Journal of the American Society for Mass Spectrometry最新文献

{"title":"Monitoring Epoxidized Soybean Oil Degradation Using Liquid Chromatography-Mass Spectrometry and <i>In Silico</i> Spectral Libraries.","authors":"Paul D Hutchins, Camila A Saez Cabezas, Joshua S Enokida, Yushan Hu, Yuming Lai, Victoria Mazure, Marie Martin, Kelly Setula, John R Stutzman, James H Wade","doi":"10.1021/jasms.4c00212","DOIUrl":"10.1021/jasms.4c00212","url":null,"abstract":"<p><p>Epoxidized soybean oil (ESO) is routinely used as a bioderived plasticizer and stabilizer in polyvinyl chloride (PVC), as it prolongs material integrity during dehydrochlorination. During this process, the epoxide moieties of ESO are progressively converted to chlorohydrins, which amplify ESO's inherent structural complexity. Past characterization efforts utilized separation-mass spectrometry (MS) analysis of the hydrolyzed acyl chains to simplify the complexity. However, this approach significantly increases the complexity of sample preparation and cannot directly monitor the chlorination of individual ESO species during aging. Here, we present a comprehensive LC-MS/MS data acquisition and <i>in silico</i> spectral library identification workflow optimized for intact ESO byproduct analysis. Detailed MS/MS fragmentation rules derived from synthesized standards were coupled with improved fragment ion intensity modeling capabilities to generate a high-fidelity spectral library for rapid ESO byproduct identification. Identification confidence was further bolstered by using retention time modeling to filter spurious MS/MS matches. Finally, we paired this informatic approach with an optimized extraction procedure and reversed-phase separation to generate a detailed timeline of more than 400 ESO species and byproducts during PVC thermal aging. These developments significantly improve our ability to detect, characterize, and understand ESO degradation in complex PVC formulations with new levels of molecular resolution.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141750808","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":"Exploring Ion Mobility Mass Spectrometry Data File Conversions to Leverage Existing Tools and Enable New Workflows.","authors":"Sarah M Stow, Bryson C Gibbons, Leonard C Rorrer Iii, Lauren Royer, Rebecca S Glaskin, Gordon W Slysz, Ruwan T Kurulugama, John C Fjeldsted, Daniel DeBord, Aivett Bilbao","doi":"10.1021/jasms.4c00220","DOIUrl":"10.1021/jasms.4c00220","url":null,"abstract":"<p><p>Ion mobility (IM) is often combined with LC-MS experiments to provide an additional dimension of separation for complex sample analysis. While highly complex samples are better characterized by the full dimensionality of LC-IM-MS experiments to uncover new information, downstream data analysis workflows are often not equipped to properly mine the additional IM dimension. For many samples the data acquisition benefits of including IM separations are all that is necessary to uncover sample information and the full dimensionality of the data is not required for data analysis. Postacquisition reduction and adaptation of the dimensions of LC-IM-MS and IM-MS experiments into an LC-MS format opens the possibility to use a plethora of existing software tools. In this work, we developed data file conversion tools to reduce the complexity of IM data analysis. Three data file transformations are introduced in the PNNL PreProcessor software: (1) mapping the IM axis to the LC axis for IM-MS data, (2) converting the drift time vs <i>m</i>/<i>z</i> space to CCS/z vs <i>m</i>/<i>z</i> space, and (3) transforming All Ions IM/MS mobility aligned fragmentation data to a standard LC-MS DDA data file format. These new data file conversions are demonstrated with corresponding lipidomics and proteomics workflows that leverage existing LC-MS data analysis software to highlight the benefits of the data transformations.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141756490","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":"Cool Classical EI - A New Standard in EI and Its Many Benefits.","authors":"Benny Neumark, Oneg Elkabets, Aviv Amirav","doi":"10.1021/jasms.4c00265","DOIUrl":"10.1021/jasms.4c00265","url":null,"abstract":"<p><p>GC-MS with Cold EI improves all of the central GC-MS performance aspects, but it is known mostly for its provision of enhanced molecular ions. This occasionally leads to the misconception that, like chemical ionization, Cold EI is a supplementary ion source to standard EI. However, Cold EI is a highly superior replacement ion source to standard EI. While Cold EI mass spectra are the most informative and fully compatible with mass spectral library (such as NIST) identification, in some cases, the Cold EI mass spectra with their enhanced molecular ions result in a \"picture\" that is not as one is used to seeing. In this paper, we describe the \"Cool Classical