Journal of Proteome Research最新文献_第10页

Comprehensive Protein Inference Analysis with PyProteinInference Elucidates Biological Understanding of Tandem Mass Spectrometry Data.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-28 DOI: 10.1021/acs.jproteome.4c00734

Trent B Hinkle, Corey E Bakalarski

{"title":"Comprehensive Protein Inference Analysis with PyProteinInference Elucidates Biological Understanding of Tandem Mass Spectrometry Data.","authors":"Trent B Hinkle, Corey E Bakalarski","doi":"10.1021/acs.jproteome.4c00734","DOIUrl":"10.1021/acs.jproteome.4c00734","url":null,"abstract":"Selection and application of protein inference algorithms can have a significant impact on the data output from tandem mass spectrometry (MS/MS) experiments. However, this critical step is often taken for granted, with many studies simply utilizing the inference method embedded within the end-to-end software pipeline employed for analysis without consideration of the particular algorithm's suitability for the experiment at hand or its effects on the resulting data. Although many individual inference algorithms have been demonstrated, few unified tools are available that allow the researcher to quickly apply a variety of different inference algorithms to meet the needs of their analysis, are agnostic of other tools in the analysis pipeline, and are easy to use for the bench biologist. PyProteinInference provides a comprehensive suite of tools that enable researchers to apply different inference algorithms and compute protein-level set-based false discovery rates (FDR) from MS/MS data through a unified interface. Here, we describe the software and its application to a traditional protein inference benchmarking data set and to a K562 whole-cell lysate to demonstrate its utility in facilitating conclusions about underlying biological mechanisms in proteomic data.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522096","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

MSConnect: Open-Source, End-to-End Platform for Automated Mass Spectrometry Data Management, Analysis, and Visualization. MSConnect：用于自动质谱数据管理、分析和可视化的端到端开源平台。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-28 DOI: 10.1021/acs.jproteome.4c00854

Xiaofeng Xie, Parker S Reyes, Hsien-Jung L Lin, G Alex Mannewitz, Thy Truong, Kei G I Webber, Samuel H Payne, Ryan T Kelly

{"title":"MSConnect: Open-Source, End-to-End Platform for Automated Mass Spectrometry Data Management, Analysis, and Visualization.","authors":"Xiaofeng Xie, Parker S Reyes, Hsien-Jung L Lin, G Alex Mannewitz, Thy Truong, Kei G I Webber, Samuel H Payne, Ryan T Kelly","doi":"10.1021/acs.jproteome.4c00854","DOIUrl":"10.1021/acs.jproteome.4c00854","url":null,"abstract":"The scale of mass spectrometry-based proteomics data sets continues to increase, and the analysis workflows are becoming more complex as various steps are carried out using a multitude of software programs developed by both commercial providers and the research community. Manually shepherding data across multiple programs and in-house-developed scripts can be error prone and labor intensive. It is also difficult for others to follow the same steps, leading to poor repeatability. We have developed an integrated data management and analysis platform termed MSConnect that enables simple and traceable processing workflows across multiple programs, thus improving repeatability and automating common backup and analysis steps from the point of data collection through summarization and visualization. The open nature of the MSConnect platform enables the diverse omics community to seamlessly integrate third-party tools or develop and automate their own unique workflows. With an open license and design architecture, MSConnect has the potential to become a community-driven platform serving a wide range of MS-based omics researchers.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522110","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

Discovery of Key Candidate Protein Biomarkers in Early-Stage Nonsmall Cell Lung Carcinoma through Quantitative Proteomics.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-27 DOI: 10.1021/acs.jproteome.4c00764

Baby Rorielyn T Dimayacyac-Esleta, Ferdinand D Mira, Lorenzo M Zarate, Ben Joshua O Porras, Dave Laurence A Juntilla, Lara Beatrice L Suñga, Venus B Pondevida, Sullian S Naval, Treah May S Sayo, Herdee Gloriane C Luna, Eloise I Prieto

