}, author={Dodds, James N. and Wang, Lingjue and Patti, Gary J. and Baker, Erin S.}, year={2022}, month={Jan} }
 @article{butler_dodds_flick_campuzano_baker_2022, title={High-Resolution Demultiplexing (HRdm) Ion Mobility Spectrometry-Mass Spectrometry for Aspartic and Isoaspartic Acid Determination and Screening}, volume={94}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.1c05533}, abstractNote={Isomeric peptide analyses are an analytical challenge of great importance to therapeutic monoclonal antibody and other biotherapeutic product development workflows. Aspartic acid (Asp, D) to isoaspartic acid (isoAsp, isoD) isomerization is a critical quality attribute (CQA) that requires careful control, monitoring, and quantitation during the drug discovery and production processes. While the formation of isoAsp has been implicated in a variety of disease states such as autoimmune diseases and several types of cancer, it is also understood that the formation of isoAsp results in a structural change impacting efficacy, potency, and immunogenic properties, all of which are undesirable. Currently, lengthy ultrahigh-performance liquid chromatography (UPLC) separations are coupled with MS for CQA analyses; however, these measurements often take over an hour and drastically limit analysis throughput. In this manuscript, drift tube ion mobility spectrometry-mass spectrometry (DTIMS-MS) and both a standard and high-resolution demultiplexing approach were utilized to study eight isomeric Asp and isoAsp peptide pairs. While the limited resolving power associated with the standard DTIMS analysis only separated three of the eight pairs, the application of HRdm distinguished seven of the eight and was only unable to separate DL and isoDL. The rapid high-throughput HRdm DTIMS-MS method was also interfaced with both flow injection and an automated solid phase extraction system to present the first application of HRdm for isoAsp and Asp assessment and demonstrate screening capabilities for isomeric peptides in complex samples, resulting in a workflow highly suitable for biopharmaceutical research needs.}, number={16}, journal={ANALYTICAL CHEMISTRY}, author={Butler, Karen E. and Dodds, James N. and Flick, Tawnya and Campuzano, Iain D. G. and Baker, Erin S.}, year={2022}, month={Apr}, pages={6191–6199} }
 @article{roman-hubers_aeppli_dodds_baker_mcfarlin_letinski_zhao_mitchell_parkerton_prince_et al._2022, title={Temporal chemical composition changes in water below a crude oil slick irradiated with natural sunlight}, volume={185}, ISSN={["1879-3363"]}, DOI={10.1016/j.marpolbul.2022.114360}, abstractNote={Photooxidation can alter the environmental fate and effects of spilled oil. To better understand this process, oil slicks were generated on seawater mesocosms and exposed to sunlight for 8 days. The molecular composition of seawater under irradiated and non-irradiated oil slicks was characterized using ion mobility spectrometry-mass spectrometry and polyaromatic hydrocarbons analyses. Biomimetic extraction was performed to quantify neutral and ionized constituents. Results show that seawater underneath irradiated oil showed significantly higher amounts of hydrocarbons with oxygen- and sulfur-containing by-products peaking by day 4-6; however, concentrations of dissolved organic carbon were similar. Biomimetic extraction indicated toxic units in irradiated mesocosms increased, mainly due to ionized components, but remained <1, suggesting limited potential for ecotoxicity. Because the experimental design mimicked important aspects of natural conditions (freshly collected seawater, natural sunlight, and relevant oil thickness and concentrations), this study improves our understanding of the effects of photooxidation during a marine oil spill.}, journal={MARINE POLLUTION BULLETIN}, author={Roman-Hubers, Alina T. and Aeppli, Christoph and Dodds, James N. and Baker, Erin S. and McFarlin, Kelly M. and Letinski, Daniel J. and Zhao, Lin and Mitchell, Douglas A. and Parkerton, Thomas F. and Prince, Roger C. and et al.}, 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} }
 @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} }
 @article{dodds_baker_2021, title={Improving the Speed and Selectivity of Newborn Screening Using Ion Mobility Spectrometry-Mass Spectrometry}, volume={93}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.1c04267}, abstractNote={Detection and diagnosis of congenital disorders is the principal aim of newborn screening (NBS) programs worldwide. Mass spectrometry (MS) has become the preferred primary testing method for high-throughput NBS sampling because of its speed and selectivity. However, the ever-increasing list of NBS biomarkers included in expanding panels creates unique analytical challenges for multiplexed MS assays due to isobaric/isomeric overlap and chimeric fragmentation spectra. Since isobaric and isomeric systems limit the diagnostic power of current methods and require costly follow-up exams due to many false-positive results, here, we explore the utility of ion mobility spectrometry (IMS) to enhance the accuracy of MS assays for primary (tier 1) screening. Our results suggest that ∼400 IMS resolving power would be required to confidently assess most NBS biomarkers of interest in dried blood spots (DBSs) that currently require follow-up testing. While this level of selectivity is unobtainable with most commercially available platforms, the separations detailed here for a commercially available drift tube IMS (Agilent 6560 with high-resolution demultiplexing, HRdm) illustrate the unique capabilities of IMS to separate many diagnostic NBS biomarkers from interferences. Furthermore, to address the need for increased speed of NBS analyses, we utilized an automated solid-phase extraction (SPE) system for ∼10 s sampling of simulated NBS samples prior to IMS-MS. This proof-of-concept work demonstrates the unique capabilities of SPE-IMS-MS for high-throughput sample introduction and enhanced separation capacity conducive for increasing speed and accuracy for NBS.