Journal of Proteome Research最新文献_第2页

Technical Considerations for Detecting Protein–Protein Interactions Using Proximity Ligation Assay 使用接近结扎法检测蛋白质相互作用的技术考虑

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-11 DOI: 10.1021/acs.jproteome.4c0085510.1021/acs.jproteome.4c00855

Zach Tower, and , Hao Chang*,

引用次数: 0

Online Alkaline-pH Reversed-Phase Nanoelectrospray-Tandem Mass Spectrometry Complements Traditional Phosphoproteomic Analysis via Influencing Charge State Distribution of Phosphopeptides 在线碱性- ph反相纳米电喷雾串联质谱法通过影响磷酸肽的电荷态分布来补充传统的磷酸蛋白质组学分析

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-10 DOI: 10.1021/acs.jproteome.4c0109110.1021/acs.jproteome.4c01091

Yuqiu Wang, Jing Gao, Wenfan Xie, Minchu Tang, Xin Chen, Lv Chen, Hongxu Chen, Zhicheng Yang, Qiang Gao, Yansheng Liu* and Hu Zhou*,

{"title":"Online Alkaline-pH Reversed-Phase Nanoelectrospray-Tandem Mass Spectrometry Complements Traditional Phosphoproteomic Analysis via Influencing Charge State Distribution of Phosphopeptides","authors":"Yuqiu Wang, Jing Gao, Wenfan Xie, Minchu Tang, Xin Chen, Lv Chen, Hongxu Chen, Zhicheng Yang, Qiang Gao, Yansheng Liu* and Hu Zhou*, ","doi":"10.1021/acs.jproteome.4c0109110.1021/acs.jproteome.4c01091","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01091https://doi.org/10.1021/acs.jproteome.4c01091","url":null,"abstract":"Phosphorylation (O-linked and N-linked) plays an important role in biological functions and cell signaling. Here, we employed a one-dimensional online alkaline-pH reversed-phase nanoelectrospray-tandem mass spectrometry (alkaline-pH-MS/MS) for the investigation of global phosphorylation. In this method, phosphopeptides were separated on a nanoflow C18 column with an alkaline-pH gradient and directly introduced to the mass spectrometer through nanoelectrospray ionization. Although the phosphosites and phosphopeptides identified by alkaline-pH-MS/MS were slightly lower than those of traditional online low-pH reversed-phase tandem MS (low-pH-MS/MS), these two methods were highly complementary to each other. This alkaline-pH-MS/MS may affect the actual polarity and CSD of phosphopeptides, consequently improving the identification of multiply phosphorylated peptides. Moreover, alkaline-pH-MS/MS was compatible with other peptide fractionation and phosphopeptide enrichment techniques, such as offline high-pH or low-pH reversed-phase liquid chromatography fractionation. The complementarity of alkaline-pH-MS/MS and low-pH-MS/MS was further demonstrated by the tandem mass tag (TMT)-based quantitative phosphoproteomic analysis of five pairs of hepatocellular carcinoma (HCC) tumors and normal adjacent tissues (NATs). Furthermore, unique information on significantly changed phosphosites was observed by alkaline-pH-MS/MS. This study provided an alternative and complementary tool for global analysis of both O- and N-phosphoproteome, which may be beneficial for the discovery of phosphoproteins with significant biological functions.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 5","pages":"2443–2453 2443–2453"},"PeriodicalIF":3.8,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143894080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proteomic Insights into the Adaptation of Acidithiobacillus ferridurans to Municipal Solid Waste Incineration Residues for Enhanced Bioleaching Efficiency. 酸性铁硫杆菌适应城市生活垃圾焚烧残渣以提高生物浸出效率的蛋白质组学研究。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-09 DOI: 10.1021/acs.jproteome.4c00527

Jiri Kucera, Klemens Kremser, Pavel Bouchal, David Potesil, Tomas Vaculovic, Dalibor Vsiansky, Georg M Guebitz, Martin Mandl

