Journal of the American Society for Mass Spectrometry最新文献

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Assignment of Disulfide Bonds in HNTX-XXI by Double-Enzymatic Digestion and Edman Degradation. 通过双酶消化和埃德曼降解法确定 HNTX-XXI 中的二硫键。
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-12-04 Epub Date: 2024-11-08 DOI: 10.1021/jasms.4c00319
Bo Chen, Juan He, Zhaotun Hu, Xiongzhi Zeng
{"title":"Assignment of Disulfide Bonds in HNTX-XXI by Double-Enzymatic Digestion and Edman Degradation.","authors":"Bo Chen, Juan He, Zhaotun Hu, Xiongzhi Zeng","doi":"10.1021/jasms.4c00319","DOIUrl":"10.1021/jasms.4c00319","url":null,"abstract":"<p><p>HNTX-XXI, a peptide toxin derived from the venom of the spider <i>Ornithoctonus hainana</i>, comprises a 64-amino-acid protein architecture that notably incorporates eight cysteine residues positioned at positions 2, 10, 14, 16, 17, 23, 36, and 63. The close spatial proximity of Cys16 and Cys17 poses a challenge in resolving their disulfide bridge configurations using standard methodologies. In this study, we introduce an innovative and highly efficient approach for delineating disulfide pairings in peptides containing adjacent cysteines. Our methodology integrates a two-step proteolytic digestion strategy utilizing trypsin and Glu-specific staphylococcal V8 protease coupled with a subsequent round of Edman degradation. This multifaceted approach enables the precise characterization of the disulfide bonds within the peptide. Specifically, targeted proteolysis by trypsin and V8, followed by reversed-phase HPLC separation of the resulting peptides, facilitated the unambiguous identification of disulfide linkages between Cys10-Cys23 and Cys14-Cys63. For the fragment containing the four remaining cysteines, a single cycle of Edman degradation was employed, strategically breaking the peptide bond between the adjacent cysteines. This pivotal step enabled the isolation and analysis of the resulting fragments. Subsequently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was utilized, revealing the presence of two additional disulfide bonds: Cys2-Cys17 and Cys16-Cys36. Collectively, these findings allow for the definitive assignment of the four disulfide linkages in HNTX-XXI as Cys2-Cys17, Cys10-Cys23, Cys14-Cys63, and Cys16-Cys36. This rapid and sensitive methodology represents a significant advancement in the structural characterization of peptide toxins with complex disulfide bond patterns, underscoring its potential for broad application in the field of venom peptide research.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"3089-3094"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142602792","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}
引用次数: 0
Single Cell MALDI-MSI Analysis of Lipids and Proteins within a Replicative Senescence Fibroblast Model. 对复制衰老成纤维细胞模型中的脂质和蛋白质进行单细胞 MALDI-MSI 分析。
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-12-04 Epub Date: 2024-10-30 DOI: 10.1021/jasms.4c00095
Emily R Sekera, Lorena Rosas, Joseph H Holbrook, Quetzalli D Angeles-Lopez, Timur Khaliullin, Mauricio Rojas, Ana L Mora, Amanda B Hummon
{"title":"Single Cell MALDI-MSI Analysis of Lipids and Proteins within a Replicative Senescence Fibroblast Model.","authors":"Emily R Sekera, Lorena Rosas, Joseph H Holbrook, Quetzalli D Angeles-Lopez, Timur Khaliullin, Mauricio Rojas, Ana L Mora, Amanda B Hummon","doi":"10.1021/jasms.4c00095","DOIUrl":"10.1021/jasms.4c00095","url":null,"abstract":"<p><p>In this study, we evaluate lipids and select proteins in human lung fibroblasts (hLFs) to interrogate changes occurring due to aging and senescence. To study single cell populations, a comparison of cells adhered onto slides using poly-d-lysine versus centrifugal force deposition was first analyzed to determine whether specific alterations were observed between preparations. The poly-d-lysine approach was then utilized to interrogate the lipidome of the cell populations and further evaluate potential applications of the MALDI-immunohistochemistry (IHC) platform for single-cell-level analyses. Two protein markers of senescence, vimentin and p21, were both observed within the fibroblast populations and quantified. Lipidomic analysis of the fibroblasts found 12 lipids significantly altered because of replicative senescence, including fatty acids, such as stearic acid, and ceramide phosphoethanolamine species (CerPE). Similar to previous reports, alterations were detected in putative fatty acid building blocks, ceramides, among other lipid species. Altogether, our results reveal the ability to detect lipids implicated in senescence and show alterations to protein expression between normal and senescent fibroblast populations, including differences between young and aged cells. This report is the first time that the MALDI-IHC system has been utilized at a single-cell level to analyze both protein expression and lipid profiles in cultured cells, with a particular focus on changes associated with aging and senescence.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"2815-2823"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542809","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}