{"title":"Discovery of Key Candidate Protein Biomarkers in Early-Stage Nonsmall Cell Lung Carcinoma through Quantitative Proteomics.","authors":"Baby Rorielyn T Dimayacyac-Esleta, Ferdinand D Mira, Lorenzo M Zarate, Ben Joshua O Porras, Dave Laurence A Juntilla, Lara Beatrice L Suñga, Venus B Pondevida, Sullian S Naval, Treah May S Sayo, Herdee Gloriane C Luna, Eloise I Prieto","doi":"10.1021/acs.jproteome.4c00764","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00764","url":null,"abstract":"Difficulties in early-stage diagnosis are among the factors contributing to the high mortality of nonsmall cell lung carcinoma (NSCLC) patients. Unfortunately, diagnostic biomarkers are currently lacking, limiting options in the clinic. To discover proteins that have potential for biomarker applications, we performed an in-depth quantitative proteomic analysis on a cohort of Filipino early-stage NSCLC lung adenocarcinoma (LUAD) patients. Differentially expressed proteins (DEPs) were obtained by using tandem mass tag (TMT) labeling and mass spectrometry (MS)-based quantitative proteomics. A total of 6240 quantified proteins were identified with 3155 significantly upregulated and 1248 significantly downregulated. Integration of the proteomic result with curated transcriptome data allowed the identification of 33 proteins with biomarker potential. This study also provided insights into relevant pathways in NSCLC LUAD, such as protein translation and metabolic pathways. Interestingly, all of the enzymes in the hexosamine biosynthetic pathway (HBP) are found to be upregulated, suggesting its important role in NSCLC LUAD. It is worthwhile to look at the potential of targeting the metabolic vulnerability of NSCLC LUAD as a new strategy in drug development. All MS data were deposited into ProteomeXchange with the identifier PXD050598.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522108","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

Categorization and Characterization of Snake Venom Variability through Intact Toxin Analysis by Mass Spectrometry

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-26 DOI: 10.1021/acs.jproteome.4c0092310.1021/acs.jproteome.4c00923

Luis L. Alonso, Julien Slagboom, Nicholas R. Casewell, Saer Samanipour and Jeroen Kool*,

{"title":"Categorization and Characterization of Snake Venom Variability through Intact Toxin Analysis by Mass Spectrometry","authors":"Luis L. Alonso, Julien Slagboom, Nicholas R. Casewell, Saer Samanipour and Jeroen Kool*, ","doi":"10.1021/acs.jproteome.4c0092310.1021/acs.jproteome.4c00923","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00923https://doi.org/10.1021/acs.jproteome.4c00923","url":null,"abstract":"The variation in venom between and within snake species has significant implications for snakebite treatment. This highlights the critical importance of studying venom composition and its variations, not only for medical purposes but also from an evolutionary perspective. This study explores analytics for characterizing venom variability, focusing on venom toxin accurate masses, and emphasizes how the complexity of studying snake venom variability can be addressed by using liquid chromatography mass spectrometry (LC-MS) analysis with bioinformatics tools. This was demonstrated by investigating LC-MS data obtained from the venoms of 15 true cobras (Naja spp.), 5 mambas (Dendroaspis spp.) and 28 vipers (Crotalus and Bothrops spp.; total of 20 Elapidae and 28 Viperidae venoms), with newly developed bioinformatics tools. The measured LC-MS data was processed in an automated fashion and sorted based on the monoisotopic accurate masses of all toxins found, their peak intensities, and their retention times in LC. The data was then investigated using bioinformatic tools, before the toxin data available in open-source databases was used to predict the class of a toxin by means of its mass. This study highlights the importance of studying venom variability, which is performed by our combinatorial approach of intact-toxin analysis and toxin grouping by accurate mass.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 3","pages":"1329–1341 1329–1341"},"PeriodicalIF":3.8,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jproteome.4c00923","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143561453","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

Clinical Response Characteristics of Salivary Proteins in the Management Strategy of Diabetes-Associated Periodontitis

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-26 DOI: 10.1021/acs.jproteome.4c0070110.1021/acs.jproteome.4c00701

Shuyuan Jia, Qin Liang, Yanling Zhang, Jing Diao, Yizhou Liu, Yulin Ye, Shaojia Xu, Wenying Yang, Ya Zhao, Bowen Ma, Xiaodong Li, Shuguo Zheng* and Chao Yuan*,

