Pub Date : 2026-01-01Epub Date: 2025-10-14DOI: 10.1016/j.ijms.2025.117543
Sarah J. Madlener , Bowei Yuan , Marc Reimann , Shaodong Zhou , Martin K. Beyer , Joost M. Bakker , Christian van der Linde
Transition metal oxides are promising candidates for water activation, a key step in hydrogen production, as they have shown their potential as catalysts. In this study, we present tag-free infrared multiple photon dissociation (IRMPD) spectra of formally singly and doubly hydrated TaO2+ cations in the 350–1650 cm−1 range, measured using the free-electron laser for intracavity experiments (FELICE). In combination with vibrational spectra obtained by quantum chemical calculations, the experimental spectra reveal that the hydroxide species TaO(OH)2+ and Ta(OH)4+ are the dominant species in the experiment. These two structures are also the lowest lying isomers, about 130 kJ mol−1 lower than the energetically closest isomers. The calculated potential energy surfaces and transition states align with earlier studies, confirming the formation of these hydroxide complexes via sequential proton transfers upon complexation of TaO2+ with one and two water molecules, respectively. This work presents the first tag free spectra of these complexes, complementing the spectroscopic picture especially in the low wavenumber region.
{"title":"Infrared multiple photon dissociation spectroscopy of TaO(OH)2+ and Ta(OH)4+ cations","authors":"Sarah J. Madlener , Bowei Yuan , Marc Reimann , Shaodong Zhou , Martin K. Beyer , Joost M. Bakker , Christian van der Linde","doi":"10.1016/j.ijms.2025.117543","DOIUrl":"10.1016/j.ijms.2025.117543","url":null,"abstract":"<div><div>Transition metal oxides are promising candidates for water activation, a key step in hydrogen production, as they have shown their potential as catalysts. In this study, we present tag-free infrared multiple photon dissociation (IRMPD) spectra of formally singly and doubly hydrated TaO<sub>2</sub><sup>+</sup> cations in the 350–1650 cm<sup>−1</sup> range, measured using the free-electron laser for intracavity experiments (FELICE). In combination with vibrational spectra obtained by quantum chemical calculations, the experimental spectra reveal that the hydroxide species TaO(OH)<sub>2</sub><sup>+</sup> and Ta(OH)<sub>4</sub><sup>+</sup> are the dominant species in the experiment. These two structures are also the lowest lying isomers, about 130 kJ mol<sup>−1</sup> lower than the energetically closest isomers. The calculated potential energy surfaces and transition states align with earlier studies, confirming the formation of these hydroxide complexes via sequential proton transfers upon complexation of TaO<sub>2</sub><sup>+</sup> with one and two water molecules, respectively. This work presents the first tag free spectra of these complexes, complementing the spectroscopic picture especially in the low wavenumber region.</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"519 ","pages":"Article 117543"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145358984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2025-10-14DOI: 10.1016/j.ijms.2025.117544
Alexander A. Makarov
{"title":"Editorial- Curt Brunnee memorial issue","authors":"Alexander A. Makarov","doi":"10.1016/j.ijms.2025.117544","DOIUrl":"10.1016/j.ijms.2025.117544","url":null,"abstract":"","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"519 ","pages":"Article 117544"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145319772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2025-11-11DOI: 10.1016/j.ijms.2025.117549
Luis Manuel Menéndez-Quintanal , Jose Manuel Matey , Marcelle D. Perretti , Nieves Rodríguez Paz
Cathinones represent one of the most prevalent classes of new psychoactive substances (NPS), largely due to the extensive variety of structural analogues. However, in forensic toxicology, their instability in post-mortem biological matrices such as blood and urine complicates their detection, making sample preservation at −20 °C essential prior to analysis. To overcome this limitation, dihydro (DH) metabolites—formed via reduction of the ketone group—have been proposed as reliable biomarkers of cathinone intake, owing to their enhanced stability. In this study, 28 DH-metabolites were synthesised through selective reduction of commercial cathinones. Their fragmentation behaviour was carefully studied using isotopically labelled analogues and analysed on different LC-HRMS platforms (Orbitrap and qTOF).
