International Journal of Mass Spectrometry最新文献_第2页

Activation of CH4 and C2H6 by Al2O2+ from 300 to 600 K

IF 1.6 3区化学 Q3 PHYSICS, ATOMIC, MOLECULAR & CHEMICAL

International Journal of Mass Spectrometry

Pub Date : 2025-02-01 DOI: 10.1016/j.ijms.2024.117384

Brendan C. Sweeny, Shaun G. Ard, Albert A. Viggiano, Nicholas S. Shuman

The kinetics of Al₂O₂⁺ + CH₄ and Al₂O₂⁺ + C₂H₆ are measured from 300 to 600 K at pressures near ∼0.35 Torr in a Selected-Ion Flow Tube apparatus. The reaction with CH₄ proceeds by hydrogen abstraction to yield an open chain AlOAlOH⁺ +CH₃. The rate constant is nearly temperature-independent at 7 ± 2 × 10⁻¹¹ cm³ s⁻¹. This competes with association, which decreases sharply with temperature (k = 3.3 ± 0.8 × 10⁻¹⁰ (T/300 K)^−3.1±0.2 cm³ s⁻¹). The reaction with C₂H₆ primarily yields Al₂O₂H₂⁺ + C₂H₄. The rate constant for this channel k_300K = 4 ± 1 × 10⁻¹⁰ cm³ s⁻¹ with a very slight negative temperature dependence. A second channel producing C₂H₅ + Al₂O₂H⁺ rises steeply with temperature (k = 10 ± 2 × 10⁻¹⁰ e^{−0.12 eV/kT} cm³ s⁻¹), and finally association decreases steeply with temperature (k = 6 ± 1.5 × 10⁻¹⁰ (T/300 K)^−3.2±0.2 cm³ s⁻¹). The reaction with methane is well-described using statistical theory based on reaction coordinates calculated using density functional theory. The total rate constant for the ethane reaction is also well-described using statistical theory, but the product branching is not, suggesting post-transition state non-statistical dynamics. One possibility is that the ethane reaction unexpectedly produces a higher energy C_2v isomer of Al₂O₂H⁺. The results support the prior interpretation that Al₂O₂⁺ activates hydrocarbons via a proton-coupled electron transfer (PCET) mechanism and not a hydrogen-atom transfer (HAT) mechanism.

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引用次数: 0

Exploring the catalytic mechanism of ATPase at the molecular level by tandem mass spectrometry

IF 1.6 3区化学 Q3 PHYSICS, ATOMIC, MOLECULAR & CHEMICAL

International Journal of Mass Spectrometry

Pub Date : 2025-02-01 DOI: 10.1016/j.ijms.2024.117393

Bin Yan , Koen K.W. van Asseldonk , Baptiste Schindler , Isabelle Compagnon , Anouk M. Rijs

The nucleotide adenosine-5′-triphosphate (ATP) is the coenzyme selected by nature to provide energy for its cellular processes through the ATP hydrolysis reaction. Although the crystal structures and the general working principles of numerous ATP hydrolases (ATPases) are generally known, this omnipresent ATP conversion reaction is not fully understood at the level of local interactions. Questions such as “How does the peptide environment of the active sites of ATPases affect their association with ATP and the consecutive reaction of ATP?” and “Why is the conversion of ATP to ADP preferred over other reactions at the active site?” await detailed answers at the molecular level. Here, tandem mass spectrometry (MS) based techniques are applied to answer these questions. Gas phase studies indicate that the conversion of ATP to ADP is a charge state driven process of which the behaviour varies dramatically with subtle changes in the ATP binding peptide. Of the peptides and peptide mimics studied, only the Ac-Arg-NH₂ form of arginine actively regulates the hydrolysis of ATP, which proceeds through the sequential release of the ADP

•

peptide complex and ADP. Relative ion activation studies of the fragmentation patterns of the ATP

•

Ac-Arg-NH₂ complex show that phosphate bond dissociation is preferred over breakage of the non-covalent bond between ATP and the peptide mimic, which coincidentally agrees with the behaviour of catalysed ATP hydrolysis reaction in solution.