EI\" mode, which produces classical EI mass spectra like standard EI. The change of Cold EI into the Cool Classical EI mode is software-based, requires no hardware change, and can be achieved even during the analysis. Several mass spectra that were obtained in the Cool Classical EI mode are presented and compared with standard EI and Cold EI mass spectra. In this paper we further demonstrate and discuss several benefits that Cold EI brings that are retained while using Cool Classical EI, including (a) much faster speed of analysis, (b) uniform response, (c) extended range of compounds amenable for analysis, (d) improved sample identification, (e) elimination of ion source related peak tailing, (f) elimination of intraion-source degradation, and (g) better signal-to-noise ratio of the sample compounds.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11311530/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141756489","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":"Selective Profiling of Carboxylic Acid in Crude Oil by Halogen Labeling Combined with Liquid Chromatography and High-Resolution Mass Spectrometry.","authors":"Khoa Huynh, Karen Louise Feilberg, Jonas Sundberg","doi":"10.1021/jasms.4c00085","DOIUrl":"10.1021/jasms.4c00085","url":null,"abstract":"<p><p>Carboxylic acids are a small but essential compound class within petroleum chemistry, influencing crude oil behaviors in production and processing and causing environmental impacts. Detailed structural information is fundamental to understanding their influence on petroleum characteristics. However, characterizing acids in crude oil remains challenging due to matrix effects, structural diversity, and low abundance. In this work, we present a new methodology for profiling carboxylic acids by liquid-liquid extraction and selective derivatization using 4-bromo-<i>N</i>-methylbenzylamine (4-BNMA) followed by liquid chromatography and electrospray ionization Orbitrap mass spectrometry (LC-ESI-Orbitrap MS). The fragmentation of 4-BNMA derivatives produces a unique product ion pair, <i>m</i>/<i>z</i> 169/171, enabling the identification of chromatographic fractions containing carboxylic acids. The mass spectra of the corresponding fractions are extracted, and the acids are further computationally isolated based on the isotopic pattern. The method was optimized and validated using acid standards and systematic experimental designs, assuring robustness and sensitivity for nontarget screening purposes. This method detected up to 380 carboxylic acids in six Danish North Sea crude oils, with up to two carboxyl and other heteroatom functionalities (NSO). The results indicated that the most populated species are fatty acids (double bond equivalent (DBE) = 1) and small aromatic acids (DBE = 2-6). The predominance and diversities of compound classes in different samples are consistent with their corresponding bulk properties. Polyfunctional acids (O_<i>x</i>, N_<i>x</i>O_<i>x</i>, and S_<i>x</i>O_<i>x</i>) were observed due to exposure to oxidation and biodegradation. Also, the approach's applicability benefits high-resolution MS analysis by simplifying data processing for crude oil and potentially other high-organic and aqueous samples.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141562341","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":"Water Plays Key Roles in Stabilities of Wild Type and Mutant Transthyretin Complexes.","authors":"Carter Lantz, Robert L Rider, Sangho D Yun, Arthur Laganowsky, David H Russell","doi":"10.1021/jasms.4c00170","DOIUrl":"10.1021/jasms.4c00170","url":null,"abstract":"<p><p>Transthyretin (TTR), a 56 kDa homotetramer that is involved in the transport of thyroxine and retinol, has been linked to amyloidosis through disassembly of tetramers to form monomers, dimers, and trimers that then reassemble into higher order oligomers and/or fibrils. Hybrid TTR (hTTR) tetramers are found in heterozygous individuals that express both wild type TTR (wt-TTR) and mutant TTR (mTTR) forms of the protein, and these states display increased rates of amyloidosis. Here we monitor subunit exchange (SUE) reactions involving homomeric and mixed tetramers using high resolution native mass spectrometry (nMS). Our results show evidence that differences in TTR primary structure alter tetramer stabilities, and hTTR products can form spontaneously by SUE reactions. In addition, we find that solution temperature has strong effects on TTR tetramer stabilities and formation of SUE products. Lower temperatures promote formation of hTTR tetramers containing L55P and V30M subunits, whereas small effects on the formation of hTTR tetramers containing F87A and T119M subunits are observed. We hypothesize that the observed temperature dependent stabilities and subsequent SUE behavior are a result of perturbations to the network of \"two kinds of water\": hydrating and structure stabilizing water molecules (Spyrakis et al. <i>J. Med. Chem.