A predictive fragmentation model was developed, allowing for the identification of anticipated MS2 fragments and the characterization of specific diagnostic ions. These ions aid in the detection of DH-metabolites during untargeted LC-HRMS analyses. In line with previously described fragmentation pathways for synthetic cathinones, DH-metabolites can produce as well odd-electron ions from even-electron precursor ions during electrospray ionization (ESI). However, compared to their parent compounds, DH-metabolites exhibit some differences in fragmentation pathways.
Understanding the fragmentation mechanisms of a compound family is essential when applying non-targeted analysis methods using LC-HRMS techniques. The development of a predictive fragmentation model can significantly improve the detection of novel, unstable emerging cathinones in post-mortem samples or in wastewater monitoring, simply by targeting their DH-metabolites.
{"title":"Fragmentation pathways of dihydro-metabolites of synthetic cathinones by high-resolution mass spectrometry on Orbitrap and quadrupole time-of-flight (qTOF) mass spectrometers","authors":"Luis Manuel Menéndez-Quintanal , Jose Manuel Matey , Marcelle D. Perretti , Nieves Rodríguez Paz","doi":"10.1016/j.ijms.2025.117549","DOIUrl":"10.1016/j.ijms.2025.117549","url":null,"abstract":"<div><div>Cathinones represent one of the most prevalent classes of new psychoactive substances (NPS), largely due to the extensive variety of structural analogues. However, in forensic toxicology, their instability in post-mortem biological matrices such as blood and urine complicates their detection, making sample preservation at −20 °C essential prior to analysis. To overcome this limitation, dihydro (DH) metabolites—formed via reduction of the ketone group—have been proposed as reliable biomarkers of cathinone intake, owing to their enhanced stability. In this study, 28 DH-metabolites were synthesised through selective reduction of commercial cathinones. Their fragmentation behaviour was carefully studied using isotopically labelled analogues and analysed on different LC-HRMS platforms (Orbitrap and qTOF).</div><div>A predictive fragmentation model was developed, allowing for the identification of anticipated MS<sup>2</sup> fragments and the characterization of specific diagnostic ions. These ions aid in the detection of DH-metabolites during untargeted LC-HRMS analyses. In line with previously described fragmentation pathways for synthetic cathinones, DH-metabolites can produce as well odd-electron ions from even-electron precursor ions during electrospray ionization (ESI). However, compared to their parent compounds, DH-metabolites exhibit some differences in fragmentation pathways.</div><div>Understanding the fragmentation mechanisms of a compound family is essential when applying non-targeted analysis methods using LC-HRMS techniques. The development of a predictive fragmentation model can significantly improve the detection of novel, unstable emerging cathinones in post-mortem samples or in wastewater monitoring, simply by targeting their DH-metabolites.</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"519 ","pages":"Article 117549"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145517063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2025-10-07DOI: 10.1016/j.ijms.2025.117535
Eugene Moskovets
The optimization of the accelerating electric field near a target plate as well as temperature of the inlet capillary in a mass spectrometer is essential for achieving a high ion yield in atmospheric pressure matrix-assisted laser desorption ionization (AP/MALDI) and atmospheric pressure/laser desorption ionization (AP/LDI). The yields of protonated rhodamine 6G ions, protonated matrix ions (M + H)+, matrix radical ions (M•)+, as well as protonated reserpine ions were studied as a function of the inlet capillary temperature in Orbitrap and electric field applied across the inlet and MALDI target plate. The findings indicated that 2,5-dihydroxybenzoic acid (DHB) generated predominantly cation radicals (M•)+ rather than protonated ions. This trend is not common for most MALDI matrices used for positive-mode MALDI-MS analysis. By changing capillary temperature, it has been found that the temperature trends observed for the (DHB + H)+/(DHB•)+ ratios in both AP/MALDI and electrospray ionization (ESI) are similar. The ion yield dependence on the electric field strength in AP/MALDI as well as low-pressure MALDI sources proved to be more complex than that suggested in the previously developed model accounting for charge neutralization in the plume mitigated by the field-driven separation of opposite charges. The laser photoionization of the matrix molecules within a thin surface layer of a matrix microcrystal followed by thermally activated proton transfer from the matrix radical cation to adjacent matrix molecules has been discussed.
