Journal of the American Society for Mass Spectrometry最新文献

{"title":"Faces of Mass Spectrometry/Ljiljana Paša-Tolić.","authors":"Anne Brenner, J D Brookbank","doi":"10.1021/jasms.4c00513","DOIUrl":"10.1021/jasms.4c00513","url":null,"abstract":"","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"232-235"},"PeriodicalIF":3.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143031798","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":"The Enzyme Effect: Broadening the Horizon of MS Optimization to Nontryptic Digestion in Proteomics.","authors":"Kinga Nagy, Péter Sándor, Károly Vékey, László Drahos, Ágnes Révész","doi":"10.1021/jasms.4c00396","DOIUrl":"10.1021/jasms.4c00396","url":null,"abstract":"<p><p>In recent years, alternative enzymes with varied specificities have gained importance in MS-based bottom-up proteomics, offering orthogonal information about biological samples and advantages in certain applications. However, most mass spectrometric workflows are optimized for tryptic digests. This raises the questions of whether enzyme specificity impacts mass spectrometry and if current methods for nontryptic digests are suboptimal. The success of peptide and protein identifications relies on the information content of MS/MS spectra, influenced by collision energy in collision-induced dissociation. We investigated this by conducting LC-MS/MS measurements with different enzymes, including trypsin, Arg-C, Glu-C, Asp-N, and chymotrypsin, at varying collision energies. We analyzed peptide scores for thousands of peptides and determined optimal collision energy (CE) values. Our results showed a linear <i>m</i>/<i>z</i> dependence for all enzymes, with Glu-C, Asp-N, and chymotrypsin requiring significantly lower energies than trypsin and Arg-C. We proposed a tailored CE selection method for these alternative enzymes, applying ca. 20% lower energy compared to tryptic peptides. This would result in a 10-15 eV decrease on a Bruker QTof instrument and a 5-6 NCE% (normalized collision energy) difference on an Orbitrap. The optimized method improved bottom-up proteomics performance by 8-32%, as measured by peptide identification and sequence coverage. The different trends in fragmentation behavior were linked to the effects of C-terminal basic amino acids for Arg-C and trypsin, stabilizing y fragment ions. This optimized method boosts the performance and provides insight into the impact of enzyme specificity. Data sets are available in the MassIVE repository (MSV000095066).</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"299-308"},"PeriodicalIF":3.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11808764/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142969198","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}

{"title":"Emission of Alkali Halide Cluster Ions from the Charged Droplets Generated from Electrospray Ionization.","authors":"Seongjae Jang, Minsu Kim, Yoonjin Kim, Junyoung Ahn, Jongcheol Seo","doi":"10.1021/jasms.4c00452","DOIUrl":"https://doi.org/10.1021/jasms.4c00452","url":null,"abstract":"<p><p>In this study, the formation and emission of alkali halide cluster ions in charged droplets generated by electrospray ionization (ESI) was investigated using mass spectrometry (MS). We focus on ion emission at the air-solution interface of charged droplets, distinguishing between two mechanisms: the ion evaporation model (IEM), where ions are released directly from the interface, and the charge residue model (CRM), where ions are generated after complete solvent evaporation. Using an iodide/chloride mixture, we analyzed how interfacial affinity influences the composition of the generated alkali halide cluster cations and anions. With the knowledge that iodides have much higher interfacial affinities than chlorides, a relative faction of iodide in the cluster ion enables us to distinguish between IEM and CRM. Small cluster anions and cations exclusively containing iodides are suggested to be from IEM, while the larger cluster ions containing more chlorides are expected to be from CRM. This work clarifies the distinctions between IEM and CRM in alkali halide cluster ion formation and also establishes a robust analytical approach for assessing interfacial affinities of ions using ESI-MS, which may potentially enhance our understanding of interfacial chemistry and its implications in atmospheric and analytical sciences.