引用次数: 0
Met4DX: A Unified and Versatile Data Processing Tool for Multidimensional Untargeted Metabolomics Data. Met4DX:用于多维非靶向代谢组学数据的统一、多功能数据处理工具。
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-12-04 Epub Date: 2024-10-14 DOI: 10.1021/jasms.4c00290
Yandong Yin, Mingdu Luo, Zheng-Jiang Zhu
{"title":"Met4DX: A Unified and Versatile Data Processing Tool for Multidimensional Untargeted Metabolomics Data.","authors":"Yandong Yin, Mingdu Luo, Zheng-Jiang Zhu","doi":"10.1021/jasms.4c00290","DOIUrl":"10.1021/jasms.4c00290","url":null,"abstract":"<p><p>Liquid chromatography-mass spectrometry (LC-MS) is a powerful tool in untargeted metabolomics, enabling the high-sensitivity and high-specificity characterization of metabolites. The integration of ion mobility (IM) with LC-MS, known as LC-IM-MS, enhances the analytical depth, facilitating more comprehensive metabolite profiling. However, the complexity of data generated by these technologies presents significant challenges in data processing. Addressing these challenges, we developed Met4DX, a unified and versatile software tool for processing both 3D and 4D untargeted metabolomics data. Met4DX incorporates a new MS1-oriented peak detection approach coupled with our bottom-up assembly algorithm, enabling highly sensitive and comprehensive peak detection in untargeted metabolomics data. Additionally, Met4DX employs a uniform quantification strategy to enhance the precision of peak integration across different samples. The software provides a user-friendly interface that simplifies data processing with default parameter sets, consolidating peak detection, alignment, quantification, and other procedures into a single streamlined workflow. Together, Met4DX offers a comprehensive solution for multidimensional metabolomics data processing, transforming raw data from diverse MS instruments into a final feature table containing quantification and identification results. We postulate Met4DX facilitates metabolite discovery in biological samples by deciphering the complex untargeted metabolomics data. Met4DX is freely available on the Internet (https://met4dx.zhulab.cn/).</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"2960-2968"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142455371","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}
引用次数: 0
Structure and Stabilities of Solution and Gas Phase Protein Complexes. 溶液和气相蛋白质复合物的结构和稳定性。
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-12-04 Epub Date: 2024-11-21 DOI: 10.1021/jasms.4c00306
Robert L Rider, Carter Lantz, Liqi Fan, David H Russell
{"title":"Structure and Stabilities of Solution and Gas Phase Protein Complexes.","authors":"Robert L Rider, Carter Lantz, Liqi Fan, David H Russell","doi":"10.1021/jasms.4c00306","DOIUrl":"10.1021/jasms.4c00306","url":null,"abstract":"<p><p>Collision-induced unfolding (CIU) has provided new levels of understanding of the stabilities and structure(s) for gas phase protein and protein complex ions formed by electrospray ionization (ESI). Variable-temperature (vT-ESI) data provide complementary information about temperature-induced folding/unfolding (TIU) reactions of solution phase ions. Results obtained by using CIU and TIU provide complementary information about stabilities of gas phase versus solution phase ions. Such comparisons may provide the most direct experimental approach to answer a long-standing question from Fred McLafferty: \"For how long, under what conditions, and to what extent, can solution structure be retained without solvent?\" Answers to this question require greater understanding of the (i) structure(s), stabilities, and dynamics of proteins/protein complexes in solution prior to ESI; (ii) effects of water removal by droplet fission and \"freeze-drying\" by evaporation of water from the nanodroplet; and (iii) potential reactions and structural changes that may occur as the ions traverse the heated capillary, the final stage in the transition to solvent-free gas phase ions. Here, we employ vT-ESI coupled with ion mobility-mass spectrometry (IM-MS) as a means to provide more detailed answers to the above-mentioned questions. Apo- and metalated-metallothionein-2A (MT), a cysteine-rich metal binding protein, and various proteoforms of transthyretin (TTR), a homotetrameric (56 kDa) retinol and thyroxine transporter protein complex were studied to examine distinct features of CIU and TIU across two different types of protein complexes. The results in this work shed light on the capabilities of CIU, TIU, and average charge state (Z<sub>avg</sub>) for probing the rugged energy landscape of native proteins and highlights the effects of water and cofactors (metal ions) on the structure and stabilities of proteins and protein complexes.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"3028-3036"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622221/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680476","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}