{"title":"Proteomic Insights into the Adaptation of Acidithiobacillus ferridurans to Municipal Solid Waste Incineration Residues for Enhanced Bioleaching Efficiency.","authors":"Jiri Kucera, Klemens Kremser, Pavel Bouchal, David Potesil, Tomas Vaculovic, Dalibor Vsiansky, Georg M Guebitz, Martin Mandl","doi":"10.1021/acs.jproteome.4c00527","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00527","url":null,"abstract":"Acidithiobacillus spp. have traditionally been utilized to extract metals from mineral ores through bioleaching. This process has recently expanded to include artificial ores, such as those derived from municipal solid waste incineration (MSWI) residues. Previous studies have indicated that microbial adaptation enhances bioleaching efficiency, prompting this study to identify proteins involved in the adaptation of A. ferridurans to MSWI residues. We employed data-independent acquisition-parallel accumulation serial fragmentation to determine the proteomic response of A. ferridurans DSM 583 to three distinct materials: bottom ash (BA), kettle ash (KA), and filter ash (FA), which represent typical MSWI residues. Our findings indicate that, irrespective of the residue type, a suite of membrane transporters, porins, efflux pumps, and specific electron and cation transfer proteins was notably upregulated. The upregulation of certain proteins involved in anaerobic pathways suggested the development of a spontaneous microaerobic environment, which minimally impacted the bioleaching efficiency. Additionally, the adaptation was most efficient at half the target FA concentration, marked by a significant increase in the detoxification and efflux systems required by microorganisms to tolerate high heavy metal concentrations. Given that metal recovery peaked at lower FA concentrations for most metals of interest, further adaptation at the level of protein expression may not be warranted for improved bioleaching outcomes.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","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 Static Myoblast Loading on Protein Secretion Linked to Tenocyte Migration. 静态肌母细胞负载对与小细胞迁移相关的蛋白质分泌的影响。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-09 DOI: 10.1021/acs.jproteome.5c00068

Junhong Li, Xin Zhou, Jialin Chen, Shaochun Zhu, Andre Mateus, Pernilla Eliasson, Paul J Kingham, Ludvig J Backman

{"title":"Impact of Static Myoblast Loading on Protein Secretion Linked to Tenocyte Migration.","authors":"Junhong Li, Xin Zhou, Jialin Chen, Shaochun Zhu, Andre Mateus, Pernilla Eliasson, Paul J Kingham, Ludvig J Backman","doi":"10.1021/acs.jproteome.5c00068","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00068","url":null,"abstract":"Exercise has been shown to promote wound healing, including tendon repair. Myokines released from the exercised muscles are believed to play a significant role in this process. In our previous study, we used an in vitro coculture and loading model to demonstrate that 2% static loading of myoblasts increased the migration and proliferation of cocultured tenocytes─two crucial aspects of wound healing. IGF-1, released from myoblasts in response to 2% static loading, was identified as a contributor to the increased proliferation. However, the factors responsible for the enhanced migration remained unknown. In the current study, we subjected myoblasts in single culture conditions to 2, 5, and 10% static loading and performed proteomic analysis of the cell supernatants. Gene Ontology (GO) analysis revealed that 2% static loading induced the secretion of NBL1, C5, and EFEMP1, which is associated with cell migration and motility. Further investigation by adding exogenous recombinant proteins to human tenocytes showed that NBL1 increased tenocyte migration but not proliferation. This effect was not observed with treatments using C5 and EFEMP1.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Deciphering N-Glycosylation Dynamics of Serum Monoclonal Immunoglobulins in Multiple Myeloma via EThcD-sceHCD-MS/MS 利用EThcD-sceHCD-MS/MS分析多发性骨髓瘤患者血清单克隆免疫球蛋白的n -糖基化动力学

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-09 DOI: 10.1021/acs.jproteome.5c0025310.1021/acs.jproteome.5c00253

Huixian Li, Wanhong Lu, Qian Jin, Jiping Sun, Li Gao, Juanjuan Hu, Yingying Ling, Wenyu Zhao, Yong Zhang* and Xinfang Xie*,

