Alena N. Joignant, Anastasia Sheridan, Ashley C. Brown and David C. Muddiman*,
{"title":"Distinguishing the Metabolic Effect of Fetal and Adult Fibrinogen on Human Fibroblast Cell Culture by IR-MALDESI Mass Spectrometry Imaging","authors":"Alena N. Joignant, Anastasia Sheridan, Ashley C. Brown and David C. Muddiman*, ","doi":"10.1021/jasms.5c0002710.1021/jasms.5c00027","DOIUrl":"https://doi.org/10.1021/jasms.5c00027https://doi.org/10.1021/jasms.5c00027","url":null,"abstract":"<p >Mass spectrometry imaging (MSI) of cells can elucidate metabolic changes with cellular and molecular specificity. Fibroblasts are mesenchymal cells that are important in tissue homeostasis and wound healing. During early wound healing, fibroblasts adhere to fibrinogen and migrate into fibrin clots, which are important interactions to stabilize early blood clots and promote subsequent tissue remodeling. It is understood that fibrinogen exists in distinct forms, fetal and adult, which have differing glycosylation and morphological effects on fibroblasts. Despite their importance to wound healing and the extracellular environment, fibroblasts are not commonly studied by MSI. While many MSI studies are conducted at the single-cell or subcellular level, there is still utility in accessing a broad view of the metabolic changes in a cell culture above single-cell spatial resolution. This enables imaging a wider area and larger number of cells directly from cell culture. In this work, dermal fibroblasts were imaged directly from cell culture chamber slides by infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI). This method enabled treating the chambers with adult or fetal fibrinogen prior to cell culture and reduced sample preparation prior to MSI. Many metabolic effects of serum and fibrinogen type were elucidated, with changes in many membrane lipids such as cholesterol and ceramides potentially contributing to the observed morphological effects of fibrinogen types on fibroblasts.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 5","pages":"1111–1119 1111–1119"},"PeriodicalIF":3.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143911441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lucas R. Abruzzi, John-Clare Laxton, Taelor M. Zarkovic and Chris G. Gill*,
{"title":"Internal Standard Utilization Strategies for Quantitative Paper Spray Mass Spectrometry","authors":"Lucas R. Abruzzi, John-Clare Laxton, Taelor M. Zarkovic and Chris G. Gill*, ","doi":"10.1021/jasms.5c0003610.1021/jasms.5c00036","DOIUrl":"https://doi.org/10.1021/jasms.5c00036https://doi.org/10.1021/jasms.5c00036","url":null,"abstract":"<p >Premixing internal standards (ISTD) with liquid samples prior to paper spray mass spectrometry (PS-MS) analysis consumes unnecessary amounts of ISTD and is not feasible for all sample types and applications. Depositing ISTD directly on the paper independently from sample has been successfully employed in the literature but can negatively affect quantitative performance. We evaluated different ISTD utilization strategies using drugs of misuse as test analytes to investigate the sources of irreproducibility and bias. Performance was assessed using both pre- and postdeposited ISTD (relative to sample loading) at different volumes with a constant final mass loading of 1 ng of each ISTD compound. Precision and accuracy were lower when using independently deposited ISTD compared to premixed ISTD (average CV = 18% vs 1% and average |bias| = 61% vs 5% for independently deposited ISTD and premixed ISTD, respectively). The use of a robotic liquid sample handling system to deposit ISTD was compared with results obtained via manually pipetting. Predeposited ISTD performed best at lower deposition volumes when a robotic liquid handler was used (average CV = 8% and 11% for 2 and 10 μL, respectively), but manual pipetting of low volume ISTD depositions performed poorly. Postdeposited ISTD was inferior to predeposited ISTD strategies, favoring larger deposition volumes regardless of deposition method (average CV = 22% and 16% for 2 and 10 μL, respectively). Systematic biases associated with each ISTD utilization strategy were effectively corrected for using strategy-matched calibrations, and AAFS (American Academy of Forensic Sciences) accuracy and precision requirements were achieved in almost all cases.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 5","pages":"1167–1174 1167–1174"},"PeriodicalIF":3.1,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143911438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jinpeng Bai, Chenxi Li, Mingmin Qian, Xian Ding, Qian Li, Yanhua Chen, Zhaoying Wang* and Zeper Abliz,