</i> 2017, 60 (16), 6781-6827; Xu et al. <i>Soft Matter</i> 2012, 8, 324-336) that stabilize wt-TTR and mTTR tetramers. The results presented in this work illustrate the utility of high resolution nMS for studies of the structures, stabilities, and dynamics of protein complexes that directly influence SUE reactions.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11311534/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141756477","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":"An Agile and Accurate Approach for N-Nitrosamines Detection and Quantification in Medicines by DART-MS.","authors":"Almir Custodio Batista Junior, Ricardo Alves Bernardo, Yuri Arrates Rocha, Boniek Gontijo Vaz, Marc Yves Chalom, Antônio Celso Jardim, Andréa Rodrigues Chaves","doi":"10.1021/jasms.4c00012","DOIUrl":"10.1021/jasms.4c00012","url":null,"abstract":"<p><p>N-nitrosamines (NAs) are prevalent mutagenic impurities in various consumer products. Their discovery in valsartan-containing medicines in 2018 prompted global regulatory agencies to set guidelines on their presence and permissible levels in pharmaceuticals. In order to determine the NAs content in medicines, efficient and sensitive analytical methods have been developed based on mass spectrometry techniques. Direct analysis in real time-mass spectrometry (DART-MS) has emerged as a prominent ambient ionization technique for pharmaceutical analysis due to its high-throughput capability, simplicity, and minimal sample preparation requirements. Thus, in this study DART-MS was evaluated for the screening and quantification of NAs in medicines. DART-MS analyses were conducted in positive ion mode, for both direct tablet analysis and solution analysis. The analytical performance was evaluated regarding linearity, precision, accuracy, limits of detection, and quantification. The DART-MS proved to be suitable for the determination of NAs in medicines, whether through direct tablet analysis or solution analysis. The analytical performance demonstrated linearity in the range from 1.00 to 200.00 ng mL^-1, limits of quantification about 1.00 ng mL^-1, precision and accuracy lower than 15%, and no significant matrix effect for six drug-related NAs. In conclusion, the DART-MS technique demonstrated to be an alternative method to determine NAs in medicines, aligning with the principles of green chemistry.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140875515","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":"Enhancing Spatial Resolution in Tandem Mass Spectrometry Ion/Ion Reaction Imaging Experiments through Image Fusion.","authors":"Zhongling Liang, Yingchan Guo, Xizheng Diao, Boone M Prentice","doi":"10.1021/jasms.4c00144","DOIUrl":"10.1021/jasms.4c00144","url":null,"abstract":"<p><p>We have recently developed a charge inversion ion/ion reaction to selectively derivatize phosphatidylserine lipids via gas-phase Schiff base formation. This tandem mass spectrometry (MS/MS) workflow enables the separation and detection of isobaric lipids in imaging mass spectrometry, but the images acquired using this workflow are limited to relatively poor spatial resolutions due to the current time and limit of detection requirements for these ion/ion reaction imaging mass spectrometry experiments. This trade-off between chemical specificity and spatial resolution can be overcome by using computational image fusion, which combines complementary information from multiple images. Herein, we demonstrate a proof-of-concept workflow that fuses a low spatial resolution (i.e., 125 μm) ion/ion reaction product ion image with higher spatial resolution (i.e., 25 μm) ion images from a full scan experiment performed using the same tissue section, which results in a predicted ion/ion reaction product ion image with a 5-fold improvement in spatial resolution. Linear regression, random forest regression, and two-dimensional convolutional neural network (2-D CNN) predictive models were tested for this workflow. Linear regression and 2D CNN models proved optimal for predicted ion/ion images of PS 40:6 and SHexCer d38:1, respectively.