{"title":"Clinical Response Characteristics of Salivary Proteins in the Management Strategy of Diabetes-Associated Periodontitis","authors":"Shuyuan Jia, Qin Liang, Yanling Zhang, Jing Diao, Yizhou Liu, Yulin Ye, Shaojia Xu, Wenying Yang, Ya Zhao, Bowen Ma, Xiaodong Li, Shuguo Zheng* and Chao Yuan*, ","doi":"10.1021/acs.jproteome.4c0070110.1021/acs.jproteome.4c00701","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00701https://doi.org/10.1021/acs.jproteome.4c00701","url":null,"abstract":"Diabetes and periodontitis, as widespread chronic diseases, often exacerbate each other’s conditions. Nonsurgical periodontal treatments can improve the oral and systemic health in these patients, with salivary proteins offering potential insights into disease mechanisms and treatment effectiveness. However, there is a lack of comprehensive data on salivary proteomics in this context. By assigning patients with diabetes-associated periodontitis to a test group (supragingival scaling, subgingival scraping and root planing) or a control group (supragingival scaling only), analyzing nonstimulated whole saliva samples using liquid chromatography-tandem mass spectrometry, and establishing the in vivo and in vitro models, we found significant differential expression of salivary proteins related to Apelin signaling pathway, hematopoietic cell profiling, stress response and immune regulation, identifying four candidate proteins: superoxide dismutase 1 (SOD1), profilin 1 (PFN1), S100 calcium-binding protein A11 (S100A11) and kallikrein-related peptidase 6 (KLK6). All four proteins were significantly elevated, with a combined area under the curve of 0.933, while SOD1 alone reached 0.915. Additionally, we observed high glucose and inflammatory conditions reduced SOD1 expression. In conclusion, SOD1 emerges as a promising regulatory target for managing diabetes and periodontitis by modulating the oral oxidative stress microenvironment.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 3","pages":"1161–1179 1161–1179"},"PeriodicalIF":3.8,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143561444","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

Tear Protein Biomarkers for Ocular Mucous Membrane Pemphigoid Uncovered Using Targeted LC-MS/MS

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-26 DOI: 10.1021/acs.jproteome.4c0092410.1021/acs.jproteome.4c00924

Maggy Lépine, Marie-Claude Robert and Lekha Sleno*,

{"title":"Tear Protein Biomarkers for Ocular Mucous Membrane Pemphigoid Uncovered Using Targeted LC-MS/MS","authors":"Maggy Lépine, Marie-Claude Robert and Lekha Sleno*, ","doi":"10.1021/acs.jproteome.4c0092410.1021/acs.jproteome.4c00924","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00924https://doi.org/10.1021/acs.jproteome.4c00924","url":null,"abstract":"Mucous membrane pemphigoid (MMP) is a multisystemic rare autoimmune disease affecting the skin and mucous membranes. Ocular involvement is characterized by chronic conjunctival inflammation causing scar formation, leading to corneal opacification and vision loss. Conjunctival biopsies are currently used to confirm diagnosis, and the associated immunosuppression treatments prescribed can have serious consequences on patients. To address these challenges, a noninvasive approach to collect patient tears using untargeted and targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses has been developed to identify a list of potential biomarkers of ocular MMP. Samples were collected on Schirmer strips and subjected to tryptic digestion and LC-MS/MS analysis. Three cohorts of patients were studied, and targeted LC-scheduled multiple reaction monitoring (LC-sMRM) methods were developed for the verification of putative biomarkers. The comparison of three groups of patients, those diagnosed with ocular MMP, non-ocular MMP, and lichen planus, another ocular cicatricial conjunctivitis disorder, yielded 56 biomarkers of interest. Proteins distinguishing MMP patients with and without ocular involvement were linked to the extracellular matrix, metabolism, and neutrophil degranulation. The comparison between MMP and lichen planus patients highlighted lower levels of metabolic enzymes in the latter. This study highlights the use of multiple patient cohorts and tailored targeted quantitative proteomics methods for the discovery of biomarkers for diagnostic and prognostic purposes.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 3","pages":"1275–1284 1275–1284"},"PeriodicalIF":3.8,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143561480","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

Isobaric Labeling Update in MaxQuant

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-25 DOI: 10.1021/acs.jproteome.4c0086910.1021/acs.jproteome.4c00869

Daniela Ferretti, Pelagia Kyriakidou, Jinqiu Xiao, Shamil Urazbakhtin, Carlo De Nart and Jürgen Cox*,