{"title":"Deciphering N-Glycosylation Dynamics of Serum Monoclonal Immunoglobulins in Multiple Myeloma via EThcD-sceHCD-MS/MS","authors":"Huixian Li, Wanhong Lu, Qian Jin, Jiping Sun, Li Gao, Juanjuan Hu, Yingying Ling, Wenyu Zhao, Yong Zhang* and Xinfang Xie*, ","doi":"10.1021/acs.jproteome.5c0025310.1021/acs.jproteome.5c00253","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00253https://doi.org/10.1021/acs.jproteome.5c00253","url":null,"abstract":"Serum glycoprotein glycosylation changes can indicate disease onset and progression. However, the site-specific N-glycosylation of monoclonal immunoglobulins (M-proteins) in multiple myeloma (MM) and its clinical implications are unclear. In this study, we isolated pathogenic micromonoclonal IgA or IgG (approximately 2 μg) from IgA-MM patients (n = 22) and IgG-MM patients (n = 30), and normal polyclonal IgA and IgG from healthy controls (HCs) (n = 16). Using EThcD-sceHCD-MS/MS, the N-glycosylation dynamics of serum M-proteins in MM were determined. Compared with polyclonal IgA1 from HCs, monoclonal IgA1 from IgA-MM patients had higher fucosylation (58.1% vs 32.1%, p < 0.001), sialylation (68.0% vs 50.8%, p = 0.011), and mannosylation (1.5% vs 0.3%, p < 0.001). While, monoclonal IgG1 from IgG-MM patients had higher fucosylation (97.8% vs 95.3%, p < 0.001). In addition, specific N-glycan abundances correlated with MM clinical features: for IgA1, HexNAc5Hex5Fuc1NeuAc1 was associated with hypocomplementemia; for IgG1, HexNAc4Hex3Fuc1 was associated with the serum albumin level (r = −0.363, p = 0.049) and estimated glomerular filtration rate (r = −0.433, p = 0.017); and HexNAc4Hex5 was associated with therapeutic prognosis. In conclusion, monoclonal IgA1 and IgG1 in MM patients and their polyclonal isotypes in HCs have distinct N-glycosylation profiles, and specific N-glycans of M-proteins are associated with MM characteristics and therapeutic prognosis.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 5","pages":"2553–2563 2553–2563"},"PeriodicalIF":3.8,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143894191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","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 Static Myoblast Loading on Protein Secretion Linked to Tenocyte Migration 静态肌母细胞负载对与小细胞迁移相关的蛋白质分泌的影响

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-09 DOI: 10.1021/acs.jproteome.5c0006810.1021/acs.jproteome.5c00068

Junhong Li*, Xin Zhou, Jialin Chen, Shaochun Zhu, Andre Mateus, Pernilla Eliasson, Paul J. Kingham and Ludvig J. Backman,

{"title":"Impact of Static Myoblast Loading on Protein Secretion Linked to Tenocyte Migration","authors":"Junhong Li*, Xin Zhou, Jialin Chen, Shaochun Zhu, Andre Mateus, Pernilla Eliasson, Paul J. Kingham and Ludvig J. Backman, ","doi":"10.1021/acs.jproteome.5c0006810.1021/acs.jproteome.5c00068","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00068https://doi.org/10.1021/acs.jproteome.5c00068","url":null,"abstract":"Exercise has been shown to promote wound healing, including tendon repair. Myokines released from the exercised muscles are believed to play a significant role in this process. In our previous study, we used an in vitro coculture and loading model to demonstrate that 2% static loading of myoblasts increased the migration and proliferation of cocultured tenocytes─two crucial aspects of wound healing. IGF-1, released from myoblasts in response to 2% static loading, was identified as a contributor to the increased proliferation. However, the factors responsible for the enhanced migration remained unknown. In the current study, we subjected myoblasts in single culture conditions to 2, 5, and 10% static loading and performed proteomic analysis of the cell supernatants. Gene Ontology (GO) analysis revealed that 2% static loading induced the secretion of NBL1, C5, and EFEMP1, which is associated with cell migration and motility. Further investigation by adding exogenous recombinant proteins to human tenocytes showed that NBL1 increased tenocyte migration but not proliferation. This effect was not observed with treatments using C5 and EFEMP1.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 5","pages":"2529–2541 2529–2541"},"PeriodicalIF":3.8,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jproteome.5c00068","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143894189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Calf Fitness Associates with Early Embryo and Recipient Metabolomes and with Calf Epigenetic Marks 犊牛健康与早期胚胎和受体代谢组以及犊牛表观遗传标记有关

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-09 DOI: 10.1021/acs.jproteome.4c0098710.1021/acs.jproteome.4c00987

Isabel Gimeno*, María Berdasco, Miguel L. Pato, Pascal Salvetti, Susana Carrocera, Aurora García and Enrique Gómez*,

