Journal of the American Society for Mass Spectrometry最新文献

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Imaging Mass Spectrometry of Sulfatide Isomers from Rat Brain Tissue Using Gas-Phase Charge Inversion Ion/Ion Reactions. 利用气相电荷反转离子/离子反应对大鼠脑组织中的硫化物异构体进行成像质谱分析
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-25 DOI: 10.1021/jasms.4c00368
Julia R Bonney, Ariana E Stratton, Yingchan Guo, Cabell B Eades, Boone M Prentice
{"title":"Imaging Mass Spectrometry of Sulfatide Isomers from Rat Brain Tissue Using Gas-Phase Charge Inversion Ion/Ion Reactions.","authors":"Julia R Bonney, Ariana E Stratton, Yingchan Guo, Cabell B Eades, Boone M Prentice","doi":"10.1021/jasms.4c00368","DOIUrl":"https://doi.org/10.1021/jasms.4c00368","url":null,"abstract":"<p><p>Sulfatides are abundant components of the brain, and dysregulation of these molecules has been linked to several diseases. In sulfatide structures, a sugar is linked to a sphingoid backbone via an α-glycosidic or β-glycosidic linkage. While sulfatides are readily generated in negative ion mode imaging mass spectrometry experiments, resolving sulfatide diastereomers is challenging; therefore, identifications are usually reported as a single sulfatide. Herein, a gas-phase charge inversion ion/ion reaction between sulfatides and a strontium tris-phenanthroline [Sr(Phen)<sub>3</sub>]<sup>2+</sup> reagent is performed to separate the diastereomers, as they form complexes containing different numbers of phenanthroline ligands. The ability to separate these diastereomers using the reaction alone, without the need for any further dissociation, allows for the workflow to be readily implemented in an imaging mass spectrometry experiment. Imaging mass spectrometry was performed on sulfatides generated directly from rat brain tissue, and both the α- and β-linked sulfatide images were obtained.</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":"142714943","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
Site-Specific Clustering of Bioactive Signaling Molecules Predicted In Situ by Space and Time Coherent Mapping for Imaging Mass Spectrometry. 通过成像质谱的时空相干图法预测生物活性信号分子的特定位点原位聚类。
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-24 DOI: 10.1021/jasms.4c00333
Jun Aoki, Masako Isokawa, Masahiro Ueda
{"title":"Site-Specific Clustering of Bioactive Signaling Molecules Predicted In Situ by Space and Time Coherent Mapping for Imaging Mass Spectrometry.","authors":"Jun Aoki, Masako Isokawa, Masahiro Ueda","doi":"10.1021/jasms.4c00333","DOIUrl":"https://doi.org/10.1021/jasms.4c00333","url":null,"abstract":"<p><p>Anatomical representation of site-specific clustering of biomolecules is a powerful way of predicting a potential interaction among signaling cascades and orchestrating molecular functions in cells and organs. The greater the number of molecules visualized simultaneously, the deeper we can understand each molecule's role in cellular metabolism and function. In the present study, we investigated site-specific localization of small biomolecules in the slug using Space and Time Coherent Mapping (STCM), a key technology in matrix-assisted laser desorption ionization time-of-flight imaging mass spectrometry. We acquired mass measurements and mass-based molecular images simultaneously under the microscope-mode instrumentation developed specifically in our laboratory. Mass images were generated in the increment of 0.2 in the mass-to-charge ratio (<i>m</i>/<i>z</i>) with spatial resolution of 2 μm. Resultant images were unique in each mass increment and allowed us to predict anatomical site-specific clustering of bioactive signaling molecules. We suggest that STCM is a useful tool to promote the compilation of comprehensive molecular maps and understand the role of individual molecules and their interactive mechanisms in situ.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142708745","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
Molecular Oxygen (O2) Artifacts in Tandem Mass Spectra. 串联质谱中的分子氧 (O2) 伪影。
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-22 DOI: 10.1021/jasms.4c00336
Yuxue Liang, Pedatsur Neta, Xiaoyu Yang, H Martin Garraffo, Tallat H Bukhari, Yi Liu, Stephen E Stein