{"title":"Isobaric Labeling Update in MaxQuant","authors":"Daniela Ferretti, Pelagia Kyriakidou, Jinqiu Xiao, Shamil Urazbakhtin, Carlo De Nart and Jürgen Cox*, ","doi":"10.1021/acs.jproteome.4c0086910.1021/acs.jproteome.4c00869","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00869https://doi.org/10.1021/acs.jproteome.4c00869","url":null,"abstract":"We present an update of the MaxQuant software for isobaric labeling data and evaluate its performance on benchmark data sets. Impurity correction factors can be applied to labels mixing C- and N-type reporter ions such as TMT Pro. Application to a single-cell multispecies mixture benchmark shows the high accuracy of the impurity-corrected results. TMT data recorded with FAIMS separation can be analyzed directly in MaxQuant without splitting the raw data into separate files per FAIMS voltage. Weighted median normalization is applied to several data sets, including large-scale human body atlas data. In the benchmark data sets, the weighted median normalization either removes or strongly reduces the batch effects between different TMT plexes and results in clustering by biology. In data sets including reference channels, we find that weighted median normalization performs as well or better when the reference channels are ignored and only the sample channel intensities are used, suggesting that the measurement of reference channels is unnecessary when using weighted median normalization in MaxQuant. We demonstrate that MaxQuant including the weighted median normalization performs well on multinotch MS3 data, as well as on phosphorylation data. MaxQuant is freely available for any purpose and can be downloaded from https://www.maxquant.org/.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 3","pages":"1219–1229 1219–1229"},"PeriodicalIF":3.8,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jproteome.4c00869","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143561642","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

Serum Metabolomics Profiling Coupled with Machine Learning Identifies Potential Diagnostic and Prognostic Candidate Markers in Meningioma Using Raman Spectroscopy, ATR-FTIR, and LC–MS/MS

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-25 DOI: 10.1021/acs.jproteome.4c0080610.1021/acs.jproteome.4c00806

Ankit Halder, Priyanka A. Jadhav, Archisman Maitra, Arghya Banerjee, Arti Hole, Sridhar Epari, Prakash Shetty, Aliasgar Moiyadi, Murali Krishna Chilkapati* and Sanjeeva Srivastava*,

{"title":"Serum Metabolomics Profiling Coupled with Machine Learning Identifies Potential Diagnostic and Prognostic Candidate Markers in Meningioma Using Raman Spectroscopy, ATR-FTIR, and LC–MS/MS","authors":"Ankit Halder, Priyanka A. Jadhav, Archisman Maitra, Arghya Banerjee, Arti Hole, Sridhar Epari, Prakash Shetty, Aliasgar Moiyadi, Murali Krishna Chilkapati* and Sanjeeva Srivastava*, ","doi":"10.1021/acs.jproteome.4c0080610.1021/acs.jproteome.4c00806","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00806https://doi.org/10.1021/acs.jproteome.4c00806","url":null,"abstract":"Meningioma, the most prevalent brain tumor, poses significant challenges due to its unclear transition from low-grade to aggressive forms, with limited knowledge about grade-specific markers. We have utilized vibrational spectroscopic techniques such as ATR-FTIR and Raman spectroscopy, alongside LC–MS/MS-based mass spectrometry to understand the systemic cues and evaluate them for clinical practice. The acquired Raman and ATR-FTIR spectra of 46 meningioma patients (27 low-grade and 19 high-grade) and 8 healthy individuals revealed 98.15% and 83.33% accuracy based on PC-LDA. The grade classification revealed an accuracy of around 70%, implying the presence of subtypes and transition phases. The observed alterations corresponded to lipids, nucleic acids, and proteins. Further, the LC–MS/MS-based study identified different derivatives of cholines, indoles, lipids, sphingosine, tryptophan, and their respective metabolic pathways as contributors in tumorigenesis and progression. Further, PRM-based targeted validation and feature selection was carried out on 43 meningioma patients and 17 healthy controls. Glycochenodeoxycholic acid, indole-3-acetic acid, trans-3-indoleacrylic acid, glycodeoxycholic acid, 5α-dihydrotestosteroneglucornide, and glycocholic acid segregated meningioma samples with an accuracy of around 90% while features like indole-3-acetic acid, stercobilin, sphingosine-1-phosphate, deoxycholic acid, and citric acid could classify grades with around 70% accuracy. These findings suggest that further validation across larger cohorts could enhance its usage in clinical settings.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 3","pages":"1180–1196 1180–1196"},"PeriodicalIF":3.8,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143561414","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 Plasticity in the Coral Montipora capitata Gamete Bundles after Parent Thermal Bleaching

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-25 DOI: 10.1021/acs.jproteome.4c0094610.1021/acs.jproteome.4c00946

Emma B. Timmins-Schiffman*, Rayhan Khanna, Tanya Brown, Jenna Dilworth, Brendan X. MacLean, Miranda C. Mudge, Samuel J. White, Carly D. Kenkel, Lisa J. Rodrigues, Brook L. Nunn and Jacqueline L. Padilla-Gamiño,