{"title":"Norm ISWSVR Enhanced Data Repeatability and Accuracy in Large-Scale Targeted Quantification Metabolomics","authors":"Jinpeng Bai, Chenxi Li, Mingmin Qian, Xian Ding, Qian Li, Yanhua Chen, Zhaoying Wang* and Zeper Abliz, ","doi":"10.1021/jasms.4c0046710.1021/jasms.4c00467","DOIUrl":"https://doi.org/10.1021/jasms.4c00467https://doi.org/10.1021/jasms.4c00467","url":null,"abstract":"<p >Targeted quantification metabolomics provides dynamic insights across various domains within the life sciences. Nevertheless, maintaining high-quality data obtained through liquid chromatography–mass spectrometry presents ongoing challenges. It is essential to develop normalization methods to correct for unwanted variations in metabolomic profiling such as batch effects and analytical drift. In this study, we assessed the normalization efficacy of Norm ISWSVR in targeted quantification metabolomics by comparing it with IS normalization and SERRF normalization. Consequently, Norm ISWSVR demonstrated exceptional efficacy in mitigating batch effects and reducing the relative standard deviation of quality control samples, in addition to correcting signal drift. Following normalization with Norm ISWSVR, the number of metabolites suitable for quantification increased with high precision. Collectively, Norm ISWSVR proves to be a robust and reliable method for enhancing data quality in targeted metabolomics, establishing itself as a promising approach for metabolomics research.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 5","pages":"1027–1033 1027–1033"},"PeriodicalIF":3.1,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143911436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
James N Dodds, Lucie C Ford, Jack P Ryan, Amie M Solosky, Ivan Rusyn, Erin S Baker
{"title":"Evaluating Ion Mobility Data Acquisition, Calibration, and Processing for Small Molecules: A Cross-Platform Assessment of Drift Tube and Traveling Wave Methodologies.","authors":"James N Dodds, Lucie C Ford, Jack P Ryan, Amie M Solosky, Ivan Rusyn, Erin S Baker","doi":"10.1021/jasms.5c00056","DOIUrl":"10.1021/jasms.5c00056","url":null,"abstract":"<p><p>As ion mobility spectrometry (IMS) separations continue to be added to analytical workflows due to their power in environmental and biological sample analyses, harmonization and capability understanding between existing and newly released instruments are desperately needed. Developments in IMS platforms often exhibit focus on increasing resolving power (R<sub>p</sub>) to better separate molecules of similar structure. While the additional separation capacity is advantageous, ensuring these developments coincide with appropriate data extraction and analysis methods is imperative to ensure routine adoption. Herein, we assess the performance of the MOBILion MOBIE in relation to a commercially available drift tube IMS-MS, the Agilent 6560, and evaluate feature extraction and analysis pipelines. Both instruments were operated using matched conditions when possible, and performance metrics of scan speed, R<sub>p</sub>, limits of detection (LOD), and propensity for isomer separation via LC-IMS-MS were evaluated. Similar scan speeds pertaining to IMS-MS frame generation were noted for both platforms, and collision cross section (CCS) values for the MOBIE were generally within ≤ 1% difference from previously reported drift tube values. Both platforms were also able to generate quantitative data (comparable limits of detection) in experiments with perfluoroalkyl substances (PFAS) mixtures in a cell-based model (both medium and cell lysates), as demonstrated in Skyline with adjusted mobility filtering parameters. Higher R<sub>p</sub> was, however, noted on the MOBIE in comparison to the 6560 (200-300 vs 45-60 CCS/ΔCCS without data processing), allowing the detection of more PFAS isomers and indicating promise toward future applications in chemical exposomics studies and biomarker discovery when molecules exhibit similar structures.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143770903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Clara Whyte Ferreira, Bastien Cabrera-Tejera, Bernard Leyh, Romain Tuyaerts, Gilles Scheen, Yannick Coffinier, Edwin De Pauw and Gauthier Eppe*,