}, number={51}, journal={ANALYTICAL CHEMISTRY}, author={Dodds, James N. and Baker, Erin S.}, year={2021}, month={Dec}, pages={17094–17102} }
 @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} }
 @article{luo_aly_mccord_strynar_chiu_dodds_baker_rusyn_2020, title={Rapid Characterization of Emerging Per- and Polyfluoroalkyl Substances in Aqueous Film-Forming Foams Using Ion Mobility Spectrometry-Mass Spectrometry}, volume={54}, ISSN={["1520-5851"]}, DOI={10.1021/acs.est.0c04798}, abstractNote={Aqueous film-forming foams (AFFF) are mixtures formulated with numerous hydrocarbon- and fluoro-containing surfactants. AFFF use leads to environmental releases of unknown per- and polyfluoroalkyl substances (PFAS). AFFF composition is seldom disclosed, and their use elicits concerns from both regulatory agencies and the public because PFAS are persistent in the environment and potentially associated with adverse health effects. In this study, we demonstrate the use of coupled liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) to rapidly characterize both known and unknown PFAS in AFFF. Ten AFFF formulations from seven brands were analyzed using LC-IMS-MS in both negative and positive ion modes. Untargeted analysis of the formulations was followed by feature identification of PFAS-like features utilizing database matching, mass defect and homologous series evaluation, and MS/MS fragmentation experiments. Across the tested AFFF formulations, we identified 33 homologous series; only ten of these homologous series have been previously reported. Among tested AFFF, the FireStopper (n = 85) contained the greatest number of PFAS-like features and Phos-Check contained zero. This work demonstrates that LC-IMS-MS-enabled untargeted analysis of complex formulations, followed by feature identification using data-processing algorithms, can be used for rapid exposure characterization of known and putative PFAS during fire suppression-related contamination events.}, number={23}, journal={ENVIRONMENTAL SCIENCE & TECHNOLOGY}, author={Luo, Yu-Syuan and Aly, Noor A. and McCord, James and Strynar, Mark J. and Chiu, Weihsueh A. and Dodds, James N. and Baker, Erin S. and Rusyn, Ivan}, year={2020}, month={Dec}, pages={15024–15034} }
 @article{aly_luo_liu_casillas_mcdonald_kaihatu_jun_ellis_gossett_dodds_et al._2020, title={Temporal and spatial analysis of per and polyfluoroalkyl substances in surface waters of Houston ship channel following a large-scale industrial fire incident}, volume={265}, ISSN={["1873-6424"]}, DOI={10.1016/j.envpol.2020.115009}, abstractNote={Firefighting foams contain per- and polyfluoroalkyl substances (PFAS) – a class of compounds widely used as surfactants. PFAS are persistent organic pollutants that have been reported in waterways and drinking water systems across the United States. These substances are of interest to both regulatory agencies and the general public because of their persistence in the environment and association with adverse health effects. PFAS can be released in large quantities during industrial incidents because they are present in most firefighting foams used to suppress chemical fires; however, little is known about persistence of PFAS in public waterways after such events. In response to large-scale fires at Intercontinental Terminal Company (ITC) in Houston, Texas in March 2019, almost 5 million liters of class B firefighting foams were used. Much of this material flowed into the Houston Ship Channel and Galveston Bay (HSC/GB) and concerns were raised about the levels of PFAS in these water bodies that have commercial and recreational uses. To evaluate the impact of the ITC incident response on PFAS levels in HSC/GB, we collected 52 surface water samples from 12 locations over a 6-month period after the incident. Samples were analyzed using liquid chromatography–mass spectrometry to evaluate 27 PFAS, including perfluorocarboxylic acids, perfluorosulfonates and fluorotelomers. Among PFAS that were evaluated, 6:2 FTS and PFOS were detected at highest concentrations. Temporal and spatial profiles of PFAS were established; we found a major peak in the level of many PFAS in the days and weeks after the incident and a gradual decline over several months with patterns consistent with the tide- and wave-associated water movements. This work documents the impact of a large-scale industrial fire, on the environmental levels of PFAS, establishes a baseline concentration of PFAS in HSC/GB, and highlights the critical need for development of PFAS water quality standards.}, number={B}, journal={Environmental Pollution}, author={Aly, N.A. and Luo, Y.-S. and Liu, Y. and Casillas, G. and McDonald, T. and Kaihatu, J. and Jun, M. and Ellis, N. and Gossett, S. and Dodds, J.N. and et al.}, year={2020}, month={Oct}, pages={115009} }