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490437","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":"Exploiting Differential Signal Filtering (DSF) and Image Structure Filtering (ISF) Methods for Untargeted Mass Spectrometry Imaging of Bacterial Metabolites.","authors":"Pierre Burguet, Raphaël La Rocca, Christopher Kune, Déborah Tellatin, Nudzejma Stulanovic, Augustin Rigolet, Johann Far, Marc Ongena, Sébastien Rigali, Loïc Quinton","doi":"10.1021/jasms.4c00129","DOIUrl":"10.1021/jasms.4c00129","url":null,"abstract":"<p><p>Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) is a label-free technique, producing images where pixels contain mass spectra. The technique allows the visualization of the spatial distribution of (bio)molecules from metabolites to proteins, on surfaces such as tissues sections or bacteria culture media. One particularly exciting example of MALDI-MSI use rests on its potential to localize ionized compounds produced during microbial interactions and chemical communication, offering a molecular snapshot of metabolomes at a given time. The huge size and the complexity of generated MSI data make the processing of the data challenging, which requires the use of computational methods. Despite recent advances, currently available commercial software relies mainly on statistical tools to identify patterns, similarities, and differences within data sets. However, grouping <i>m</i>/<i>z</i> values unique to a given data set according to microbiological contexts, such as coculture experiments, still requires tedious manual analysis. Here we propose a nontargeted method exploiting the differential signals between negative controls and tested experimental conditions, i.e., differential signal filtering (DSF), and a scoring of the ion images using image structure filtering (ISF) coupled with a fold change score between the controls and the conditions of interest. These methods were first applied to coculture experiments involving <i>Escherichia coli</i> and <i>Streptomyces coelicolor</i>, revealing specific MS signals during bacterial interaction. Two case studies were also investigated: (i) cellobiose-mediated induction for the pathogenicity of <i>Streptomyces scabiei</i>, the causative agent of common scab on root and tuber crops, and (ii) iron-repressed production of siderophores of <i>S. scabiei</i>. This report proposes guidelines for MALDI-MSI data treatment applied in the case of microbiology contexts, with enhanced ion peak annotation in specific culture conditions. The strengths and weaknesses of the methods are discussed.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141615601","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":"Compaction, Relaxation, and Linearization of Megadalton-Sized DNA Plasmids: DNA Structures Probed by CD-MS.","authors":"Lohra M Miller, Luke Hawkins, Martin F Jarrold","doi":"10.1021/jasms.4c00222","DOIUrl":"10.1021/jasms.4c00222","url":null,"abstract":"<p><p>High purity plasmid DNA is a raw material for recombinant protein production as well as an active ingredient in DNA vaccines. There are four primary plasmid structures that can be observed in a typical plasmid formulation: supercoiled, relaxed (circular), linearized, and condensed. Determining what structures are present in a sample is important, as the structure can affect activity; the supercoiled structure has the highest activity, and >90% supercoiled is desired for industry standards. Recently, charge detection mass spectrometry (CD-MS) was used to distinguish two of the structures, supercoiled and condensed, by measuring the charge deposited on the ions by positive mode electrospray. Here, CD-MS is used to probe the structures of DNA plasmids during compaction with polycations, and through enzymatic treatment to relax and linearize plasmids. We find that all four structural types for plasmid DNA have unique charging profiles that can be distinguished using CD-MS. The extent of mechanical shearing of the DNA plasmids during electrospray is strongly influenced by the structural type.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141625558","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":"Automated Identification of Ions Observed in Mass Spectra of Inorganic Compounds Using Isotopic Distribution Brute Force: Methodology and Performance Measurements.","authors":"Viacheslav V Lebedev, Daniil I Yarykin, Aleksey K Buryak","doi":"10.1021/jasms.4c00153","DOIUrl":"10.1021/jasms.4c00153","url":null,"abstract":"<p><p>This Article describes the method of isotopic distribution brute force, which can be used to identify ions registered in mass spectra of inorganic compounds in an automated manner when a library search cannot be conducted. A detailed description of the isotopic distribution brute force methodology is presented, including a discussion of computation-related difficulties. The ability of the proposed algorithm to identify various inorganic ions is tested on a small set of real-life low-resolution mass spectra of lead halides and copper halides. An evaluation of the isotopic distribution brute force performance is conducted using the low-resolution experimental mass spectra of natural rhenium sulfide and lead(II) chloride. Based on identification results and obtained performance measurements, we formulate the empirical restrictions on the input data, ensuring that the application of isotopic distribution brute force is feasible from the standpoints of search space reduction and identification time.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141747083","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}