{"title":"Molecular Oxygen (O<sub>2</sub>) Artifacts in Tandem Mass Spectra.","authors":"Yuxue Liang, Pedatsur Neta, Xiaoyu Yang, H Martin Garraffo, Tallat H Bukhari, Yi Liu, Stephen E Stein","doi":"10.1021/jasms.4c00336","DOIUrl":"https://doi.org/10.1021/jasms.4c00336","url":null,"abstract":"<p><p>Peak annotation plays an important role in mass spectral evaluation of the NIST 2023 tandem mass spectral library. While most fragment ions are formed by neutral losses, there are peaks that represent adduct ions from these fragments. Previously, we have reported two main types of addition reactions in the collision cell, namely addition of H<sub>2</sub>O and N<sub>2</sub>. Here we report a different reaction in the collision cell, with addition of O<sub>2</sub> leading to a small peak that could only be assigned to a peroxyl radical ion. For example, some protonated iodoaromatics lose an iodine atom to form a radical cation [M+H-I]<sup>+•</sup>, which reacts with O<sub>2</sub> to generate a peroxyl radical ion [M+H-I+O<sub>2</sub>]<sup>+•</sup>. Higher concentrations of O<sub>2</sub> result in higher peroxyl radical peaks, which become dominant while the precursor ions are consumed, as examined by five compounds under different concentrations of O<sub>2</sub>. The correlation of the peroxyl radical peak intensities to the concentration of O<sub>2</sub> provides a tool to estimate trace amounts of O<sub>2</sub> within the instrument. In the NIST 2023 tandem mass spectral library, the peaks for [M+H-X+O<sub>2</sub>]<sup>+·</sup> are most abundant in numbers and in intensity for X = NO<sub>2</sub> or I, are much less abundant for X = Br, and are rare for X = Cl. Other leaving groups in this library are SO<sub>3</sub>H, SO<sub>2</sub>NH<sub>2</sub>, CSNH<sub>2</sub>, CO<sub>2</sub>C<sub>6</sub>F<sub>5</sub>, SO<sub>2</sub>CH<sub>3</sub>, and COCH<sub>3</sub>. The O<sub>2</sub> addition reaction is also observed with negative ions in this library. While adducts of H<sub>2</sub>O and N<sub>2</sub> often constitute major peaks, the peaks of the peroxyl radicals under standard conditions are mostly very small and may be mistaken for noise, but their correct annotation improves the quality of the spectra and is important when comparing spectra from different instruments or conditions.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142685729","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
Hybrid Mass Spectrometry Applied across the Production of Antibody Biotherapeutics. 混合质谱法应用于抗体生物疗法的生产。
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-21 DOI: 10.1021/jasms.4c00253
Emilia Christofi, Mark O'Hanlon, Robin Curtis, Arghya Barman, Jeff Keen, Tibor Nagy, Perdita Barran
{"title":"Hybrid Mass Spectrometry Applied across the Production of Antibody Biotherapeutics.","authors":"Emilia Christofi, Mark O'Hanlon, Robin Curtis, Arghya Barman, Jeff Keen, Tibor Nagy, Perdita Barran","doi":"10.1021/jasms.4c00253","DOIUrl":"https://doi.org/10.1021/jasms.4c00253","url":null,"abstract":"<p><p>Post expression from the host cells, biotherapeutics undergo downstream processing steps before final formulation. Mass spectrometry and biophysical characterization methods are valuable for examining conformational and stoichiometric changes at these stages, although typically not used in biomanufacturing, where stability is assessed via bulk property studies. Here we apply hybrid MS methods to understand how solution condition changes impact the structural integrity of a biopharmaceutical across the processing pipeline. As an exemplar product, we use the model IgG1 antibody, mAb4. Flexibility, stability, aggregation propensity, and bulk properties are evaluated in relation to perfusion media, purification stages, and formulation solutions. Comparisons with Herceptin, an extensively studied IgG1 antibody, were conducted in a mass spectrometry-compatible solution. Despite presenting similar charge state distributions (CSD) in native MS, mAb4, and Herceptin show distinct unfolding patterns in activated ion mobility mass spectrometry (aIM-MS) and differential scanning fluorimetry (DSF). Herceptin's greater structural stability and aggregation onset temperature (<i>T</i><sub>agg</sub>) are attributed to heavier glycosylation and kappa-class light chains, unlike the lambda-class light chains in mAb4. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) revealed that mAb4 undergoes substantial structural changes during purification, marked by high flexibility, low melting temperature (Tm), and prevalent repulsive protein-protein interactions but transitions to a compact and stable structure in high-salt and formulated environments. Notably, in formulation, the third constant domain (CH3) of the heavy chain retains flexibility and is a region of interest for aggregation. Future work could translate features of interest from comprehensive studies like this to targeted approaches that could be utilized early in the development stage to aid in decision-making regarding targeted mutations or to guide the design space of bioprocesses and formulation choices.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142685728","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