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引用次数: 0

Ion mobility-assisted free radical-initiated peptide sequencing 离子迁移辅助自由基启动肽测序。

IF 1.6 3区化学 Q3 PHYSICS, ATOMIC, MOLECULAR & CHEMICAL

International Journal of Mass Spectrometry

Pub Date : 2025-02-01 DOI: 10.1016/j.ijms.2024.117396

Kemi E. Osho, Keshari Kunwor, Nicholas B. Borotto

Free radical-initiated peptide sequencing (FRIPS) is a tandem mass spectrometry technique (MS/MS) that enables radical-based dissociation on instruments only capable of collisional activation. In FRIPS, peptides are chemically-derivatized with a compound that undergoes homolytic cleavage and generates radicals upon collisional activation. These radicals then propagate through the peptide backbone enabling the sequencing of peptide ions. This MS/MS technique has shown promise in sequencing post-translationally modified peptides, but it is typically performed in an MS³ workflow and single-step MS/MS approaches result in the generation of both collisional- and radical-driven dissociation products and highly complex spectra. Recently, our group developed a method to dissociate peptide ions prior to ion mobility analysis within a trapped-ion mobility spectrometry (TIMS) device. In this work, we examine if this “CIDtims” technique can initiate the homolytic cleavage of the FRIPS precursor. We then examine if the resultant ion mobility separation results in additional assignments of product ions and improved sequence coverage. We demonstrate that activation within the TIMS device does indeed promote robust radical initiation and fragmentation of peptide cations and that the generated product ions are mobility separated enabling facile assignment and increased sequence coverage.

自由基启动肽测序（FRIPS）是一种串联质谱技术（MS/MS），能够在仅能够碰撞激活的仪器上进行基于自由基的解离。在FRIPS中，肽是由一种化合物化学衍生的，该化合物经过均裂裂解并在碰撞激活时产生自由基。然后，这些自由基通过肽主链传播，从而实现肽离子的排序。这种MS/MS技术在测序翻译后修饰肽方面显示出前景，但它通常在MS3工作流程中进行，单步MS/MS方法导致产生碰撞和自由基驱动的解离产物和高度复杂的光谱。最近，我们的团队开发了一种方法，在离子迁移率分析之前，在捕获离子迁移率光谱（TIMS）设备中解离肽离子。在这项工作中，我们研究了这种“CIDtims”技术是否可以启动FRIPS前体的均溶裂解。然后，我们检查所产生的离子迁移分离是否会导致产品离子的额外分配和改进的序列覆盖。我们证明了TIMS装置内的激活确实促进了自由基的激活和肽阳离子的断裂，并且生成的产物离子是可迁移的，可以方便地分配和增加序列覆盖。

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引用次数: 0

Deep cross-modal learning between tandem mass spectrometry and molecular fingerprints for metabolite identification

IF 1.6 3区化学 Q3 PHYSICS, ATOMIC, MOLECULAR & CHEMICAL

International Journal of Mass Spectrometry

Pub Date : 2025-02-01 DOI: 10.1016/j.ijms.2024.117388

Chaofu Wang , Ping Xu , Lingyun Xue , Yian Liu , Ming Yan , Anqi Chen , Shundi Hu , Luhong Wen

Metabolite annotation plays a key role in metabolomics. To enable structural annotation of unknown tandem mass spectra, the prediction of molecular fingerprints using MS/MS is currently of great interest. However, current methods still present challenges in terms of redundancy and high dimensionality of fingerprint features, which can affect the accuracy and speed of annotation results. Therefore, we propose a dual-tower model structure consisting of an MS/MS feature extractor and a fingerprint feature extractor, which can directly compute the correlation between MS/MS and molecular fingerprints without needing to predict molecular fingerprints. Moreover, the fingerprint feature extractor, consisting of two MLPs, effectively reduces fingerprint redundancy. Both feature extractors are simultaneously optimized by contrastive learning. We trained and tested our method using data downloaded from the GNPS. The trained model was then used to search molecular structure databases such as PubChem. Experimental results show that our method outperforms MetFID, FingerScorer, MatFrag, DeepMass and CFM-ID in top-k evaluation.