{"title":"A Practical Approach for Internal Energy Tuning in LDI-MS: Porous Silicon Substrates as a Case Study","authors":"Clara Whyte Ferreira, Bastien Cabrera-Tejera, Bernard Leyh, Romain Tuyaerts, Gilles Scheen, Yannick Coffinier, Edwin De Pauw and Gauthier Eppe*, ","doi":"10.1021/jasms.4c0046210.1021/jasms.4c00462","DOIUrl":"https://doi.org/10.1021/jasms.4c00462https://doi.org/10.1021/jasms.4c00462","url":null,"abstract":"<p >This study presents a methodical procedure for optimizing laser desorption/ionization mass spectrometry (LDI-MS) supports using porous silicon (PSi) substrates. The approach involves the use of substituted benzyl-pyridinium salts (thermometer ions) to obtain one metric that assesses analyte fragmentation (the effective temperature of vibration). Porous silicon substrates were synthesized via electrochemical etching of p-type silicon wafers (10–20 mΩ·cm), with etching parameters adjusted to vary porosity while maintaining a layer thickness between 700 and 1200 nm. The results revealed that PSi substrates with 40–60% porosity achieved the lowest fragmentation levels. This finding was validated through the analysis of N-acetyl glucosamine, a carbohydrate, which confirmed the effective temperature trend. Further analysis involving peptides, specifically P14R and a peptide mix (Peptide Calibration Standard II, Bruker), demonstrated that the optimized PSi substrates enabled the desorption and ionization of peptides with a maximum mass at <i>m</i>/<i>z</i> 2465, corresponding to ACTH clip 1–17. These results highlight the critical role of substrate porosity in minimizing analyte fragmentation and enhancing LDI-MS performance.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 5","pages":"1008–1016 1008–1016"},"PeriodicalIF":3.1,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143911437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Michelle Rajkovic, Thorsten Benter, Walter Wißdorf
{"title":"Investigation of Surface-Induced Dissociation Processes via Molecular Dynamics Simulations of Wall Collisions of Large Droplets Produced by Electrospray Ionization.","authors":"Michelle Rajkovic, Thorsten Benter, Walter Wißdorf","doi":"10.1021/jasms.4c00449","DOIUrl":"10.1021/jasms.4c00449","url":null,"abstract":"<p><p>Electrospray ionization is one of the most utilized ionization techniques in atmospheric pressure mass spectrometry. Recent experimentally reported results are in disagreement with fundamentals revolving around ESI droplet sizes and their lifetimes. Specifically, much larger droplet sizes and longer lifetimes have been experimentally observed to exist in typical ESI ion sources. Experiments involving a custom scan mode on a triple quadrupole system have shown that high-mass fragments of large ESI droplets can be observed in mass spectra. Initial hypotheses rationalizing these results were focused on the creation of droplet fragments by collision-induced dissociation (CID). The collision energy accumulated by CID is most likely too small to lead to the observed mass spectra. In response, surface-induced dissociation (SID) was proposed as an additional mechanism to provide large amounts of collision energy to the droplets. The present work thus investigates the possible fragmentation pathways and dynamics of droplet fragments resulting from aspirated ESI droplets upon surface collisions through classical molecular dynamics simulations. Different types of collisions are simulated, where the impact of the simulated droplet fragments is either frontal or angled. The resulting fragmentation dynamics are thoroughly analyzed, showing the possibility for charged fragments to be liberated through SID events. A second, much larger droplet fragment is employed to illustrate the altered collision dynamics found for such larger aggregates, where no charged clusters are released through the surface collision. Since approximated force fields have to be used to model the interactions between the particles observed in the simulation, a sensitivity study is carried out regarding the critical parameters governing such processes. Further modifications of the MD system have to be carried out, including more realistic walls and much larger ESI droplets, to clarify the possibility of charged fragment releases from larger droplet fragments through SID.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"760-770"},"PeriodicalIF":3.