Journal of Proteome Research最新文献_第7页

Multiomics Reveals the Mechanism of Natranaerobius thermophilus Adaptation to Combined Hypersaline, Alkaline, and Elevated Temperature Environments. 多组学揭示嗜热纳特拉纳菌适应高盐、碱性和高温联合环境的机制。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-07-22 DOI: 10.1021/acs.jproteome.5c00395

Qinghua Xing, Xinyi Tao, Shanshan Zhang, Noha M Mesbah, Xinwei Mao, Xiaomeng Guo, Qingping Hu, Haisheng Wang, Baisuo Zhao

{"title":"Multiomics Reveals the Mechanism of Natranaerobius thermophilus Adaptation to Combined Hypersaline, Alkaline, and Elevated Temperature Environments.","authors":"Qinghua Xing, Xinyi Tao, Shanshan Zhang, Noha M Mesbah, Xinwei Mao, Xiaomeng Guo, Qingping Hu, Haisheng Wang, Baisuo Zhao","doi":"10.1021/acs.jproteome.5c00395","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00395","url":null,"abstract":"The halophilic alkalithermophile N. thermophilus grows optimally at the combined extremes of 3.3-3.9 M Na+, pH 9.5, and 53 °C. This study aims to uncover its unique adaptations to the combined extremes of high salt, alkaline pH, and high temperature. Due to the difficulties of genetic manipulation, we used a multiomics approach to reveal the comprehensive transcriptomic, proteomic, and metabolomic landscapes of N. thermophilus under the triple extremes. Specifically, two distinct conditions were evaluated: high salt-alkaline-thermal (HSAT, 4 M Na+/ pH 9.8/52 °C) stress and low salt-alkaline-thermal (LSAT, 3 M Na+/ pH 8.8/42 °C) stress. Under HSAT stress, N. thermophilus increased the level of saturated fatty acids and uncharged polar lipids to remodel its cell membrane, enhanced Na+-driven flagellar motility, accumulated various compatible solutes, redirected amino acid metabolism for energy, and adjusted the activity of ion transporters and chaperones. These findings exemplify the \"No Free Lunch\" principle in polyextremophiles. By examining changes in gene, protein, and metabolic regulation levels in N. thermophilus under the simultaneous influence of three extremes, this study provides a comprehensive analysis of the survival mechanisms of polyextremophiles in hypersaline, alkaline, and high-temperature environments. Our findings offer valuable insights into the origins of life on Earth and the potential for extraterrestrial life.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144688365","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 Comparison between Hyphae and Spores Reveals Pathogenicity of Mucor Irregularis. 菌丝和孢子的蛋白质组学比较揭示了不规则毛霉的致病性。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-07-21 DOI: 10.1021/acs.jproteome.5c00214

Meijie Zhang, Xiaowei Zhou, Yuhan Zhang, Ge Song, Xiaofang Li, Weida Liu, Guanzhao Liang

{"title":"Proteomic Comparison between Hyphae and Spores Reveals Pathogenicity of Mucor Irregularis.","authors":"Meijie Zhang, Xiaowei Zhou, Yuhan Zhang, Ge Song, Xiaofang Li, Weida Liu, Guanzhao Liang","doi":"10.1021/acs.jproteome.5c00214","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00214","url":null,"abstract":"Mucor irregularis, an emerging causative agent of disfiguring mucormycosis, demonstrates distinct clinical manifestations between hyphae and spore forms, though the pathogenic determinants between these two forms remain elusive. Utilizing TMT (tandem mass tag)-based quantitative proteomics (ProteomeXchange: PXD055430), we conducted a comparative analysis of these morphotypes, followed by Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment and protein-protein interaction network construction. Critically, we identified the following: (i) tRNA sulfur modification (NCS6) in spore dormancy maintenance; (ii) adenylate kinase (adenylate kinase 1)-mediated energy metabolism during germination; and (iii) COQ3-dependent mitochondrial function in spore germination. This first proteomic profiling of M. irregularis morphotypes delineates distinct phase-specific adaptations. Notably, the ribosomal and dormancy-associated machinery as NCS6 in spores contrasts sharply with the metabolic activation and upregulated virulence determinants as PAC1 in hyphae. Findings highlight NAT10 critical for spore readiness and RhoGEF GTPases central to hyphal invasion as particularly promising candidate therapeutic targets. Building upon this foundation, future investigations must now delineate the immunomodulatory roles of these effector proteins during host invasion to advance mucormycosis management strategies.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144681671","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