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-21 DOI: 10.1021/jasms.4c0030610.1021/jasms.4c00306
Robert L. Rider, Carter Lantz, Liqi Fan and David H. Russell*, 
{"title":"Structure and Stabilities of Solution and Gas Phase Protein Complexes","authors":"Robert L. Rider,&nbsp;Carter Lantz,&nbsp;Liqi Fan and David H. Russell*,&nbsp;","doi":"10.1021/jasms.4c0030610.1021/jasms.4c00306","DOIUrl":"https://doi.org/10.1021/jasms.4c00306https://doi.org/10.1021/jasms.4c00306","url":null,"abstract":"<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":"35 12","pages":"3028–3036 3028–3036"},"PeriodicalIF":3.1,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/jasms.4c00306","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142761118","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
Systematic Optimization of Activity-Based Protein Profiling for Identification of Polysorbate-Degradative Enzymes in Biotherapeutic Drug Substance down to 10 ppb
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-21 DOI: 10.1021/jasms.4c0038710.1021/jasms.4c00387
Taku Tsukidate, Anita P. Liu, Shannon Rivera, Alyssa Q. Stiving, Jonathan Welch and Xuanwen Li*, 
{"title":"Systematic Optimization of Activity-Based Protein Profiling for Identification of Polysorbate-Degradative Enzymes in Biotherapeutic Drug Substance down to 10 ppb","authors":"Taku Tsukidate,&nbsp;Anita P. Liu,&nbsp;Shannon Rivera,&nbsp;Alyssa Q. Stiving,&nbsp;Jonathan Welch and Xuanwen Li*,&nbsp;","doi":"10.1021/jasms.4c0038710.1021/jasms.4c00387","DOIUrl":"https://doi.org/10.1021/jasms.4c00387https://doi.org/10.1021/jasms.4c00387","url":null,"abstract":"<p >The identification and control of high-risk host cell proteins (HCPs) in biotherapeutics development are crucial for ensuring product quality and shelf life. Specifically, HCPs with hydrolase activity can cause the degradation of excipient polysorbates (PS), leading to a decrease in the shelf life of the drug product. In this study, we systematically optimized every step of an activity-based protein profiling (ABPP) workflow to identify trace amounts of active polysorbate-degradative enzymes (PSDEs) in biotherapeutic process intermediates. Evaluation of various parameters during sample preparation pinpointed the optimal pH level and fluorophosphonate (FP)-biotin concentration. Moreover, the combined use of a short liquid chromatography gradient and the fast-scanning parallel accumulation–serial fragmentation (PASEF) methodology increased sample throughput without compromising identification coverage. Tuning the trapped ion mobility spectrometry (TIMS) parameters further enhanced sensitivity. In addition, we evaluated various data acquisition modes, including PASEF combined with data-dependent acquisition (DDA PASEF), data-independent acquisition (diaPASEF), or parallel reaction monitoring (prm-PASEF). By employing the newly optimized ABPP workflow, we successfully identified PSDEs at a concentration as low as 10 ppb in a drug substance sample. Finally, the new workflow enabled us to detect a PSDE that could not be detected with the original workflow during a PS degradation root-cause investigation.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"35 12","pages":"3256–3264 3256–3264"},"PeriodicalIF":3.1,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142760995","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
Subcellular Proteomic Mapping of Lysine Lactylation
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-21 DOI: 10.1021/jasms.4c0036610.1021/jasms.4c00366
Qiuyu Bao, Ning Wan*, Zimeng He, Ji Cao, Wenjie Yuan, Haiping Hao* and Hui Ye*, 
{"title":"Subcellular Proteomic Mapping of Lysine Lactylation","authors":"Qiuyu Bao,&nbsp;Ning Wan*,&nbsp;Zimeng He,&nbsp;Ji Cao,&nbsp;Wenjie Yuan,&nbsp;Haiping Hao* and Hui Ye*,&nbsp;","doi":"10.1021/jasms.4c0036610.1021/jasms.4c00366","DOIUrl":"https://doi.org/10.1021/jasms.4c00366https://doi.org/10.1021/jasms.4c00366","url":null,"abstract":"<p >Protein lactylation is a novel post-translational modification (PTM) involved in many important physiological processes such as macrophage polarization, immune regulation, and tumor cell growth. However, traditional methodologies for studying lactylation have predominantly relied on peptide enrichment from whole-cell lysates, which tend to favor the detection of high-abundance peptides, thus limiting the identification of low-abundance lactylated peptides. To address this limitation, here, we