{"title":"Influence of acceleration field and inlet temperature on ion yields of small molecules in atmospheric pressure MALDI","authors":"Eugene Moskovets","doi":"10.1016/j.ijms.2025.117535","DOIUrl":"10.1016/j.ijms.2025.117535","url":null,"abstract":"<div><div>The optimization of the accelerating electric field near a target plate as well as temperature of the inlet capillary in a mass spectrometer is essential for achieving a high ion yield in atmospheric pressure matrix-assisted laser desorption ionization (AP/MALDI) and atmospheric pressure/laser desorption ionization (AP/LDI). The yields of protonated rhodamine 6G ions, protonated matrix ions (M + H)<sup>+</sup>, matrix radical ions (M•)<sup>+</sup>, as well as protonated reserpine ions were studied as a function of the inlet capillary temperature in Orbitrap and electric field applied across the inlet and MALDI target plate. The findings indicated that 2,5-dihydroxybenzoic acid (DHB) generated predominantly cation radicals (M•)<sup>+</sup> rather than protonated ions. This trend is not common for most MALDI matrices used for positive-mode MALDI-MS analysis. By changing capillary temperature, it has been found that the temperature trends observed for the (DHB + H)<sup>+</sup>/(DHB•)<sup>+</sup> ratios in both AP/MALDI and electrospray ionization (ESI) are similar. The ion yield dependence on the electric field strength in AP/MALDI as well as low-pressure MALDI sources proved to be more complex than that suggested in the previously developed model accounting for charge neutralization in the plume mitigated by the field-driven separation of opposite charges. The laser photoionization of the matrix molecules within a thin surface layer of a matrix microcrystal followed by thermally activated proton transfer from the matrix radical cation to adjacent matrix molecules has been discussed.</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"519 ","pages":"Article 117535"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145263346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2025-09-27DOI: 10.1016/j.ijms.2025.117534
Lynne P. Heilbrun , Anabel Rodriguez , L. Aubree Shay , David Gimeno Ruiz de Porras , Inkyu Han , Kristin Favela
Background
Semi-volatile organic chemicals (SVOCs) have been studied in shed baby teeth as a potential tool to identify environmental triggers of autism. However, these targeted studies are limited by the availability of standards, leaving a vast number of chemicals unexplored for autism risk.
Objective
We explored the use of two-dimensional gas chromatography time-of-flight mass spectrometry (GCxGC-TOFMS) as a viable and accurate method for identifying and quantifying a wide range of low-level SVOCs in deciduous teeth.
Methods
Tooth samples were derived from The Autism Tooth Fairy Study. Ground tooth samples (n = 44) were analyzed using GCxGC-TOFMS. Targeted and non-targeted analyses were performed. Targeted compounds were reviewed against reference spectra for identification, and non-targets were manually curated using the National Institute of Standards and Technology Library data, as available. Kovat's retention index was used for identifications without a reference standard.
Results
From the 44 tooth samples analyzed, 11,971 total endogenous and exogenous features were cataloged, including unknowns without a suitable library match. Of the 203 compounds detected, 106 high-fidelity matched compounds were identified spanning 45 subclasses of toxicants. Eighty-nine of these compounds are known developmental toxicants or endocrine disruptors. The remaining compounds were toxicants with acute or chronic toxicity data but had no developmental or endocrine-disrupting activity data.
Conclusion
This study demonstrates the utility of GCxGC-TOFMS for detecting a wide range of SVOCs in children's teeth, identifying a substantial number of developmental toxicants and other toxic chemicals. The detection of these compounds highlights critical gaps in our understanding of children's chemical exposures.