Acute Metabolic Effects in Brazilian A-29 Fighter Pilots by NMR-Based Metabolomics. 基于核磁共振代谢组学的巴西A-29战斗机飞行员急性代谢效应

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-07-21 DOI: 10.1021/acs.jproteome.5c00129

Roberta Verissimo França de Oliveira, Grace Barros de Sá, Alanny Cristine Dos Santos Pinheiro, Antonia Claudia Jácome da Câmara, Palmielly Diógenes, Adriano Percival Calderaro Calvo, Laila Ribeiro Fernandes, Luísa Soares da Silva, Rafael Loureiro Simões, Verônica Morandi, Gilson Costa Dos Santos, Paulo Farinatti

{"title":"Acute Metabolic Effects in Brazilian A-29 Fighter Pilots by NMR-Based Metabolomics.","authors":"Roberta Verissimo França de Oliveira, Grace Barros de Sá, Alanny Cristine Dos Santos Pinheiro, Antonia Claudia Jácome da Câmara, Palmielly Diógenes, Adriano Percival Calderaro Calvo, Laila Ribeiro Fernandes, Luísa Soares da Silva, Rafael Loureiro Simões, Verônica Morandi, Gilson Costa Dos Santos, Paulo Farinatti","doi":"10.1021/acs.jproteome.5c00129","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00129","url":null,"abstract":"Operating an aircraft imposes significant physical and mental demands on pilots, particularly those in military aviation. These challenges include circadian disruptions, irregular working hours, and exposure to G-forces. This study investigates the acute metabolic effects of flight in the A-29 fighter pilots of the Brazilian Air Force (FAB). Blood, urine, and saliva samples were collected from 32 pilots, trainees (n = 12; aged 23-26 years) and instructors (n = 20; aged 25-41 years), immediately before and after flights. Assessments included anthropometric measurements, complete blood count (CBC), circulating endothelial cells (CECs), coagulogram, lipidogram, urinalysis, and nuclear magnetic resonance (NMR)-based metabolomics. After flights, trainees showed a 12% increase in the number of segmented neutrophils, while instructors exhibited a 15% increase in the number of lymphocyte counts. Serum lactate levels decreased in both groups (23% in trainees and 12% in instructors). Salivary glucose increased by 49% in trainees, whereas instructors demonstrated decreases in metabolites such as choline (23%) and lactate (15%). Urinary trigonelline levels increased by 53% in instructors. The observed changes were more pronounced in instructors vs trainees, indicating a degree of metabolic adaptation associated with greater flight experience. These findings highlight NMR-based metabolomics as a valuable tool for monitoring acute metabolic changes in fighter pilots.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673323","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

OCIAD2 Promotes Cancer Progression via Metabolic Reprogramming in Lung Adenocarcinoma. OCIAD2在肺腺癌中通过代谢重编程促进癌症进展。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-07-21 DOI: 10.1021/acs.jproteome.5c00273

Yi-Hui Huang, Wen-Hsin Chang, Chi-Ya Shen, Kang-Yi Su, Gee-Chen Chang, Jin-Shing Chen, Wen-Yao Lee, Yu-Ju Chen, Sung-Liang Yu

{"title":"OCIAD2 Promotes Cancer Progression via Metabolic Reprogramming in Lung Adenocarcinoma.","authors":"Yi-Hui Huang, Wen-Hsin Chang, Chi-Ya Shen, Kang-Yi Su, Gee-Chen Chang, Jin-Shing Chen, Wen-Yao Lee, Yu-Ju Chen, Sung-Liang Yu","doi":"10.1021/acs.jproteome.5c00273","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00273","url":null,"abstract":"Given the limited proteomic insights and high incidence of lung adenocarcinoma, further investigation of uncharacterized proteins in cancer progression remains crucial. In this study, a poorly characterized protein, OCIA domain-containing 2 (OCIAD2), encoded by chromosome 4 was identified as being upregulated in lung adenocarcinoma from our previous proteogenomics data using the Taiwan Cancer Moonshot cohort. OCIAD2 was highly expressed in tumor tissues in 95.5% of lung adenocarcinoma patients in our cohort, with elevated expression correlating with worse survival. Functional studies revealed that the silencing of the OCIAD2 decreased cell migration, invasion, and colony-forming abilities. Gene Set Enrichment Analysis (GSEA) indicated the involvement of OCIAD2 in oxidative phosphorylation (OXPHOS). Subsequently, mitochondrial metabolic assay demonstrated that OCIAD2 impairs OXPHOS function, accompanied by a metabolic shift toward glycolysis. These findings suggest that OCIAD2 promotes cancer progression through metabolic reprogramming, highlighting the role of OCIAD2 as a potential biomarker and therapeutic target for lung adenocarcinoma.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673361","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