{"title":"Calf Fitness Associates with Early Embryo and Recipient Metabolomes and with Calf Epigenetic Marks","authors":"Isabel Gimeno*, María Berdasco, Miguel L. Pato, Pascal Salvetti, Susana Carrocera, Aurora García and Enrique Gómez*, ","doi":"10.1021/acs.jproteome.4c0098710.1021/acs.jproteome.4c00987","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00987https://doi.org/10.1021/acs.jproteome.4c00987","url":null,"abstract":"We used metadata to explore the metabolic interplay between culture medium from in vitro-produced bovine embryos transferred fresh or frozen, recipient blood plasma, and calf fitness, alongside gene expression and methylation in calf lymphocytes. Principal component (PC) analysis (PCA) identified covariates that were depicted in Debiased Sparse Partial Correlation networks and analyzed as enriched pathways. Four PCs explained 13.77, 9.58, 7.73 and 5.84% variability. PC1 clustered only mother weight and two embryonic metabolites. PC2, PC3 and PC4 associated 10, 17, and 5 calf features with 10, 6, and 16 embryonic and 2, 20, and 5 recipient metabolites, respectively. Subsequently, gene methylation and expression, and calf fitness were analyzed by PCA. Three PCs covered 100% variability. PC1 associated acid–base balance, protein metabolism, Cl–, and Ca2+ with IGF2 and IL1R1 expression, and IL4 and IL12B methylation. PC2 linked H19 expression and methylation with growth and biochemical traits. PC3 clustered growth, hydration, and redox balance, with IGF2, IGF2R, IL1R1 and IL3 methylation, and H19, IGF2, IGF2R and IL12B expression. Gene methylation connected with embryo metabolites through networks via K+, Cl–, HCO3– and TCO2. Calf fitness parallels the early metabolic fingerprints of the embryo and recipient, allowing embryo transfer decision-making based on calf health.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 5","pages":"2386–2402 2386–2402"},"PeriodicalIF":3.8,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143894192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proteomic Insights into the Adaptation of Acidithiobacillus ferridurans to Municipal Solid Waste Incineration Residues for Enhanced Bioleaching Efficiency 酸性铁硫杆菌适应城市生活垃圾焚烧残渣以提高生物浸出效率的蛋白质组学研究

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-09 DOI: 10.1021/acs.jproteome.4c0052710.1021/acs.jproteome.4c00527

Jiri Kucera*, Klemens Kremser, Pavel Bouchal, David Potesil, Tomas Vaculovic, Dalibor Vsiansky, Georg M. Guebitz and Martin Mandl,

{"title":"Proteomic Insights into the Adaptation of Acidithiobacillus ferridurans to Municipal Solid Waste Incineration Residues for Enhanced Bioleaching Efficiency","authors":"Jiri Kucera*, Klemens Kremser, Pavel Bouchal, David Potesil, Tomas Vaculovic, Dalibor Vsiansky, Georg M. Guebitz and Martin Mandl, ","doi":"10.1021/acs.jproteome.4c0052710.1021/acs.jproteome.4c00527","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00527https://doi.org/10.1021/acs.jproteome.4c00527","url":null,"abstract":"Acidithiobacillus spp. have traditionally been utilized to extract metals from mineral ores through bioleaching. This process has recently expanded to include artificial ores, such as those derived from municipal solid waste incineration (MSWI) residues. Previous studies have indicated that microbial adaptation enhances bioleaching efficiency, prompting this study to identify proteins involved in the adaptation of A. ferridurans to MSWI residues. We employed data-independent acquisition-parallel accumulation serial fragmentation to determine the proteomic response of A. ferridurans DSM 583 to three distinct materials: bottom ash (BA), kettle ash (KA), and filter ash (FA), which represent typical MSWI residues. Our findings indicate that, irrespective of the residue type, a suite of membrane transporters, porins, efflux pumps, and specific electron and cation transfer proteins was notably upregulated. The upregulation of certain proteins involved in anaerobic pathways suggested the development of a spontaneous microaerobic environment, which minimally impacted the bioleaching efficiency. Additionally, the adaptation was most efficient at half the target FA concentration, marked by a significant increase in the detoxification and efflux systems required by microorganisms to tolerate high heavy metal concentrations. Given that metal recovery peaked at lower FA concentrations for most metals of interest, further adaptation at the level of protein expression may not be warranted for improved bioleaching outcomes.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 5","pages":"2243–2255 2243–2255"},"PeriodicalIF":3.8,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jproteome.4c00527","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143894190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MSIght: A Modular Platform for Improved Confidence in Global, Untargeted Mass Spectrometry Imaging Annotation. MSIght：一个模块化平台，用于提高全球非靶向质谱成像注释的信心。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-08 DOI: 10.1021/acs.jproteome.4c01140