{"title":"Methods for a comprehensive targeted and suspect screen survey of exogenous chemicals in shed baby teeth","authors":"Lynne P. Heilbrun , Anabel Rodriguez , L. Aubree Shay , David Gimeno Ruiz de Porras , Inkyu Han , Kristin Favela","doi":"10.1016/j.ijms.2025.117534","DOIUrl":"10.1016/j.ijms.2025.117534","url":null,"abstract":"<div><h3>Background</h3><div>Semi-volatile organic chemicals (SVOCs) have been studied in shed baby teeth as a potential tool to identify environmental triggers of autism. However, these targeted studies are limited by the availability of standards, leaving a vast number of chemicals unexplored for autism risk.</div></div><div><h3>Objective</h3><div>We explored the use of two-dimensional gas chromatography time-of-flight mass spectrometry (GCxGC-TOFMS) as a viable and accurate method for identifying and quantifying a wide range of low-level SVOCs in deciduous teeth.</div></div><div><h3>Methods</h3><div>Tooth samples were derived from The Autism Tooth Fairy Study. Ground tooth samples (n = 44) were analyzed using GCxGC-TOFMS. Targeted and non-targeted analyses were performed. Targeted compounds were reviewed against reference spectra for identification, and non-targets were manually curated using the National Institute of Standards and Technology Library data, as available. Kovat's retention index was used for identifications without a reference standard.</div></div><div><h3>Results</h3><div>From the 44 tooth samples analyzed, 11,971 total endogenous and exogenous features were cataloged, including unknowns without a suitable library match. Of the 203 compounds detected, 106 high-fidelity matched compounds were identified spanning 45 subclasses of toxicants. Eighty-nine of these compounds are known developmental toxicants or endocrine disruptors. The remaining compounds were toxicants with acute or chronic toxicity data but had no developmental or endocrine-disrupting activity data.</div></div><div><h3>Conclusion</h3><div>This study demonstrates the utility of GCxGC-TOFMS for detecting a wide range of SVOCs in children's teeth, identifying a substantial number of developmental toxicants and other toxic chemicals. The detection of these compounds highlights critical gaps in our understanding of children's chemical exposures.</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"519 ","pages":"Article 117534"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145263477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2025-10-24DOI: 10.1016/j.ijms.2025.117545
Jinyang Li , Shuqi Li , Yongliang Cui , Sen Zhang , Guanxin Yao , Xianyi Zhang , Xianglei Kong
The selection of precursor is essential for the generation of various endohedral metallofullerenes (EMFs) in the laser ablation mass spectrometry experiments. Herein, natural graphite sheets without any pretreatment were applied in the laser ablation experiments with a Fourier transform ion cyclotron resonance (FT ICR) mass spectrometer. EMF ions of were identified in the mass spectrum. Although the distributions of the mono- and di- EMF ions are somewhat similar to those previously observed with the precursor of graphene/CaCl2, the tri-EMF ions of (2n = 92–132) and tetra-EMF ions of (2n = 110–124) were also observed, which have not been reported before. The presence of these Ca-related impurities not only indicates that laser ablation mass spectrometry can be an effective means of identifying natural graphite but also suggests that well-designed doping can provide a long-lasting and enduring pathway for the generation of new EMFs.
{"title":"Generation of endohedral metallofullerene ions of Ca1-4C2n+ (44 ≤ 2n ≤ 132) by laser ablation of natural graphite sheets without pretreatment","authors":"Jinyang Li , Shuqi Li , Yongliang Cui , Sen Zhang , Guanxin Yao , Xianyi Zhang , Xianglei Kong","doi":"10.1016/j.ijms.2025.117545","DOIUrl":"10.1016/j.ijms.2025.117545","url":null,"abstract":"<div><div>The selection of precursor is essential for the generation of various endohedral metallofullerenes (EMFs) in the laser ablation mass spectrometry experiments. Herein, natural graphite sheets without any pretreatment were applied in the laser ablation experiments with a Fourier transform ion cyclotron resonance (FT ICR) mass spectrometer. EMF ions of <span><math><mrow><msubsup><mrow><msub><mtext>Ca</mtext><mrow><mn>1</mn><mo>−</mo><mn>4</mn></mrow></msub><mo>@</mo><mi>C</mi></mrow><mrow><mn>2</mn><mi>n</mi></mrow><mo>+</mo></msubsup><mspace></mspace><mrow><mo>(</mo><mrow><mn>44</mn><mo>≤</mo><mn>2</mn><mi>n</mi><mo>≤</mo><mn>132</mn></mrow><mo>)</mo></mrow></mrow></math></span> were identified in the mass spectrum. Although the distributions of the