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254451","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":"Structural Categorization of Adenine, Guanine, and Xanthine Derivatives Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry with 5-Nitrosalicylic Acid and 1,5-Diaminonaphtalene.","authors":"Tohru Yamagaki, Mika Nobuhara","doi":"10.1021/jasms.4c00405","DOIUrl":"10.1021/jasms.4c00405","url":null,"abstract":"<p><p>In this study, we analyzed purine derivatives using multimatrix variation matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) with α-cyano-4-hydroxycinnamic acid (CHCA), 1,5-diaminonaphtalene (DAN), 5-formylsalicylic acid (FSA), and 5-nitrosalicylic acid (NSA) as matrices. Further, we focused on the abstraction/attachment of hydrogen from/to analytes and detected [M - H]⁺, [M + 2H]^+• and/or [M + 3H]⁺ in MALDI MS spectra of compounds containing nitrogen and/or carbonyl oxygen. Although [M - H]⁺ generation of purine compounds in MALDI MS with conventional matrices was challenging, NSA-MALDI MS effectively yielded the [M - H]⁺species of purine derivatives compared with CHCA, FSA, and DAN, and the [M - H]⁺/[M + H]⁺ ratios reflected their structures, such as the substituting groups and positions. We speculated that the molecular ion [M]^+• generated and the subsequent hydrogen radical abstraction proceeded by NSA matrix from the α-carbon of the amine group. The nitro group (-NO₂) of NSA can withdraw hydrogen radicals in photochemical reactions. The [M - H]⁺ of adenosine, guanosine, and inosine suggested that hydrogen abstraction occurred in the ribose unit. The xanthine isomer of paraxanthine was distinguished from those of theophylline and theobromine using their [M - H]⁺/[M + H]⁺ ratios obtained with NSA-MALDI MS. Additionally, [M + 2H]^+• generated in DAN-MALDI MS of xanthine derivatives due to their carbonyl groups. The relative abundances of [M + 2H]^+• of xanthine derivatives were much higher than those of the other purine derivatives such as adenine derivatives which generated [M + 3H]⁺ in their DAN-MALDI MS. DAN induced the hydrogen attachment of purine compounds because the amine group (-NH₂) of DAN can give hydrogen radicals in photochemical reactions. NSA- and DAN-MALDI MS characterized purine derivatives and were useful for their structure categorization.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"329-339"},"PeriodicalIF":3.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11808777/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142926193","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}

{"title":"Investigation into Drug-Induced Liver Damage Using Multimodal Mass Spectrometry Imaging.","authors":"Bryn Flinders, Lennart Huizing, Bhanu Singh, Heng-Keang Lim, Marjolein van Heerden, Filip Cuyckens, Ron M A Heeren, Rob J Vreeken","doi":"10.1021/jasms.4c00313","DOIUrl":"10.1021/jasms.4c00313","url":null,"abstract":"<p><p>Drug toxicity during the development of candidate pharmaceuticals is the leading cause of discontinuation in preclinical drug discovery and development. Traditionally, the cause of the toxicity is often determined by histological examination, clinical pathology, and the detection of drugs and/or metabolites by liquid chromatography-mass spectrometry (LC-MS). While these techniques individually provide information on the pathological effects of the drug and the detection of metabolites, they cannot provide specific molecular spatial information without additional experiments. Matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) is a powerful, label-free technique for the simultaneous detection of pharmaceuticals, metabolites, and endogenous chemical species in tissue sections, which makes it suitable for mechanistic toxicological studies to directly correlate the distribution of the drug and its metabolites with histological findings. This capability was demonstrated by the analysis of the liver from dogs dosed with discontinued drug compound B and its N-desmethyl metabolite, compound A. Histological examination showed multifocal hepatocellular necrosis, bile duct hyperplasia, periportal fibrosis, and chronic inflammation. MALDI-MSI analysis of liver tissue dosed with only compound A indicated that liver lesions were associated exclusively with the parent compound, whereas liver lesions with compound B showed the presence of the parent compound and its two metabolites (compound A and an N-oxide metabolite). Using both positive and negative ion modes, simultaneous detection and identification of endogenous molecular markers of the connective tissue, blood vessels, liver parenchyma, and bile duct epithelium was achieved, allowing optimal visualization of histological lesions by mass spectrometry imaging.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"265-276"},"PeriodicalIF":3.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11808762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998184","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}