{"title":"Deep cross-modal learning between tandem mass spectrometry and molecular fingerprints for metabolite identification","authors":"Chaofu Wang , Ping Xu , Lingyun Xue , Yian Liu , Ming Yan , Anqi Chen , Shundi Hu , Luhong Wen","doi":"10.1016/j.ijms.2024.117388","DOIUrl":"10.1016/j.ijms.2024.117388","url":null,"abstract":"<div><div>Metabolite annotation plays a key role in metabolomics. To enable structural annotation of unknown tandem mass spectra, the prediction of molecular fingerprints using MS/MS is currently of great interest. However, current methods still present challenges in terms of redundancy and high dimensionality of fingerprint features, which can affect the accuracy and speed of annotation results. Therefore, we propose a dual-tower model structure consisting of an MS/MS feature extractor and a fingerprint feature extractor, which can directly compute the correlation between MS/MS and molecular fingerprints without needing to predict molecular fingerprints. Moreover, the fingerprint feature extractor, consisting of two MLPs, effectively reduces fingerprint redundancy. Both feature extractors are simultaneously optimized by contrastive learning. We trained and tested our method using data downloaded from the GNPS. The trained model was then used to search molecular structure databases such as PubChem. Experimental results show that our method outperforms MetFID, FingerScorer, MatFrag, DeepMass and CFM-ID in top-k evaluation.</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"508 ","pages":"Article 117388"},"PeriodicalIF":1.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143135564","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}

引用次数: 0

The development of a novel double-focusing thermal ionization mass spectrometer

IF 1.6 3区化学 Q3 PHYSICS, ATOMIC, MOLECULAR & CHEMICAL

International Journal of Mass Spectrometry

Pub Date : 2025-01-23 DOI: 10.1016/j.ijms.2025.117408

Xianglong Yuan , Xiaopan Shen , Lubaiyang Liu , Feiteng Li , Lili Jiang , Lihua Zhai , Hu Deng , Leixin Yan , Zhiming Li

Unlike traditional Thermal Ionization Mass Spectrometers (TIMS) with single-focusing magnetic mass analyzers (such as Triton, Phoenix, Nu TIMS, etc.), a newly developed Double-Focusing Thermal Ionization Mass Spectrometer (DF-TIMS) enhances the system stability by mitigating accelerating high-voltage noise and drift. Featuring a Nier-Johnson type double-focusing mass analyzer, the instrument includes a laminated magnet with a 250 mm radius and a cylindrical Electrostatic Analyzer (ESA) with a 350 mm radius, achieving a mass dispersion of 560 mm. It is equipped with of 16 Faraday cups and 4 full-size discrete dynode secondary electron multipliers (SEM), combined with variable dispersion double quadrupole zoom optics, allowing for multi-collection of isotopes with up to 20 % mass dispersion, such as isotopes of Lithium, Boron and Calcium. Additionally, a compact and advanced Retarding Filter enhances abundance sensitivity from < 2 ppm to < 5 ppb. Automated tuning and measurement improve efficiency for both positive and negative ions. With a 0.2 mm source slit and a 1 mm receiving slit, DF-TIMS achieves a resolution over 470 and a peak shape factor below 0.3. System stability is less than 15 ppm/30 min credit to the double-focusing design. Each Faraday cup operates with a dynamic range of 0–50 V, featuring Root Mean Square (RMS) noise (4s integration, 10¹¹ Ω high resistance) under 20 μV and baseline drift below 1 × 10⁻¹⁶ A/h. The instrument has been applied extensively, delivering internal precision and external precision for Strontium and Neodymium measurements under 5 ppm, meeting stringent isotopic ratio analysis requirements in nuclear science and geoscience.

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引用次数: 0

Influence of mass spectrometry source settings on native protein ion mobility mass spectrometry measurements

IF 1.6 3区化学 Q3 PHYSICS, ATOMIC, MOLECULAR & CHEMICAL

International Journal of Mass Spectrometry

Pub Date : 2025-01-20 DOI: 10.1016/j.ijms.2025.117411

Mack Shih, Patrick J. Faustino, Thomas F. O'Connor, Jinhui Zhang

Ion mobility mass spectrometry is emerging as a useful tool to probe native protein structural information. Advance ion mobility methods like collision-induced unfolding (CIU) can be used to characterize proteins’ conformational dynamics. The impact of instrument source conditions on the native protein conformations is not well characterized or standardized. High values of drying gas temperature and gas flow parameters on the Agilent IM-QTOF instrument were shown to apply collision-induced unfolding (CIU) effects on protein ions ionized from physiological solution condition. Ion conformation heat maps of model proteins ubiquitin, myoglobin, and bovine serum albumin were obtained using a novel CIU method utilizing high drying gas temperature and varying drying gas flow. Protein charge states also increased as drying gas flow was increased at high temperature indicating a thermal heating element. Overall, drying gas temperature and gas flow on IM-QTOF and the associated impacts on ionic structure need to be considered when using ion mobility mass spectrometry technology to assess protein structure.