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143673151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mapping Binding Domains of Viral and Allergenic Proteins with Dual-Cleavable Cross-Linking Technology.","authors":"Akash Talukder, Saiful M Chowdhury","doi":"10.1021/jasms.4c00398","DOIUrl":"10.1021/jasms.4c00398","url":null,"abstract":"<p><p>The dual-cleavable nature of the cross-linking technology (DUCCT) enhances the reliable identification of cross-linked peptides via mass spectrometry. The DUCCT approach uses a cross-linking agent that can be selectively cleaved by two different tandem mass spectrometry techniques: collision-induced dissociation (CID) and electron transfer dissociation (ETD). This results in distinct signatures in two independent mass spectra for the same cross-linked precursor, leading to unambiguous identification and the validation of the spectra. In this study, we expanded the application of the DUCCT cross-linker to evaluate the binding domains of a specific cat dander allergen, Fel d 1, which exists as the Fel d 1 A and B protein complex, and a viral spike protein from SARS-CoV-2, which invades host cells. To assess the cross-linked products obtained by DUCCT, we utilized a software tool called Cleave-XL, which effectively identified cross-linked sites using data from CID and ETD. Dual cleavable cross-linking studies identified cross-linked peptides in these complexes, which have been reported in bioinformatics analysis and proposed for immunotherapy using synthetic peptides. A benchmark study was also conducted using a commercial cross-linker disuccinimidyl suberate (DSS). Overall, we expect that DUCCT cross-linking technology will greatly facilitate the rapid screening of binding interfaces, thereby advancing structural biology and cell signaling investigations.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"721-731"},"PeriodicalIF":3.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kaylie I Kirkwood-Donelson, Prashant Rai, Lalith Perera, Michael B Fessler, Alan K Jarmusch
{"title":"Bromine-Based Derivatization of Carboxyl-Containing Metabolites for Liquid Chromatography-Trapped Ion Mobility Spectrometry-Mass Spectrometry.","authors":"Kaylie I Kirkwood-Donelson, Prashant Rai, Lalith Perera, Michael B Fessler, Alan K Jarmusch","doi":"10.1021/jasms.5c00023","DOIUrl":"10.1021/jasms.5c00023","url":null,"abstract":"<p><p>The analysis of small carboxyl-containing metabolites (CCMs), such as tricarboxylic acid (TCA) cycle intermediates, provides highly useful information about the metabolic state of cells. However, their detection using liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) methods can face sensitivity and specificity challenges given their low ionization efficiency and the presence of isomers. Ion mobility spectrometry (IMS), such as trapped ion mobility spectrometry (TIMS), provides additional specificity, but further signal loss can occur during the mobility separation process. We, therefore, developed a solution to boost CCM ionization and chromatographic separation as well as leverage specificity of IMS. Inspired by carbodiimide-mediated coupling of carboxylic acids with 4-bromo-<i>N</i>-methylbenzylamine (4-BNMA) for quantitative analysis, we newly report the benefits of this reagent for TIMS-based measurement. We observed a pronounced (orders of magnitude) increase in signal and enhanced isomer separations, particularly by LC. We found that utilization of a brominated reagent, such as 4-BNMA, offered unique benefits for untargeted CCM measurement. Derivatized CCMs displayed shifted mobility out of the metabolite and lipid region of the TIMS-MS space as well as characteristic isotope patterns, which were leveraged for data mining with Mass Spectrometry Query Language (MassQL) and indication of the number of carboxyl groups. The utility of our LC-ESI-TIMS-MS/MS method with 4-BMA derivatization was demonstrated via the characterization of alterations in CCM expression in bone marrow-derived macrophages upon activation with lipopolysaccharide. While metabolic reprogramming in activated macrophages has been characterized previously, especially with respect to TCA cycle intermediates, we report a novel finding that isomeric itaconic, mesaconic, and citraconic acid increase after 24 h, indicating possible roles in the inflammatory response.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"888-899"},"PeriodicalIF":3.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11970421/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Samantha A. Mehnert, Katherine J. Lee and Scott A. McLuckey*,