Comparative Analysis of Platelet-Derived Extracellular Vesicle Protein Extraction Methodologies for Mass Spectrometry. 血小板来源的细胞外囊泡蛋白质谱提取方法的比较分析。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-07-21 DOI: 10.1021/acs.jproteome.5c00089

Carmen Ráez-Meseguer, Andreu Miquel Amengual-Tugores, Maria Antònia Forteza-Genestra, Francisca Orvay-Pintos, Rosa M Gomila, Gabriel Martorell-Crespí, Javier Calvo, Antoni Gayà, Marta Monjo, Joana Maria Ramis

{"title":"Comparative Analysis of Platelet-Derived Extracellular Vesicle Protein Extraction Methodologies for Mass Spectrometry.","authors":"Carmen Ráez-Meseguer, Andreu Miquel Amengual-Tugores, Maria Antònia Forteza-Genestra, Francisca Orvay-Pintos, Rosa M Gomila, Gabriel Martorell-Crespí, Javier Calvo, Antoni Gayà, Marta Monjo, Joana Maria Ramis","doi":"10.1021/acs.jproteome.5c00089","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00089","url":null,"abstract":"The aim of this study is to present a comparative study of different methodologies for the extraction of proteins from platelet-derived extracellular vesicles (pEVs) prior to subsequent mass spectrometry (MS) analysis. pEVs were isolated by size exclusion chromatography (SEC) from human platelet lysates (PL) and characterized by identifying specific markers by Western blot, visualizing morphology by transmission electron microscopy (TEM) and analyzing concentration and size via nanoparticle tracking analysis (NTA). Protein isolation was performed through three different methodologies based on SDS-polyacrylamide gel electrophoresis (SDS-PAGE), organic solvent precipitation (OSP), or magnetic beads (MB), followed by protein digestion and sample acquisition by LC-MS/MS. Clustering of the samples according to methodology is observed in the principal component analysis (PCA), although no significant differences in terms of normalized abundances are reached. Similarly, a small number of proteins were identified as unique by each methodology, with 91.3% coincidence among all three procedures. In addition, the bioinformatic results of the enrichment analysis and the numbers of proteins already identified in the Vesiclepedia database are highly similar for the three methodologies. Overall, all three methodologies analyzed are optimal for the extraction of proteins from pEV and could be considered according to their intrinsic characteristics, in accordance with the research requirements.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144681670","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

Mitochondrial Oxidative Stress Alters the Phosphoproteome and Reverses Epithelial-Mesenchymal Transition in Human Breast Cancer Cells via the β-Catenin/c-Myc Axis. 线粒体氧化应激通过β-Catenin/c-Myc轴改变人乳腺癌细胞的磷酸化蛋白质组和逆转上皮-间质转化

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-07-21 DOI: 10.1021/acs.jproteome.5c00386

Shivani R Nandha, Pooja K Melwani, Deepak Sharma, Santosh K Sandur, Rahul Checker

{"title":"Mitochondrial Oxidative Stress Alters the Phosphoproteome and Reverses Epithelial-Mesenchymal Transition in Human Breast Cancer Cells via the β-Catenin/c-Myc Axis.","authors":"Shivani R Nandha, Pooja K Melwani, Deepak Sharma, Santosh K Sandur, Rahul Checker","doi":"10.1021/acs.jproteome.5c00386","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00386","url":null,"abstract":"Mitochondrial redox status plays a critical role in cancer progression, yet the effects of mitochondrial oxidative stress on the epithelial-mesenchymal transition (EMT), a key step in metastasis, remain elusive. We have investigated the phosphoproteomic landscape of breast cancer cells exposed to mitochondrial oxidative stress induced by mitochondria-targeted curcumin (mitocurcumin (MC)) and explored its potential as a druggable target. Mitocurcumin led to altered cell morphology, reduced migration, and shift to a cobblestone-like epithelial morphology, indicating EMT reversal. Label-free mass spectrometry-based global phosphoproteomic analysis revealed upregulation of phosphoproteins involved in DNA damage-related processes, transcription termination, and induction of oxidative stress, while downregulated phosphoproteins were linked to translation and amino acid metabolism. Processes related to EMT reversal, such as cytoskeleton organization, cell-cell adhesion, focal adhesion assembly and cell-cell junction organization/assembly, and establishment/maintenance of epithelial cell apical-basal polarity, were enriched. The RAC2/RAC3 GTPase cycle, important for cell migration, was downregulated, along with the Wnt/β-catenin signaling pathway. A decrease in the levels of mesenchymal markers, β-catenin, and its target gene, c-Myc, confirmed the suppression of the mesenchymal phenotype. In conclusion, mitochondrial oxidative stress inhibits the migratory capacity of breast cancer cells by targeting the β-catenin/c-Myc axis, indicating its potential as a novel druggable target to prevent cancer metastasis.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673360","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 Signatures of Choroidal Neovascularization via Integrated LC-FAIMS-MS/MS Workflow. 基于LC-FAIMS-MS/MS集成工作流的脉络膜新生血管的蛋白质组学特征。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-07-19 DOI: 10.1021/acs.jproteome.5c00363