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引用次数: 0

Synthesis of bis(guanidinylated-methylcytosine) and its effect toward nucleobase binding

IF 1.6 3区化学 Q3 PHYSICS, ATOMIC, MOLECULAR & CHEMICAL

International Journal of Mass Spectrometry

Pub Date : 2025-01-20 DOI: 10.1016/j.ijms.2025.117409

Scott M. Simpson , Eric J. Commendatore , Hou U. Ung

The synthesis, characterization, and binding interactions of novel 4-(bis(4,5-dihydro-1H-imidazole-2-yl)amino)-1-methylpyrimidin-2(1H)-one (compound A) with two i-motif forming DNA oligomers (telomeric and hypoxia-inducible factor 1 (HIF-1α) DNA sequences) is reported. DFT-D3 calculations are used to explore binding energies and structural bonding characteristics of compound A with various nucleobases and 1-methylcytosine. Results show a significant increase in DNA melting temperatures with the addition of compound A to both telomeric and HIF-1α DNA sequences. Other ligands have shown the ability to bind and increase i-motif stability. Compound A differs in that it possesses a modified cytosine base core, while lacking the ribose sugar to achieve a significant increase in the melting temperatures of both telomeric and HIF-1α sequences.

引用次数: 0

Structural differentiation of protein charge state conformers via gas-phase ion/ion cross-linking mass spectrometry

IF 1.6 3区化学 Q3 PHYSICS, ATOMIC, MOLECULAR & CHEMICAL

International Journal of Mass Spectrometry

Pub Date : 2025-01-18 DOI: 10.1016/j.ijms.2025.117410

Woo-Young Kang, Arup Mondal, Alberto Perez, Boone M. Prentice

Determining structures of multiply charged protein ions in mass spectrometry is critical for understanding the relationship between condensed-phase protein structures found in biological environments and gas-phase structures produced during electrospray ionization (ESI). The determination of collision cross-sections (CCSs) via ion mobility-mass spectrometry (IM-MS) has been used to study conformational changes as a function of protein charge state; however, this approach provides limited structural information on the overall topology of analytes. Recently developed gas-phase cross-linking mass spectrometry (XL-MS) performed via ion/ion reactions can probe local tertiary structures, providing an additional dimension to MS-based gas-phase structural biology studies. Herein, we demonstrate the conformational differentiation of alcohol-denatured, ESI-generated ubiquitin ions with varying charges (6+ through 11+) using gas-phase XL-MS. Gas-phase N-hydroxysulfosuccinimide (NHS) ester chemistry is performed using sodiated ethylene glycol bis(sulfosuccinimidyl succinate) (sulfo-EGS) cross-linkers to covalently modify neutral and charged basic amino acid residues. This method provides sufficient sensitivity to detect subtle conformational changes in local tertiary structures specific to each charge state. These results reveal that 6+ through 8+ charge states of ubiquitin adopt folded conformations, while the 9+ through 11+ charge states exhibit unfolded structures. This trend is consistent with the bimodal charge state distribution observed in the ESI mass spectrum of alcohol-denatured ubiquitin. Overall, this gas-phase XL-MS method enables the examination of conformational changes in gas-phase proteins of varying charge states at the local tertiary structural motif level, providing a novel gas-phase structural biology approach that complements existing MS-based methods.