mono- and di- EMF ions are somewhat similar to those previously observed with the precursor of graphene/CaCl<sub>2</sub>, the tri-EMF ions of <span><math><mrow><msub><mtext>Ca</mtext><mn>3</mn></msub><mo>@</mo><msubsup><mi>C</mi><mrow><mn>2</mn><mi>n</mi></mrow><mo>+</mo></msubsup></mrow></math></span> (2n = 92–132) and tetra-EMF ions of <span><math><mrow><msub><mtext>Ca</mtext><mn>4</mn></msub><mo>@</mo><msubsup><mi>C</mi><mrow><mn>2</mn><mi>n</mi></mrow><mo>+</mo></msubsup></mrow></math></span> (2n = 110–124) were also observed, which have not been reported before. The presence of these Ca-related impurities not only indicates that laser ablation mass spectrometry can be an effective means of identifying natural graphite but also suggests that well-designed doping can provide a long-lasting and enduring pathway for the generation of new EMFs.</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"519 ","pages":"Article 117545"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145358983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2025-09-10DOI: 10.1016/j.ijms.2025.117526
Daniil D. Odintsov , Sergey S. Poteshin
In the last few years, high-resolution time-of-flight mass analyzers (TOF-MA) have been intensively developed. Their development requires tools that provide very accurate calculation of ion trajectories in electric fields, since an error on the scale of hundreds of picoseconds at millisecond flight times (10−10 %) already leads to noticeable distortions of the result. The main apparatus for calculating such systems is the aberration theory, but it has a limitation in the accuracy of calculations, since it is based on expansion in a series, and taking into account the next order of expansion significantly complicates the formulas. In this regard, using the example of calculating ion trajectories for TOF-MA with sector electrostatic fields, a comparison of the results, obtained using the aberration theory was carried out with the results of modeling in Simion. Results of the comparison indicate the possibility of applicability of the program for calculating multi-turn mass analyzers (MT-MA). Using the developed program, MT-MA with a resolution of 470,000 was calculated.
{"title":"Comparison of the results of the aberration approach for the calculation of electrostatic TOF mass analyzers with simulation in SIMION","authors":"Daniil D. Odintsov , Sergey S. Poteshin","doi":"10.1016/j.ijms.2025.117526","DOIUrl":"10.1016/j.ijms.2025.117526","url":null,"abstract":"<div><div>In the last few years, high-resolution time-of-flight mass analyzers (TOF-MA) have been intensively developed. Their development requires tools that provide very accurate calculation of ion trajectories in electric fields, since an error on the scale of hundreds of picoseconds at millisecond flight times (10<sup>−10</sup> %) already leads to noticeable distortions of the result. The main apparatus for calculating such systems is the aberration theory, but it has a limitation in the accuracy of calculations, since it is based on expansion in a series, and taking into account the next order of expansion significantly complicates the formulas. In this regard, using the example of calculating ion trajectories for TOF-MA with sector electrostatic fields, a comparison of the results, obtained using the aberration theory was carried out with the results of modeling in Simion. Results of the comparison indicate the possibility of applicability of the program for calculating multi-turn mass analyzers (MT-MA). Using the developed program, MT-MA with a resolution of 470,000 was calculated.</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"519 ","pages":"Article 117526"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145048038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2025-10-30DOI: 10.1016/j.ijms.2025.117547
Younes Valadbeigi
This study presents a comprehensive computational investigation of protonation behavior, proton affinity (PA), pKa values, and collision cross sections (CCS) for fifteen neonicotinoid pesticides using density functional theory with B3LYP, ωB97X-D, and M06-2X functionals. Protonation sites were systematically evaluated in both gas and aqueous phases. CCS values of the resulting protonated species were computed via the trajectory method using MOBCAL-MPI, showing excellent agreement with experimental data and enabling site-specific protonation prediction. All neonicotinoids except nithiazine had PA values above 900 kJ mol−1, confirming strong gas-phase basicity. Predicted pKa values of the conjugate acids of neonicotinoids were consistently below 7, indicating low aqueous-phase basicity of the neonicotinoids.