Lauren Fields, Hannah N Miles, Alexis E Adrian, Elliot Patrenets, William A Ricke, Lingjun Li

{"title":"MSIght: A Modular Platform for Improved Confidence in Global, Untargeted Mass Spectrometry Imaging Annotation.","authors":"Lauren Fields, Hannah N Miles, Alexis E Adrian, Elliot Patrenets, William A Ricke, Lingjun Li","doi":"10.1021/acs.jproteome.4c01140","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01140","url":null,"abstract":"Mass spectrometry imaging (MSI) has gained popularity in clinical analyses due to its high sensitivity, specificity, and throughput. However, global profiling experiments are often still restricted to LC-MS/MS analyses that lack spatial localization due to low-throughput methods for on-tissue peptide identification and confirmation. Additionally, the integration of parallel LC-MS/MS peptide confirmation, as well as histological stains for accurate mapping of identifications, presents a large bottleneck for data analysis, limiting throughput for untargeted profiling experiments. Here, we present a novel platform, termed MSIght, which automates the integration of these multiple modalities into an accessible and modular platform. Histological stains of tissue sections are coregistered to their respective MSI data sets to improve spatial localization and resolution of identified peptides. MS/MS peptide identifications via untargeted LC-MS/MS are used to confirm putative MSI identifications, thus generating MS images with greater confidence in a high-throughput, global manner. This platform has the potential to enable large-scale clinical cohorts to utilize MSI in the future for global proteomic profiling that uncovers novel biomarkers in a spatially resolved manner, thus widely expanding the utility of MSI in clinical discovery.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MSIght: A Modular Platform for Improved Confidence in Global, Untargeted Mass Spectrometry Imaging Annotation MSIght：一个模块化平台，用于提高全球非靶向质谱成像注释的信心

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-08 DOI: 10.1021/acs.jproteome.4c0114010.1021/acs.jproteome.4c01140

Lauren Fields, Hannah N. Miles, Alexis E. Adrian, Elliot Patrenets, William A. Ricke and Lingjun Li*,

{"title":"MSIght: A Modular Platform for Improved Confidence in Global, Untargeted Mass Spectrometry Imaging Annotation","authors":"Lauren Fields, Hannah N. Miles, Alexis E. Adrian, Elliot Patrenets, William A. Ricke and Lingjun Li*, ","doi":"10.1021/acs.jproteome.4c0114010.1021/acs.jproteome.4c01140","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01140https://doi.org/10.1021/acs.jproteome.4c01140","url":null,"abstract":"Mass spectrometry imaging (MSI) has gained popularity in clinical analyses due to its high sensitivity, specificity, and throughput. However, global profiling experiments are often still restricted to LC-MS/MS analyses that lack spatial localization due to low-throughput methods for on-tissue peptide identification and confirmation. Additionally, the integration of parallel LC-MS/MS peptide confirmation, as well as histological stains for accurate mapping of identifications, presents a large bottleneck for data analysis, limiting throughput for untargeted profiling experiments. Here, we present a novel platform, termed MSIght, which automates the integration of these multiple modalities into an accessible and modular platform. Histological stains of tissue sections are coregistered to their respective MSI data sets to improve spatial localization and resolution of identified peptides. MS/MS peptide identifications via untargeted LC-MS/MS are used to confirm putative MSI identifications, thus generating MS images with greater confidence in a high-throughput, global manner. This platform has the potential to enable large-scale clinical cohorts to utilize MSI in the future for global proteomic profiling that uncovers novel biomarkers in a spatially resolved manner, thus widely expanding the utility of MSI in clinical discovery.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 5","pages":"2478–2490 2478–2490"},"PeriodicalIF":3.8,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143894187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0