{"title":"Enthalpies and Entropies of Activation for sn-1/sn-2 Acyl Chain Loss in Glycerophospholipid Anions via Dipolar DC Kinetics","authors":"Samantha A. Mehnert, Katherine J. Lee and Scott A. McLuckey*, ","doi":"10.1021/jasms.4c0047710.1021/jasms.4c00477","DOIUrl":"https://doi.org/10.1021/jasms.4c00477https://doi.org/10.1021/jasms.4c00477","url":null,"abstract":"<p >Glycerophospholipids (GPs) have been observed to prefer losing a particular fatty acyl chain over the other, with the preference for the chain in either the <i>sn-</i>1 or <i>sn-</i>2 position being different between various GP classes. It has been assumed that the <i>sn</i> preference results from the entropic favorability of the transition state conformation; however, this has not been measured previously. Here, we demonstrate the application of our previously established collision-based activation method to GP fragmentation. The method utilizes a dipolar direct current (DDC) potential across a pair of opposing rods to force ions out of the center of the ion trap, causing them to undergo radio frequency (RF) heating by absorbing power from the trapping RF field. We confirmed that the previous assumption holds for some species studied here, wherein the ΔH<sup>‡</sup> values were nearly identical and the ΔS<sup>‡</sup> values showed greater differences between the <i>sn</i> positions. However, some species and ion types seem to be more driven by ΔH<sup>‡</sup>. Additionally, the loss of the fatty acyl chains as neutrals rather than ions should also be considered if one is to thoroughly weigh which chain is indeed the preferred loss, as including all forms of acyl chain loss results in an overall favorability for the acyl chain in the <i>sn-</i>2 position to be lost. The driving force behind these different losses seems to be a mixture of entropic and enthalpic reasons, with the identity and presence of the headgroup playing an important role in the observed fragmentation and the measured activation parameters.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 5","pages":"1041–1051 1041–1051"},"PeriodicalIF":3.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143911255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Aurore L Schneiders, Johann Far, Lidia Belova, Allison Fry, Adrian Covaci, Erin S Baker, Edwin De Pauw, Gauthier Eppe
{"title":"Structural Characterization of Dimeric Perfluoroalkyl Carboxylic Acid Using Experimental and Theoretical Ion Mobility Spectrometry Analyses.","authors":"Aurore L Schneiders, Johann Far, Lidia Belova, Allison Fry, Adrian Covaci, Erin S Baker, Edwin De Pauw, Gauthier Eppe","doi":"10.1021/jasms.5c00007","DOIUrl":"10.1021/jasms.5c00007","url":null,"abstract":"<p><p>Per- and polyfluoroalkyl substances (PFAS) are contaminants of increasing concern, with over seven million compounds currently inventoried in the PubChem PFAS Tree. Recently, ion mobility spectrometry has been combined with liquid chromatography and high-resolution mass spectrometry (LC-IMS-HRMS) to assess PFAS. Interestingly, using negative electrospray ionization, perfluoroalkyl carboxylic acids (PFCAs) form homodimers ([2M-H]<sup>-</sup>), a phenomenon observed with trapped, traveling wave, and drift-tube IMS. In addition to the limited research on their effect on analytical performance, there is little information on the conformations these dimers can adopt. This study aimed to propose most probable conformations for PFCA dimers. Based on qualitative analysis of how collision cross section (CCS) values change with the mass-to-charge ratio (<i>m</i>/<i>z</i>) of PFCA ions, the PFCA dimers were hypothesized to likely adopt a V-shaped structure. To support this assumption, <i>in silico</i> geometry optimizations were performed to generate a set of conformers for each possible dimer. A CCS value was then calculated for each conformer using the trajectory method with Lennard-Jones and ion-quadrupole potentials. Among these conformers, at least one of the ten lowest-energy conformers identified for each dimer exhibited theoretical CCS values within a ±2% error margin compared to the experimental data, qualifying them as plausible structures for the dimers. Our findings revealed that the fluorinated alkyl chains in the dimers are close to each other due to a combination of C-F···O=C and C-F···F-C stabilizing interactions. These findings, together with supplementary investigations involving environmentally relevant cations, may offer valuable insights into the interactions and environmental behavior of PFAS.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"850-861"},"PeriodicalIF":3.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143565636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}