employed subcellular fractionation to separate proteins and map lactylated peptides from each isolated subcellular fraction using a model cell line. In brief, we identified 1,217 lysine lactylation (Kla) sites on 553 proteins across four subcellular fractions. Subsequent pathway enrichment analysis revealed that Kla proteins participate in distinct pathways depending on the subcellular contexts. In addition, this subcellular fractionation method enabled the discovery of 36 previously unreported Kla proteins and 223 novel Kla sites, many of which are present in low abundance. Notably, several proteins contain multiple newly identified Kla sites, exemplified by the transcriptional regulator ATRX. Furthermore, our results indicate the possibility of PTM crosstalk between Kla and other PTMs such as ubiquitination and sumoylation. In conclusion, subcellular fractionation facilitates the identification of Kla proteins that have been previously uncovered and could be overlooked by affinity enrichment of whole-cell lysates.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"35 12","pages":"3221–3232 3221–3232"},"PeriodicalIF":3.1,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142760997","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
Enrichable Protein Footprinting for Structural Proteomics
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-20 DOI: 10.1021/jasms.4c0036210.1021/jasms.4c00362
Jamison D. Wolfer, Benjamin B. Minkoff, Heather L. Burch and Michael R. Sussman*, 
{"title":"Enrichable Protein Footprinting for Structural Proteomics","authors":"Jamison D. Wolfer,&nbsp;Benjamin B. Minkoff,&nbsp;Heather L. Burch and Michael R. Sussman*,&nbsp;","doi":"10.1021/jasms.4c0036210.1021/jasms.4c00362","DOIUrl":"https://doi.org/10.1021/jasms.4c00362https://doi.org/10.1021/jasms.4c00362","url":null,"abstract":"<p >Protein footprinting is a useful method for studying protein higher order structure and conformational changes induced by interactions with various ligands via addition of covalent modifications onto the protein. Compared to other methods that provide single amino acid-level structural resolution, such as cryo-EM, X-ray diffraction, and NMR, mass spectrometry (MS)-based methods can be advantageous as they require lower protein amounts and purity. As with other MS-based proteomic methods, such as post-translational modification analysis, enrichment techniques have proven necessary for both optimal sensitivity and sequence coverage when analyzing highly complex proteomes. Currently used reagents for footprinting via covalent labeling, such as hydroxyl radicals and carbodiimide-based methods, do not yet have a suitable enrichment method, limiting their applicability to whole proteome analysis. Here, we report a method for enrichable covalent labeling built upon the GEE/EDC system commonly used to covalently label aspartic acid and glutamic acid residues. Novel labeling reagents containing alkynyl functionality can be “clicked” to any azido-containing molecule with copper-catalyzed azide–alkyne cycloaddition (CuAAC), allowing for enrichment or further labeling. Multiple azide- and alkyne-containing GEE-like molecules were tested, and the most efficient method was determined to be the EDC-facilitated coupling of glycine propargyl amide (GPA) to proteins. The pipeline we report includes clicking via CuAAC to a commercially available biotin-azide containing a photocleavable linker, followed by enrichment using a streptavidin resin and subsequent cleavage under ultraviolet light. The enrichment process was optimized through the screening of clickable amines, coupling reagents, and enrichment scaffolds and methods with pure model proteins and has also been applied to complex mixtures of proteins isolated from the model plant, <i>Arabidopsis thaliana</i>, suggesting that our method may ultimately be used to measure protein conformation on a proteomic scale.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"35 12","pages":"3192–3202 3192–3202"},"PeriodicalIF":3.1,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142760961","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
Automated Single Cell Phenotyping of Time-of-Flight Secondary Ion Mass Spectrometry Tissue Images
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-19 DOI: 10.1021/jasms.4c0032810.1021/jasms.4c00328
Sweta Bajaj, Spencer Tolleson, Aida Zarfeshani, Monirath Hav, Sean C. Pawlowski, Danielle E. Lyons, Raghav Padmanabhan, Jay G. Tarolli and Máté Levente Nagy*, 