{"title":"Proton affinity, pKa, and collision cross section of neonicotinoid pesticides: A DFT approach","authors":"Younes Valadbeigi","doi":"10.1016/j.ijms.2025.117547","DOIUrl":"10.1016/j.ijms.2025.117547","url":null,"abstract":"<div><div>This study presents a comprehensive computational investigation of protonation behavior, proton affinity (PA), pK<sub>a</sub> values, and collision cross sections (CCS) for fifteen neonicotinoid pesticides using density functional theory with B3LYP, ωB97X-D, and M06-2X functionals. Protonation sites were systematically evaluated in both gas and aqueous phases. CCS values of the resulting protonated species were computed via the trajectory method using MOBCAL-MPI, showing excellent agreement with experimental data and enabling site-specific protonation prediction. All neonicotinoids except nithiazine had PA values above 900 kJ mol<sup>−1</sup>, confirming strong gas-phase basicity. Predicted pK<sub>a</sub> values of the conjugate acids of neonicotinoids were consistently below 7, indicating low aqueous-phase basicity of the neonicotinoids.</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"519 ","pages":"Article 117547"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145413021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Database-searching based precursor ion identification in tandem mass spectrometry data analysis is limited to the search space. Once a single amino acid variation (SAAV) or a modification is not included to the search space, then its observed spectra will not be annotated correctly. Several methods have been developed to identify and localize post-translational modifications (PTMs); however, few methods have been introduced to identify peptide sequences with amino acid mutations. Here, we present our approach to detect SAAVs, called SeVa (standing for Sequence Variation). SeVa is based on the High-Resolution Exact P-Value (HR-XPV) method (doi:10.1002/pmic.202300145), which builds an exact empirical null distribution by implicitly scoring the spectra against all possible amino acid sequences in high-resolution fragmentation settings. SeVa extracts the amino acid sequence from HR-XPV, which produces the highest score. The SeVa peptides identified are subjected to a homology search against a proteome database containing shuffled decoy protein sequences. This step increases the sensitivity of the results and the decoy identifications can be used to estimate the FDR. We tested SeVa with two experimental datasets related to immunopeptidomics (PXD017407) and cancer (PDC000224), and our method identified 781 and 15,764 peptide sequences with mutations at 1.68% and 0.52% of FDRs.
{"title":"Single amino acid variation identification in high resolution tandem mass spectrometry data in bottom up proteomics","authors":"Kishankumar Bhimani , Arina Peresadina , Karina Burmak , Kartik Joshi , Attila Kertesz-Farkas","doi":"10.1016/j.ijms.2025.117532","DOIUrl":"10.1016/j.ijms.2025.117532","url":null,"abstract":"<div><div>Database-searching based precursor ion identification in tandem mass spectrometry data analysis is limited to the search space. Once a single amino acid variation (SAAV) or a modification is not included to the search space, then its observed spectra will not be annotated correctly. Several methods have been developed to identify and localize post-translational modifications (PTMs); however, few methods have been introduced to identify peptide sequences with amino acid mutations. Here, we present our approach to detect SAAVs, called SeVa (standing for <u>Se</u>quence <u>Va</u>riation). SeVa is based on the High-Resolution Exact P-Value (HR-XPV) method (doi:10.1002/pmic.202300145), which builds an exact empirical null distribution by implicitly scoring the spectra against all possible amino acid sequences in high-resolution fragmentation settings. SeVa extracts the amino acid sequence from HR-XPV, which produces the highest score. The SeVa peptides identified are subjected to a homology search against a proteome database containing shuffled decoy protein sequences. This step increases the sensitivity of the results and the decoy identifications can be used to estimate the FDR. We tested SeVa with two experimental datasets related to immunopeptidomics (PXD017407) and cancer (PDC000224), and our method identified 781 and 15,764 peptide sequences with mutations at 1.68% and 0.52% of FDRs.</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"519 ","pages":"Article 117532"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145217932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The negative and positive ions formed on the surface of the heated Re, W, and Mo under ambient atmosphere were measured by mass spectrometry. Heated metal surfaces are quickly oxidized under ambient atmospheric pressure with the presence of oxygen and moisture in the air. Metal oxides of Re2O7, WO3, and MoO3 formed on the heated Re, W, and Mo surfaces reacted with water (moisture in the air) to form ReO4−, WO3−OH, and MoO3−OH, respectively. The formation of WO3−OH and MoO3−OH were followed by successive dehydration condensation reactions to form (WO3)n−OH (n = 0–14) and (MoO3)n−OH (n = 0–41), i.e., (WO3)n−1−OH + HOWO2OH → (WO3)n−OH + H2O and (MoO3)n−1−OH + HOMoO3OH → (MoO3)n−OH + H2O, respectively. The magic number of n = 6 was observed for (WO3)n−OH and (MoO3)n−OH, likely due to the formation of a cyclic intramolecular hydrogen bond between the terminal O− and OH in O−(WO3)5WO2OH. No dehydrated condensed ions were detected for Re because the primary ion ReO4− does not have a hydroxyl group for the occurrence of dehydration reactions. Evidence for the desorption of metal oxides of Re2O7, WO3, and MoO3 as neutral forms was not obtained. This suggests that these neutral products react almost instantly with water to form metallic acids on the surface followed by the formation of polyoxometalate anions.