 @article{eugenia monge_dodds_baker_edison_fernandez_2019, title={Challenges in Identifying the Dark Molecules of Life}, volume={12}, ISSN={["1936-1327"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85067284122&partnerID=MN8TOARS}, DOI={10.1146/annurev-anchem-061318-114959}, abstractNote={ Metabolomics is the study of the metabolome, the collection of small molecules in living organisms, cells, tissues, and biofluids. Technological advances in mass spectrometry, liquid- and gas-phase separations, nuclear magnetic resonance spectroscopy, and big data analytics have now made it possible to study metabolism at an omics or systems level. The significance of this burgeoning scientific field cannot be overstated: It impacts disciplines ranging from biomedicine to plant science. Despite these advances, the central bottleneck in metabolomics remains the identification of key metabolites that play a class-discriminant role. Because metabolites do not follow a molecular alphabet as proteins and nucleic acids do, their identification is much more time consuming, with a high failure rate. In this review, we critically discuss the state-of-the-art in metabolite identification with specific applications in metabolomics and how technologies such as mass spectrometry, ion mobility, chromatography, and nuclear magnetic resonance currently contribute to this challenging task. }, journal={ANNUAL REVIEW OF ANALYTICAL CHEMISTRY, VOL 12}, author={Eugenia Monge, Maria and Dodds, James N. and Baker, Erin S. and Edison, Arthur S. and Fernandez, Facundo M.}, year={2019}, pages={177–199} }
 @article{dodds_baker_2019, title={Ion Mobility Spectrometry: Fundamental Concepts, Instrumentation, Applications, and the Road Ahead}, volume={30}, ISSN={["1879-1123"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85073982332&partnerID=MN8TOARS}, DOI={10.1007/s13361-019-02288-2}, abstractNote={Ion mobility spectrometry (IMS) is a rapid separation technique that has experienced exponential growth as a field of study. Interfacing IMS with mass spectrometry (IMS-MS) provides additional analytical power as complementary separations from each technique enable multidimensional characterization of detected analytes. IMS separations occur on a millisecond timescale, and therefore can be readily nested into traditional GC and LC/MS workflows. However, the continual development of novel IMS methods has generated some level of confusion regarding the advantages and disadvantages of each. In this critical insight, we aim to clarify some common misconceptions for new users in the community pertaining to the fundamental concepts of the various IMS instrumental platforms (i.e., DTIMS, TWIMS, TIMS, FAIMS, and DMA), while addressing the strengths and shortcomings associated with each. Common IMS-MS applications are also discussed in this review, such as separating isomeric species, performing signal filtering for MS, and incorporating collision cross-section (CCS) values into both targeted and untargeted omics-based workflows as additional ion descriptors for chemical annotation. Although many challenges must be addressed by the IMS community before mobility information is collected in a routine fashion, the future is bright with possibilities.}, number={11}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Dodds, James N. and Baker, Erin S.}, year={2019}, month={Nov}, pages={2185–2195} }
 @misc{burnum-johnson_zheng_dodds_ash_fourches_nicora_wendler_metz_waters_jansson_et al._2019, title={Ion mobility spectrometry and the omics: Distinguishing isomers, molecular classes and contaminant ions in complex samples}, volume={116}, ISSN={["1879-3142"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85065908529&partnerID=MN8TOARS}, DOI={10.1016/j.trac.2019.04.022}, abstractNote={Ion mobility spectrometry (IMS) is a widely used analytical technique providing rapid gas phase separations. IMS alone is useful, but its coupling with mass spectrometry (IMS-MS) and various front-end separation techniques has greatly increased the molecular information achievable from different omic analyses. IMS-MS analyses are specifically gaining attention for improving metabolomic, lipidomic, glycomic, proteomic and exposomic analyses by increasing measurement sensitivity (e.g. S/N ratio), lowering the detection limit, and amplifying peak capacity. Numerous studies including national security-related analyses, disease screenings and environmental evaluations are illustrating that IMS-MS is able to extract information not possible with MS alone. Furthermore, IMS-MS has shown great utility in salvaging molecular information for low abundance molecules of interest when high concentration contaminant ions are present in the sample by reducing detector suppression. This review highlights how IMS-MS is currently being used in omic analyses to distinguish structurally similar molecules, isomers, molecular classes and contaminant ions.}, journal={TRAC-TRENDS IN ANALYTICAL CHEMISTRY}, author={Burnum-Johnson, Kristin E. and Zheng, Xueyun and Dodds, James N. and Ash, Jeremy and Fourches, Denis and Nicora, Carrie D. and Wendler, Jason P. and Metz, Thomas O. and Waters, Katrina M. and Jansson, Janet K. and et al.}, year={2019}, month={Jul}, pages={292–299} }