{"title":"Automated Single Cell Phenotyping of Time-of-Flight Secondary Ion Mass Spectrometry Tissue Images","authors":"Sweta Bajaj,&nbsp;Spencer Tolleson,&nbsp;Aida Zarfeshani,&nbsp;Monirath Hav,&nbsp;Sean C. Pawlowski,&nbsp;Danielle E. Lyons,&nbsp;Raghav Padmanabhan,&nbsp;Jay G. Tarolli and Máté Levente Nagy*,&nbsp;","doi":"10.1021/jasms.4c0032810.1021/jasms.4c00328","DOIUrl":"https://doi.org/10.1021/jasms.4c00328https://doi.org/10.1021/jasms.4c00328","url":null,"abstract":"<p >Existing analytical techniques are being improved or applied in new ways to profile the tissue microenvironment (TME) to better understand the role of cells in disease research. Fully understanding the complex interactions between cells of many different types and functions is often slowed by the intense data analysis required. Multiplexed Ion Beam Imaging (MIBI) has been developed to simultaneously characterize 50+ cell types and their functions within the TME with a subcellular spatial resolution, but this results in complex data sets that are challenging to qualitatively analyze. Deep Learning (DL) techniques were used to build the MIBIsight workflow, which can process images containing thousands of cells into easily digestible reports and plots to enable researchers to easily summarize data sets in a study and make informed conclusions. Here we present the three types of DL models that have been trained with annotated MIBI images that have been pathologist validated as well as the associated workflow for the evolution of raw mass spectral data into actionable reports and plots.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"35 12","pages":"3126–3134 3126–3134"},"PeriodicalIF":3.1,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142761348","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
Impact of Hydrothermal Fluids on Hydrocarbon Generation and Solid Bitumen Formation in the Kongdian Formation, Huanghua Depression, China
IF 3.1 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2024-11-18 DOI: 10.1021/jasms.4c0040310.1021/jasms.4c00403
Yufu Han, Yuanjia Han, Li Wang, Dietrich A. Volmer and Yulin Qi*, 
{"title":"Impact of Hydrothermal Fluids on Hydrocarbon Generation and Solid Bitumen Formation in the Kongdian Formation, Huanghua Depression, China","authors":"Yufu Han,&nbsp;Yuanjia Han,&nbsp;Li Wang,&nbsp;Dietrich A. Volmer and Yulin Qi*,&nbsp;","doi":"10.1021/jasms.4c0040310.1021/jasms.4c00403","DOIUrl":"https://doi.org/10.1021/jasms.4c00403https://doi.org/10.1021/jasms.4c00403","url":null,"abstract":"<p >Hydrothermal fluid plays a crucial role in the generation and migration of hydrocarbons within sedimentary basins. Herein, we employed bulk analysis and high-resolution mass spectrometry techniques to investigate the transformation dynamics from source rock to hydrocarbons under conditions influenced by magmatic activities in the Kongdian Formation, Huanghua Depression, China. The results revealed that hydrocarbon generation in the Ek<sub>2</sub> shale of the study area was significantly influenced by abnormal heating from hydrothermal fluids. High temperatures associated with these fluids accelerated the conversion of organic matter within source rocks, enhancing hydrocarbon generation rates. Subsequently, the hydrocarbons migrated into fracture networks, where they solidified as low-reflectance solid bitumen, forming trapped fractures of pyrobitumen and authigenic mineral aggregates leached from thermal fluid. High aliphatic fractions were noted in the source rock extracts, while extracts from low-reflectance solid bitumen exhibited higher aromatic fraction. Aliphatic and aromatic compounds in extracts from both the low-reflectance solid bitumen and the source rock exhibited similar maturities and origins. Regarding polar compounds, the compound classes O<sub>1</sub>, O<sub>2</sub>, N<sub>1</sub>O<sub>1</sub>, and N<sub>1</sub>O<sub>2</sub> showed higher abundances in source rock extracts compared to those in low-reflectance solid bitumen, while the S<sub>1</sub> and N<sub>1</sub> classes showed the opposite trend. Thus, fractionation clearly occurs when hydrocarbons expelled from source rocks by thermal fluids solidify into low-reflectance solid bitumen. This unique study provides valuable insights into understanding the fate of hydrocarbons originating from source rocks heated by thermal fluids, and explores the potential for unconventional oil in regions with intense hydrothermal alteration.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"35 12","pages":"3274–3285 3274–3285"},"PeriodicalIF":3.1,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142761228","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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