引用次数: 0
Covalent Labeling Automated Data Analysis Platform for High Throughput in R (coADAPTr): A Proteome-Wide Data Analysis Platform for Covalent Labeling Experiments. 共价标记高通量 R 语言自动数据分析平台(coADAPTr):共价标记实验的全蛋白质组数据分析平台。
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-12-04 Epub Date: 2024-10-02 DOI: 10.1021/jasms.4c00196
Raquel L Shortt, Lindsay K Pino, Emily E Chea, Carolina Rojas Ramirez, Daniel A Polasky, Alexey I Nesvizhskii, Lisa M Jones
{"title":"Covalent Labeling Automated Data Analysis Platform for High Throughput in R (coADAPTr): A Proteome-Wide Data Analysis Platform for Covalent Labeling Experiments.","authors":"Raquel L Shortt, Lindsay K Pino, Emily E Chea, Carolina Rojas Ramirez, Daniel A Polasky, Alexey I Nesvizhskii, Lisa M Jones","doi":"10.1021/jasms.4c00196","DOIUrl":"10.1021/jasms.4c00196","url":null,"abstract":"<p><p>Covalent labeling methods coupled to mass spectrometry have emerged in recent years for studying the higher order structure of proteins. Quantifying the extent of modification of proteins in multiple states (i.e., ligand free vs ligand-bound) can provide information on protein interaction sites and regions of conformational change. Though there are several software platforms that are used to quantify the extent of modification, the process can still be time-consuming, particularly for proteome-wide studies. Here, we present an open-source software for quantitation called Covalent labeling Automated Data Analysis Platform for high Throughput in R (coADAPTr). coADAPTr tackles the need for more efficient data analysis in covalent labeling mass spectrometry for techniques such as hydroxyl radical protein footprinting (HRPF). Traditional methods like Excel's Power Pivot (PP) are cumbersome and time-intensive, posing challenges for large-scale analyses. coADAPTr simplifies analysis by mimicking the functions used in the previous quantitation platform using PowerPivot in Microsoft Excel but with fewer steps, offering proteome-wide insights with enhanced graphical interpretations. Several features have been added to improve the fidelity and throughput compared to those of PowerPivot. These include filters to remove any duplicate data and the use of the arithmetic mean rather than the geometric mean for quantitation of the extent of modification. Validation studies confirm coADAPTr's accuracy and efficiency while processing data up to 200 times faster than conventional methods. Its open-source design and user-friendly interface make it accessible for researchers exploring intricate biological phenomena via HRPF and other covalent labeling MS methods. coADAPTr marks a significant leap in structural proteomics, providing a versatile and efficient platform for data interpretation. Its potential to transform the field lies in its seamless handling of proteome-wide data analyses, empowering researchers with a robust tool for deciphering complex structural biology data.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"3301-3307"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142363933","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}
引用次数: 0
Development of Peptide Identification System for ToF-SIMS Spectra Using Supervised Machine Learning. 利用监督机器学习为 ToF-SIMS 光谱开发多肽识别系统
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-12-04 Epub Date: 2024-10-12 DOI: 10.1021/jasms.4c00310
Satoka Aoyagi, Miya Fujita, Hidemi Itoh, Hiroto Itoh, Takaharu Nagatomi, Masayuki Okamoto, Tomikazu Ueno
{"title":"Development of Peptide Identification System for ToF-SIMS Spectra Using Supervised Machine Learning.","authors":"Satoka Aoyagi, Miya Fujita, Hidemi Itoh, Hiroto Itoh, Takaharu Nagatomi, Masayuki Okamoto, Tomikazu Ueno","doi":"10.1021/jasms.4c00310","DOIUrl":"10.1021/jasms.4c00310","url":null,"abstract":"<p><p>Time-of-flight secondary ion mass spectrometry (ToF-SIMS) data interpretation for organic materials is complicated because of various fragment ions produced from each molecule and the overlapping of certain mass peaks from different molecules. Fragmentation mechanisms in SIMS are complex because different sputtering and ionization processes can simultaneously occur. Therefore, a prediction system that can identify materials in a sample is required. A novel prediction system for peptides based on ToF-SIMS and amino-acid-based teaching information (labels) for supervised machine learning was developed. To develop the prediction system for general organic materials, the annotation of materials is crucial to creating effective labels for supervised learning. Peptides are composed of 20 amino acid residues, which can be used as labels. We previously