{"title":"Thermal desorption of preformed polyoxometalate anions on the heated oxidized Re, W, and Mo under ambient atmospheric pressure studied by mass spectrometry","authors":"Kenzo Hiraoka , Stephanie Rankin-Turner , Dilshadbek T. Usmanov , Satoshi Ninomiya","doi":"10.1016/j.ijms.2025.117550","DOIUrl":"10.1016/j.ijms.2025.117550","url":null,"abstract":"<div><div>The negative and positive ions formed on the surface of the heated Re, W, and Mo under ambient atmosphere were measured by mass spectrometry. Heated metal surfaces are quickly oxidized under ambient atmospheric pressure with the presence of oxygen and moisture in the air. Metal oxides of Re<sub>2</sub>O<sub>7</sub>, WO<sub>3</sub>, and MoO<sub>3</sub> formed on the heated Re, W, and Mo surfaces reacted with water (moisture in the air) to form ReO<sub>4</sub><sup>−</sup>, WO<sub>3</sub><sup>−</sup>OH, and MoO<sub>3</sub><sup>−</sup>OH, respectively. The formation of WO<sub>3</sub><sup>−</sup>OH and MoO<sub>3</sub><sup>−</sup>OH were followed by successive dehydration condensation reactions to form (WO<sub>3</sub>)<sub>n</sub><sup>−</sup>OH (n = 0–14) and (MoO<sub>3</sub>)<sub>n</sub><sup>−</sup>OH (n = 0–41), i.e., (WO<sub>3</sub>)<sub>n−1</sub><sup>−</sup>OH + HOWO<sub>2</sub>OH → (WO<sub>3</sub>)<sub>n</sub><sup>−</sup>OH + H<sub>2</sub>O and (MoO<sub>3</sub>)<sub>n−1</sub><sup>−</sup>OH + HOMoO<sub>3</sub>OH → (MoO<sub>3</sub>)<sub>n</sub><sup>−</sup>OH + H<sub>2</sub>O, respectively. The magic number of n = 6 was observed for (WO<sub>3</sub>)<sub>n</sub><sup>−</sup>OH and (MoO<sub>3</sub>)<sub>n</sub><sup>−</sup>OH, likely due to the formation of a cyclic intramolecular hydrogen bond between the terminal O<sup>−</sup> and OH in O<sup>−</sup>(WO<sub>3</sub>)<sub>5</sub>WO<sub>2</sub>OH. No dehydrated condensed ions were detected for Re because the primary ion ReO<sub>4</sub><sup>−</sup> does not have a hydroxyl group for the occurrence of dehydration reactions. Evidence for the desorption of metal oxides of Re<sub>2</sub>O<sub>7</sub>, WO<sub>3</sub>, and MoO<sub>3</sub> as neutral forms was not obtained. This suggests that these neutral products react almost instantly with water to form metallic acids on the surface followed by the formation of polyoxometalate anions.</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"519 ","pages":"Article 117550"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145517062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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