{"title":"Proteomic Plasticity in the Coral Montipora capitata Gamete Bundles after Parent Thermal Bleaching","authors":"Emma B. Timmins-Schiffman*, Rayhan Khanna, Tanya Brown, Jenna Dilworth, Brendan X. MacLean, Miranda C. Mudge, Samuel J. White, Carly D. Kenkel, Lisa J. Rodrigues, Brook L. Nunn and Jacqueline L. Padilla-Gamiño, ","doi":"10.1021/acs.jproteome.4c0094610.1021/acs.jproteome.4c00946","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00946https://doi.org/10.1021/acs.jproteome.4c00946","url":null,"abstract":"Coral reefs are vital to marine biodiversity and human livelihoods, but they face significant threats from climate change. Increased ocean temperatures drive massive “bleaching” events, during which corals lose their symbiotic algae and the important metabolic resources those algae provide. Proteomics is a crucial tool for understanding coral function and tolerance to thermal stress, as proteins drive physiological processes and accurately represent cell functional phenotypes. We examined the physiological condition of coral (Montipora capitata) gametes from parents that either experienced thermal bleaching or were nonbleached controls by comparing data dependent (DDA) and data independent (DIA) acquisition methods and peptide quantification (spectral counting and area-under-the-curve, AUC) strategies. For DDA, AUC captured a broader dynamic range than spectral counting. DIA yielded better coverage of low abundance proteins than DDA and a higher number of proteins, making it the more suitable method for detecting subtle, yet biologically significant, shifts in protein abundance in gamete bundles. Gametes from bleached corals showed a broadscale decrease in metabolic proteins involved in carbohydrate metabolism, citric acid cycle, and protein translation. This metabolic plasticity could reveal how organisms and their offspring acclimatize and adapt to future environmental stress, ultimately shaping the resilience and dynamics of coral populations.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 3","pages":"1317–1328 1317–1328"},"PeriodicalIF":3.8,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143561415","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

Heterogeneities of Site-Specific N-Glycosylation in the Hippocampus of Depression-like Behavior Models in Mice Induced by Acute Stress and Chronic Stress

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-24 DOI: 10.1021/acs.jproteome.4c0065510.1021/acs.jproteome.4c00655

Pengyu Ren, Longhui Fu, Xiaojuan Gong, Li Jia, Boqiang Lyu, Mengke Wang, Siyuan Zhang, Shisheng Sun, Na Zhao, Zongben Xu and Jie Zhu*,

{"title":"Heterogeneities of Site-Specific N-Glycosylation in the Hippocampus of Depression-like Behavior Models in Mice Induced by Acute Stress and Chronic Stress","authors":"Pengyu Ren, Longhui Fu, Xiaojuan Gong, Li Jia, Boqiang Lyu, Mengke Wang, Siyuan Zhang, Shisheng Sun, Na Zhao, Zongben Xu and Jie Zhu*, ","doi":"10.1021/acs.jproteome.4c0065510.1021/acs.jproteome.4c00655","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00655https://doi.org/10.1021/acs.jproteome.4c00655","url":null,"abstract":"It is well established that acute and chronic stress contributes to the onset and progression of depression, but the underlying mechanisms have not been elucidated. Here an integrated N-glycoproteomic and proteomic analysis was performed to investigate heterogeneities of glycoprotein and site-specific glycosylation between the hippocampi of control, acute stress-affected (AS), and chronic mild stress-affected (CMS) mice. 1063 unique intact N-glycopeptides, 116 N-glycan compositions, and 512 glycosylation sites were identified. CMS and AS had significant effects on glycosylation. CMS reduced multiantenna glycosylation (N8H8 and N6H5F1S1) more strongly, while AS reduced multiantenna glycosylation (N5H3F1) more strongly. CMS inhibited high-mannose synthesis with high polymerization (N2H9 and N2H8), while AS inhibited high-mannose synthesis with low polymerization (N2H6, H2H5). Furthermore, 26 and 39 glycosylation-related genes (GRGs) were identified in the AS and CMS groups, separately. Functional enrichment analysis for GRGs in the AS and CMS groups exhibited that the up-regulated functions were leading edge membrane and cell adhesion molecule binding; meanwhile, the down-regulated functions were cAMP signaling pathways. Finally, tSNE analysis based on ScRNA-seq revealed that core GRGs were highly expressed in astrocytes. All of these findings improve our understanding of glycosylation in stress-related depression, providing valuable data resources for depression pathogenesis exploration and novel therapeutic target discovery.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 3","pages":"1039–1052 1039–1052"},"PeriodicalIF":3.8,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143561540","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