Bintao Xie, Liujun Ding, Qin Zhang, Xiaohua Chen, Kai Wang, Jineng Lv, Jing Wang, Lue Xiang, Jia Qu, Qi Chen

{"title":"Proteomic Signatures of Choroidal Neovascularization via Integrated LC-FAIMS-MS/MS Workflow.","authors":"Bintao Xie, Liujun Ding, Qin Zhang, Xiaohua Chen, Kai Wang, Jineng Lv, Jing Wang, Lue Xiang, Jia Qu, Qi Chen","doi":"10.1021/acs.jproteome.5c00363","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00363","url":null,"abstract":"The multicellular retinal pigment epithelium/choroid (RC) tissue is pivotal in maintaining retinal homeostasis and is closely associated with sight-threatening eye diseases. However, the limited sample amount, particularly in mice, poses a great challenge in comprehensively characterizing the functional proteins of the RC in disease models. This study utilized a state-of-the-art FAIMS device coupled with an Orbitrap Fusion Lumos mass spectrometer to systematically optimize the LC, FAIMS, and MS/MS acquisition parameters for in-depth proteomic analysis of the difficultly obtained RC samples. In a mouse model of neovascular age-related macular degeneration (nvAMD), the optimized workflow effectively increased the coverage of the proteome, which enabled the identification of 7047 proteins, compared to 5500 identified by conventional LC-MS/MS. Combined with multiomics data sets across species, differential expression analysis revealed 295 significantly altered proteins in the nvAMD model, including key regulators of extracellular matrix (ECM) remodeling (HTRA1, CCDC80) and immune response (SYK, CTSS). Functional enrichment and protein-protein interaction (PPI) network analysis highlighted critical pathways involved in neutrophil chemotaxis, ECM organization, and PI3K-Akt signaling, uncovering potential crosstalk between immune dysregulation and ECM degradation in choroidal neovascularization (CNV) progression. In conclusion, the optimized LC-FAIMS-MS/MS technique presented in this study offers an enhanced depth of proteomic analysis for the RC tissue, revealing novel insights into the molecular mechanisms of nvAMD and identifying new potential therapeutic targets.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144666645","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

Transcriptome-Proteome Profiling in Burkholderia thailandensis during the Transition from Exponential to Stationary Phase. 泰国伯克霍尔德菌从指数期过渡到固定期的转录组-蛋白质组分析。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-07-18 DOI: 10.1021/acs.jproteome.5c00223

Ahmed Al-Tohamy, Fabrizio Donnarumma, Anne Grove

{"title":"Transcriptome-Proteome Profiling in Burkholderia thailandensis during the Transition from Exponential to Stationary Phase.","authors":"Ahmed Al-Tohamy, Fabrizio Donnarumma, Anne Grove","doi":"10.1021/acs.jproteome.5c00223","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00223","url":null,"abstract":"Burkholderia thailandensis is closely related to, and a surrogate for, highly pathogenic Burkholderia species. Like other bacterial cells, it commonly exists in the stationary phase, for instance, within a host cell. Understanding the molecular mechanisms that characterize the transition from exponential to stationary phases is therefore critical to understanding responses to stress or nutrient limitation. We present here an integrated transcriptomic and proteomic analysis of mRNA and protein abundance changes during entry into the stationary phase. We identified 928 differentially accumulating mRNAs and 832 differentially accumulating proteins. mRNAs encoding proteins involved in benzoate degradation and O-antigen nucleotide sugar biosynthesis were elevated in the stationary phase, whereas processes such as translation and flagellar biosynthesis were downregulated. Proteins related to fatty acid degradation and butanoate metabolism accumulated in the stationary phase along with proteins involved in the synthesis of secondary metabolites. Markedly downregulated proteins in the stationary phase included ribosomal proteins as well as the house-keeping iron-sulfur biogenesis proteins. An only modest correlation between transcriptome and proteome changes was seen, and the RpoS sigma factor was not significantly increased during the stationary phase; RpoS is typically abundant during the stationary phase and critical for expression of stress-response genes. Our data point to distinct adaptive mechanisms, possibly including post-translational regulation.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144663840","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