developed a peptide prediction system using Random Forest, a supervised machine-learning method. However, only the amino acids contained in the target peptide were predicted, and the amino acid sequence was unable to be assumed. In this study, the amino acid sequence of the test peptide was determined by adding the information on two adjacent amino acids to the labels. Once the prediction system learned the target peptide spectra, the peptides in the newly obtained ToF-SIMS spectra could be identified. The new prediction system also provides useful information for the identification of unknown peptides. The prediction results indicate that two adjacent permutations of amino acids are effective pieces of teaching information for expressing the amino acid sequence of a peptide.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"3057-3062"},"PeriodicalIF":3.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11623169/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142455370","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}
引用次数: 0
Assessing Antiparasitic Compounds Persistence in Cattle Hair by DART-MS. 利用 DART-MS 评估牛毛中抗寄生虫化合物的持久性。
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-27 DOI: 10.1021/jasms.4c00422
Almir Custodio Batista Junior, Lanaia Ítala Louzeiro Maciel, Yuri Arrates Rocha, Gabriela Guimarães Souza, Boniek Gontijo Vaz, Welber Daniel Zanetti Lopes, Ana Flávia Machado Botelho, Marc Yves Chalom, Andréa Rodrigues Chaves
{"title":"Assessing Antiparasitic Compounds Persistence in Cattle Hair by DART-MS.","authors":"Almir Custodio Batista Junior, Lanaia Ítala Louzeiro Maciel, Yuri Arrates Rocha, Gabriela Guimarães Souza, Boniek Gontijo Vaz, Welber Daniel Zanetti Lopes, Ana Flávia Machado Botelho, Marc Yves Chalom, Andréa Rodrigues Chaves","doi":"10.1021/jasms.4c00422","DOIUrl":"https://doi.org/10.1021/jasms.4c00422","url":null,"abstract":"<p><p>This study introduces an alternative strategy for evaluating antiparasitic persistence compounds in cattle hair by Direct Analysis in Real Time Mass Spectrometry (DART-MS). The developed DART-MS method aimed to determine fenthion, chlorpyrifos, and cypermethrin in cattle hair samples. DART-MS analyses were performed in positive ion mode, and parameters related to the DART source were evaluated. The analytical performance demonstrated the efficiency of the optimized DART-MS method for fenthion, chlorpyrifos, and cypermethrin quantification in the evaluated samples, meeting criteria for precision, accuracy and limits of detection. Overall, the DART-MS method provided a fast and efficient analysis for determination of antiparasitic agents in cattle hair, which contributes to the evaluation of drug administration protocols and dosage intervals, and aids the safety and advancement of the livestock sector.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142724590","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}
引用次数: 0
Infrared Photoactivation Enables nano-DESI MS of Protein Complexes in Tissue on a Linear Ion Trap Mass Spectrometer. 红外光活化技术可在线性离子阱质谱仪上对组织中的蛋白质复合物进行纳米 DESI MS 分析。
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-27 DOI: 10.1021/jasms.4c00377
Oliver J Hale, Todd H Mize, Helen J Cooper
{"title":"Infrared Photoactivation Enables nano-DESI MS of Protein Complexes in Tissue on a Linear Ion Trap Mass Spectrometer.","authors":"Oliver J Hale, Todd H Mize, Helen J Cooper","doi":"10.1021/jasms.4c00377","DOIUrl":"https://doi.org/10.1021/jasms.4c00377","url":null,"abstract":"<p><p>Native mass spectrometry analysis of proteins directly from tissues can be performed by using nanospray-desorption electrospray ionization (nano-DESI). Typically, supplementary collisional activation is essential to decluster protein complex ions from solvent, salt, detergent, and lipid clusters that comprise the ion beam. As an alternative, we have implemented declustering by infrared (IR) photoactivation on a linear ion trap mass spectrometer equipped with a CO<sub>2</sub> laser (λ = 10.6 μm). The prototype system demonstrates declustering of intact protein complex ions up to approximately 50 kDa in molecular weight that were sampled directly from brain and eye lens tissues by nano-DESI. For example, signals for different metal binding states of hSOD1<sup>G93A</sup> homodimers (approximately 32 kDa) separated by only approximately 6 Th (10+ ions) were resolved with IR declustering, but not with collisional activation. We found IR declustering to outperform collisional activation in its ability to reduce chemical background attributable to nonspecific clusters in the nano-DESI ion beam. The prototype system also demonstrates <i>in situ</i> native MS on a low-cost mass spectrometer and the potential of linear ion trap mass spectrometers for this type of analysis.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142738244","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}
引用次数: 0