{"title":"Direct Implementation of MSⁿ Using Frequency Scanning Collision Induced Dissociation in a Digital Ion Trap Mass Spectrometer.","authors":"Jie Ren, Pingping Chen, Yunjing Zhang, Xingli He, Lingfeng Li, Peng Li","doi":"10.1021/jasms.4c00395","DOIUrl":"10.1021/jasms.4c00395","url":null,"abstract":"<p><p>Tandem mass spectrometry (MSⁿ) is one of the most effective methods to obtain the structures of organic molecules, enabling the observation of multigenerational ion fragments. Collision-induced dissociation (CID) is currently the most mature technique for mass spectrometry analysis. Ion trap mass spectrometry (ITMS) is favored for on-site detection field, due to its ability of MSⁿ analysis with a single trap and its small size. However, conventional MSⁿ analysis in ITMS requires repeated isolation and excitation processes multiple times, causing high complexity of the entire scanning process. Additionally, the fragment ion detection in ITMS is limited by low-mass cutoff (LMCO) and the weak fragmentation yield. In this study, a method named reverse scanning-collision induced dissociation (RS-CID) is proposed, which involves increasing RF and AC frequencies while maintaining RF voltage constant during the CID process. Twelve representative illegal drugs were analyzed adopting this method, enhancing the intensities of low-mass fragment ions compared to conventional dissociation method. Moreover, experimental results with ketamine and methamphetamine show that RS-CID effectively reduces the LMCO effect and slightly improves CID efficiency. It also enables direct acquisition of their multigeneration fragment ions spectra in a single sequence of ion injection, cooling, isolation, RS-CID, cooling, mass scanning and empty. The experiments to distinguish between the isomers ab-4en-pinaca and adb-3en-butinaca as well as the isomeric compounds 5f-cumyl-pegaclone and cumyl-pipetinaca were also successful by this method. In summary, RS-CID enables MSⁿ analysis in a single sequence and improves the low-mass fragment ions intensity. It can simplify workflows, achieve faster analysis and provide more valuable mass spectral information.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"309-317"},"PeriodicalIF":3.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875593","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":"NIST Mass Spectral Libraries in the Context of the Circular Economy of Plastics.","authors":"Yamil Simón-Manso, Edward P Erisman, Tytus D Mak, Meghan C Burke, Adam Zuber, Xiaoyu Yang, Yuxue Liang, Pedatsur Neta, Tallat Bukhari, Antony J Williams, Joshua A Young, Samanthi Wickramasekara, William E Wallace, Stephen E Stein","doi":"10.1021/jasms.4c00349","DOIUrl":"10.1021/jasms.4c00349","url":null,"abstract":"<p><p>The Mass Spectrometry Data Center (MSDC) has recently started improving existing libraries and creating new ones for identifying and analyzing plastics-related compounds (PRC) and materials (PRM) as part of the NIST circular economy program. PRC are small molecules of dissimilar chemical nature; hence, to increase coverage, we have used three types of ionizations: EI, ESI, and APCI. PRM are solids that include polymers, polymer mixtures, and commercial plastics, so we have used pyrolysis-gas chromatography (py-GC-MS) to create a new searchable library. First, we have increased the coverage of the existing libraries by including as many as possible commercially available PRC. Then, for testing the libraries and to deconvolute complex PRM mixtures, we have analyzed extractable and leachable (E&L) samples and pyrolysis products from one hundred standards of the most common polymers and some of their mixtures using LC-MS/MS, GC-MS, and py-GC-MS. In collaboration with the FDA, the EPA, and other non-government institutions, we are applying techniques, libraries, and tools to areas of interest to the circular economy of plastics, health risk assessments, and environmental challenges.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"439-445"},"PeriodicalIF":3.