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引用次数: 0

Determining organophosphorus pesticides in agriculture: A combined approach of ion-mobility spectrometry with robust principal component analysis and multivariate adaptive regression splines

IF 1.6 3区化学 Q3 PHYSICS, ATOMIC, MOLECULAR & CHEMICAL

International Journal of Mass Spectrometry

Pub Date : 2025-01-10 DOI: 10.1016/j.ijms.2025.117407

Abdollah Azad, Mohammadreza Khanmohammadi Khorrami, Mahsa Mohammadi

The high toxicity and widespread use of organophosphorus pesticides (OPPs) in agriculture make their accurate detection and quantification a critical challenge. Traditional analytical techniques like gas chromatography (GC) and high-performance liquid chromatography (HPLC) face limitations due to their cost, time-consuming procedures, and labor intensity. This study explores a novel analytical approach that utilizes robust principal component analysis (rPCA) and multivariate adaptive regression splines (MARS) to enable the determination of OPPs using ion mobility spectrometry (IMS). IMS data were compressed using rPCA to identify the principal components (PCs) that best capture the relevant information.

Kenard Stone algorithm was employed to create the calibration and test sets for model development and validation, respectively. The calibration set (containing 35 samples and 6 PCs) was used to train the rPCA-MARS model. Principal Component Regression (PCR) and Partial Least Squares Regression (PLS-R) models were compared for their ability to predict the quantitative values of OPPs to the rPCA-MARS model. The efficiency of the rPCA-MARS model was evaluated using several metrics: R-squared (R²), R² estimated by generalized cross-validation (R²_GCV), adjusted R-squared (R²_adj), sum of squared errors (SSE), and mean square error (MSE). The optimal rPCA-MARS model utilized 7 basis functions to effectively characterize the OPPs values.

The linear rPCA-MARS model for Ethion performs well on both the calibration and test sets. The piecewise-cubic rPCA-MARS model achieved excellent performance on the calibration set, with R² = 0.995, R²_adj = 0.994, and SSE = 0.368. The test set results were equally impressive, showing R² = 0.993, R²_adj = 0.993, and SSE = 0.220. The cubic rPCA-MARS model exhibited exceptional predictive performance and generalizability, achieving a low MSE of 0.012 and a high R²_GCV of 0.992. These results underscore the superior predictive capability of the rPCA-MARS framework for Ethion determination in this study. Building on the success with Ethion, the rPCA-MARS model shows promise for predicting concentrations of Malathion and Phosalone.This finding highlights the model's potential for broader applications in OPPs analysis in agriculture. This paves the way for developing rapid, cost-effective, and environmentally friendly methods for monitoring and managing OPPs within agricultural ecosystems.

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引用次数: 0

Extraction anode lens effects in gas phase peptide cation-electron reactions

IF 1.6 3区化学 Q3 PHYSICS, ATOMIC, MOLECULAR & CHEMICAL

International Journal of Mass Spectrometry

Pub Date : 2024-12-23 DOI: 10.1016/j.ijms.2024.117390

Steven A. DeFiglia , Teresa Lee , Neven N. Mikawy , Carson W. Szot , Kristina Håkansson

Gas phase cation-electron reactions, from electron capture dissociation (ECD; <1 eV electrons) to electron ionization dissociation (>∼26 eV electrons), are highly beneficial for biomolecular structural characterization. These techniques offer high sequence coverage, labile posttranslational modification retention, and sidechain loss fragments which can differentiate isomeric residues. For optimum performance, careful tuning of electron energy, flux, and irradiation time is required to reach efficiency at a particular energy regime. The cathode bias voltage (CBV) is the primary determinant of electron energy, while several parameters including CBV, extraction anode lens voltage (LV), and cathode heating current determine electron flux. We present an in-depth examination of how the interplay of these parameters at variable irradiation times results in differing peptide cation-electron reaction regimes. A particularly interesting finding was the prominent high energy fragmentation pathways observed at low (∼−1.0 V) CBV and high (>50 V) LV, as compared with conventional (∼5 V) LV for peptide ECD. Specifically, high LV resulted in tandem ionization, observed for both singly- and doubly protonated peptides, alongside increased sequence coverage for both charge states from complex spectra containing a multitude of a/b/c′/d/w/x/y′/z•-type terminal fragments as well as internal fragments and a large number of neutral losses. Electron flux and energy measurements as well as electron irradiation at constant flux showed that an increased number of higher energy electrons are present at high vs. low LV, i.e., the observed “lens effect” is likely due to the presence of high energy electrons under such conditions. This extraction anode lens effect may explain previous observations of unexpected internal fragments from ECD.

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引用次数: 0