Biological Function Assignment across Taxonomic Levels in Mass-Spectrometry-Based Metaproteomics via a Modified Expectation Maximization Algorithm. 基于改进期望最大化算法的质谱宏蛋白质组学生物功能分配

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-07-18 DOI: 10.1021/acs.jproteome.4c01125

Gelio Alves, Aleksey Y Ogurtsov, Yi-Kuo Yu

{"title":"Biological Function Assignment across Taxonomic Levels in Mass-Spectrometry-Based Metaproteomics via a Modified Expectation Maximization Algorithm.","authors":"Gelio Alves, Aleksey Y Ogurtsov, Yi-Kuo Yu","doi":"10.1021/acs.jproteome.4c01125","DOIUrl":"10.1021/acs.jproteome.4c01125","url":null,"abstract":"A major challenge in mass-spectrometry-based metaproteomics is accurately identifying and quantifying biological functions across the full taxonomic lineage of microorganisms. This issue stems from what we refer to as the \"shared confidently identified peptide problem″. To address this issue, most metaproteomics tools rely on the lowest common ancestor (LCA) algorithm to assign biological functions, which often leads to incomplete biological function assignments across the full taxonomic lineage of identified microorganisms. To overcome this limitation, we implemented an expectation-maximization (EM) algorithm, along with a biological function database, within the MiCId workflow. Using synthetic datasets, our study demonstrates that the enhanced MiCId workflow achieves better control over false discoveries and improved accuracy in microorganism identification and biomass estimation compared to Unipept and MetaGOmics. Additionally, the updated MiCId offers improved accuracy and better control of false discoveries in biological function identification compared to Unipept, along with reliable computation of function abundances across the full taxonomic lineage of identified microorganisms. Reanalyzing human oral and gut microbiome datasets using the enhanced MiCId workflow, we show that the results are consistent with those reported in the original publications, which were analyzed using the Galaxy-P platform with MEGAN5 and the MetaPro-IQ approach with Unipept, respectively.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144657878","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

Evaluation of the False Discovery Rate in Library-Free Search by DIA-NN Using In Vitro Human Proteome. 基于体外人类蛋白质组的DIA-NN无库搜索错误发现率评估。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-07-18 DOI: 10.1021/acs.jproteome.5c00036

Kongxin Gu, Masanaga Kenko, Koji Ogawa, Naoki Goshima, Takeshi Masuda, Shingo Ito, Sumio Ohtsuki

{"title":"Evaluation of the False Discovery Rate in Library-Free Search by DIA-NN Using In Vitro Human Proteome.","authors":"Kongxin Gu, Masanaga Kenko, Koji Ogawa, Naoki Goshima, Takeshi Masuda, Shingo Ito, Sumio Ohtsuki","doi":"10.1021/acs.jproteome.5c00036","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00036","url":null,"abstract":"Recently, deep-learning-based in silico spectral libraries have gained increasing attention. Several data-independent acquisition (DIA) software tools have integrated this feature, known as a library-free search, thereby making DIA analysis more accessible. However, controlling the false discovery rate (FDR) is challenging owing to the vast amount of peptide information in in silico libraries. In this study, we introduced a stringent method to evaluate FDR control using DIA software. Recombinant proteins were synthesized from full-length human cDNA libraries and analyzed by using liquid chromatography-mass spectrometry and DIA software. The results were compared with known protein sequences to calculate the FDR. Notably, we compared the identification performance of DIA-NN versions 1.8.1, 1.9.2, and 2.1.0. Versions 1.9.2 and 2.10 identified more peptides than version 1.8.1, and versions 1.9.2 and 2.1.0 used a more conservative identification approach, thus significantly improving the FDR control. Across the synthesized recombinant protein mixtures, the average FDR at the precursor level was 0.538% for version 1.8.1, 0.389% for version 1.9.2, and 0.385% for version 2.1.0; at the protein level, the FDRs were 2.85%, 1.81%, and 1.81%, respectively. Collectively, our data set provides valuable insights for comparing FDR controls across DIA software and aiding bioinformaticians in enhancing their tools.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144657879","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