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142926192","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":"A Fast-Pass, Desorption Electrospray Ionization Mass Spectrometry Strategy for Untargeted Metabolic Phenotyping.","authors":"Hawkins S Shepard, Jody C May, Baltazar E Zuniga, Joshua P Abraham, Brian F Pfleger, Jamey D Young, John A McLean","doi":"10.1021/jasms.4c00459","DOIUrl":"10.1021/jasms.4c00459","url":null,"abstract":"<p><p>Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) provides direct analytical readouts of small molecules that can be used to characterize the metabolic phenotypes of genetically engineered bacteria. In an effort to accelerate the time frame associated with the screening of mutant libraries, we have developed a high-throughput DESI-MSI analytical workflow implementing a single raster line-scan strategy that facilitates the collection of location-resolved molecular information from engineered strains on a subminute time scale. Evaluation of this \"Fast-Pass\" DESI-MSI phenotyping workflow on analytical standards demonstrated the capability of acquiring full metabolic profiling information with a throughput of ∼40 s per sample. This Fast-Pass strategy was implemented in the analysis of genetically edited <i>Escherichia coli</i> strains that have been engineered to produce various free-fatty acids (FFAs) for applications relevant to biofuels. Due to the untargeted nature of DESI-MSI, the investigation of these strains yielded molecular information for both global metabolites and targeted detection of accumulated bioproducts, allowing simultaneous readouts of strain-specific chemical profiles and comparative measurements of FFA production levels.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"400-408"},"PeriodicalIF":3.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11808754/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143051148","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}

{"title":"Reactivity of [CpFe(CO)₂]⁺ with Nitrogen-Containing Heterocyclic Compounds in the Gas Phase: Ligand Exchange and Dehydrogenation.","authors":"Robert King, Allan J Canty, Richard A J O'Hair, Victor Ryzhov","doi":"10.1021/jasms.4c00437","DOIUrl":"https://doi.org/10.1021/jasms.4c00437","url":null,"abstract":"<p><p>A previous gas-phase study has uncovered formal catalytic cycles for the dehydrogenation of model liquid organic hydrogen carriers (LOHCs) pyrrolidine, <i>N</i>-methylpyrrolidine, and piperidine by the coordinatively unsaturated half-sandwich cyclopentadienyl iron cation, [CpFe]⁺. That work is extended here to the well-known condensed-phase [CpFe(CO)₂]⁺ cation, which was generated via electrospray ionization for gas-phase reactions with model LOHCs in a linear ion trap mass spectrometer, in which the helium bath gas was seeded with 0.1% carbon monoxide. The initial ion-molecule reaction (IMR) was exothermic enough to expel one CO molecule from the complex to form [CpFe(CO)L]⁺ (L = pyrrolidine, <i>N</i>-methylpyrrolidine, or piperidine). Collision-induced dissociation (CID) of these cations revealed two fragmentation pathways: (i) removal of another CO molecule leading to the species [CpFeL]⁺ that was studied previously; (ii) dehydrogenation of the ligand L (except for L= <i>N</i>-methylpyrrolidine). Two new formal catalytic cycles (for dehydrogenation of pyrrolidine and piperidine) were found that operate via a combination of IMR and CID experiments and which rely on the presence of CO for re-ligation of iron complexes. Density functional theory calculations were performed to compute the structures of all species observed as well as the reaction energetics.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 2","pages":"379-388"},"PeriodicalIF":3.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143187896","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":"Nextflow4MS-DIAL: A Reproducible Nextflow-Based Workflow for Liquid Chromatography-Mass Spectrometry Metabolomics Data Processing.","authors":"Xinsong Du, Amanda Dobrowolski, Mathias Brochhausen, Timothy J Garrett, William R Hogan, Dominick J Lemas","doi":"10.1021/jasms.4c00364","DOIUrl":"10.1021/jasms.4c00364","url":null,"abstract":"<p><p>Reproducibility in untargeted metabolomics data processing remains a significant challenge due to software limitations and the complex series of steps required. To address these issues, we developed Nextflow4MS-DIAL, a reproducible workflow for liquid chromatography-mass spectrometry (LC-MS) metabolomics data processing, validated with publicly available data from MetaboLights (MTBLS733). Nextflow4MS-DIAL automates LC-MS data processing to minimize human errors from manual data handling. The workflow supports software containerization, ensuring computational reproducibility and enabling collaborative research. Nextflow4MS-DIAL is compatible with any Unix-like system and supports multiple job schedulers, offering flexibility and ease of use. The Nextflow4MS-DIAL workflow is available under the permissive MIT license: https://github.com/Nextflow4Metabolomics/nextflow4ms-dial.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"433-438"},"PeriodicalIF":3.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142930356","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}