Photochemical and Collision-Induced Cross-Linking of Asp, Glu, Asn, and Gln Residues in Peptide-Nitrile Imine Conjugate Ions in the Gas Phase. 气相中肽-腈-亚胺共轭离子中 Asp、Glu、Asn 和 Gln 树脂的光化学和碰撞诱导交联。
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-27 DOI: 10.1021/jasms.4c00394
Mikuláš Vlk, Jiahao Wan, Marianna Nytka, Tuan Ngoc Kim Vu, Karel Lemr, František Tureček
{"title":"Photochemical and Collision-Induced Cross-Linking of Asp, Glu, Asn, and Gln Residues in Peptide-Nitrile Imine Conjugate Ions in the Gas Phase.","authors":"Mikuláš Vlk, Jiahao Wan, Marianna Nytka, Tuan Ngoc Kim Vu, Karel Lemr, František Tureček","doi":"10.1021/jasms.4c00394","DOIUrl":"https://doi.org/10.1021/jasms.4c00394","url":null,"abstract":"<p><p>Peptide conjugates furnished with a 2,5-diaryltetrazolecarbonyl tag at the C-terminal lysine, which we call peptide-<i>tet</i>-K, were found to undergo efficient cross-linking of Asp, Glu, Asn, and Gln residues to transient nitrile-imine intermediates produced by photodissociation and collision-induced dissociation (CID) of the tetrazole ring in gas-phase ions. UV photodissociation (UVPD) at 213 nm achieved cross-linking conversion yields of 37 and 61% for DAAAK-<i>tet</i>-K and EAAAK-<i>tet</i>-K, respectively. The yields for NAAAK-<i>tet</i>-K and QAAAK-<i>tet</i>-K were 29 and 57%, respectively. Even higher cross-link yields were found for CID-MS<sup>3</sup> of stable denitrogenated ions, (peptide-<i>tet</i>-K-N<sub>2</sub> + H)<sup>+</sup>, that were in the 69-83% range. Different types of cross-links were distinguished by CID-MS<sup>n</sup> that showed a distinct series of backbone fragment ions, loss of N-terminal groups, and loss of phenylhydrazine from the modified nitrile imines. The Asp and Glu side-chain carboxyl groups were major participants in cross-linking that resulted in proton and oxygen transfer to the nitrile imine group. Other types of cross-linking involved Asn and Gln <i>C</i>ONH<sub>2</sub> groups and backbone amides. Cyclic ion mobility-mass spectrometry was used to separate NAAAK-<i>tet</i>-K and QAAAK-<i>tet</i>-K conformers and products of their collision-induced denitrogenation. Linear nitrile-imine and cross-linked ion structures were identified by comparing the experimental collision cross sections (CC<i>S</i><sub>exp</sub>) to those for structures obtained by combined Born-Oppenheimer molecular dynamics and density functional theory (DFT) calculations. The formation of cross-links was found to be energetically favorable and involved proton-facilitated nucleophilic attack at the nitrile-imine carbon atom.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142738255","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}
引用次数: 0
Studying Structural Details in Complex Samples: II. High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Coupled to High Resolution Tandem Mass Spectrometry (MS/MS). 研究复杂样本中的结构细节:II.高场不对称波形离子迁移谱(FAIMS)与高分辨率串联质谱(MS/MS)联用。
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-25 DOI: 10.1021/jasms.4c00227
Alessandro Vetere, Wolfgang Schrader
{"title":"Studying Structural Details in Complex Samples: II. High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Coupled to High Resolution Tandem Mass Spectrometry (MS/MS).","authors":"Alessandro Vetere, Wolfgang Schrader","doi":"10.1021/jasms.4c00227","DOIUrl":"https://doi.org/10.1021/jasms.4c00227","url":null,"abstract":"<p><p>The elucidation of structural motifs in extremely complex mixtures is very difficult since the standard methods for structural elucidation are not capable to provide significant information on a single molecule. The best method for the analysis of complex mixtures is ultrahigh resolution mass spectrometry, but the utilization of this method alone does not provide significant information about structural details. Here, a combination with a separation method is necessary. While chromatography is a well-established technique, it has some disadvantages in regard to the separation of complex mixtures, as often no separation of individual isomers is possible. Therefore, here the combination of an ion mobility separation with ultrahigh resolution mass spectrometry is evaluated. As a sample matrix, crude oil is used because it is an excellent matrix to develop new analytical techniques on complex samples. Crude oil is the most complex natural sample known, but only little information is available on the structural identity or functionalities due to a high number of structural isomers or isobars. A lab-built APPI/APLI-FAIMS source was revised to optimize ion transmission and used to follow up on the ion mobility of crude oil constituents after photoionization. An MS/MS approach using collision-induced dissociation (CID) was used to elucidate structural motifs of the transmitted isomers.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142714944","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}
引用次数: 0
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