Proteomes最新文献_第2页

Comparison of the Trapping Efficiency for Tryptic Peptides on Particle-Packed and Micro-Pillar Trap Columns for Proteomics Analyses. 蛋白质组学分析中颗粒填充柱和微柱陷阱柱对色氨酸捕获效率的比较

IF 3.6

Proteomes Pub Date : 2026-02-18 DOI: 10.3390/proteomes14010010

Jadranka Miletić Vukajlović, Bojana Ilić, Bella Bruszel, Tanja Panić-Janković, Goran Mitulović

{"title":"Comparison of the Trapping Efficiency for Tryptic Peptides on Particle-Packed and Micro-Pillar Trap Columns for Proteomics Analyses.","authors":"Jadranka Miletić Vukajlović, Bojana Ilić, Bella Bruszel, Tanja Panić-Janković, Goran Mitulović","doi":"10.3390/proteomes14010010","DOIUrl":"10.3390/proteomes14010010","url":null,"abstract":"Background: Low-volume trapping columns are essential for sample enrichment, desalting, and injection profile focusing on nano-LC-MS-based proteomics. They enable higher sample loading, improve chromatographic performance, and protect the analytical column by removing salts and contaminants. Recently, monolithic trap columns with micropillar architecture have emerged as alternatives to conventionally packed traps. This study compares the performance of a packed and a micropillar monolithic trap column for the analysis of tryptic peptides.Methods: A tryptic digest of HeLa cell lysate was analyzed under identical LC-MS conditions using both trap types. Peptides were detected at 214 nm and analyzed by nano-ESI on a Q Exactive Plus Orbitrap. Data were searched against the human UniProt database (February 2023) using FragPipe v20.0, and statistical evaluation of MaxLFQ intensities was performed in Perseus using Welch's t-test and clustering analysis.Results: Over 2500 proteins were identified with both setups. The packed trap column yielded more total peptides, particularly those with post-translational modifications and higher hydrophilicity, whereas the monolithic column favored peptides of intermediate hydrophobicity. Chromatographic profiles confirmed a slight reduction in the trapping efficiency of hydrophilic peptides by the monolithic trap.Conclusions: Trap column design significantly influences peptide recovery and proteome coverage.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"14 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13030385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147532280","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Scout-Triggered Multiple Reaction Monitoring Enables Robust Quantification of Host Cell Proteins Across Bioprocess Matrices. 侦察兵触发的多重反应监测使宿主细胞蛋白在生物过程矩阵的稳健定量。

IF 3.6

Proteomes Pub Date : 2026-02-17 DOI: 10.3390/proteomes14010009

Julie Flecheux, Chloé Bardet, Laura Herment, Tanguy Fortin, Jérôme Lemoine

{"title":"Scout-Triggered Multiple Reaction Monitoring Enables Robust Quantification of Host Cell Proteins Across Bioprocess Matrices.","authors":"Julie Flecheux, Chloé Bardet, Laura Herment, Tanguy Fortin, Jérôme Lemoine","doi":"10.3390/proteomes14010009","DOIUrl":"10.3390/proteomes14010009","url":null,"abstract":"Background: Host cell proteins (HCPs) are process-related impurities that must be monitored in biopharmaceutical products due to their potential impact on product quality and patient safety. Targeted LC-MS/MS approaches such as multiple reaction monitoring (MRM) enable protein-specific HCP quantification but are difficult to apply in highly multiplexed assays because of retention time (RT) variability across complex bioprocess matrices.Methods: Here, we show that conventional RT-scheduled MRM workflows lack transferability when applied to heterogeneous drug substances and process intermediates. Using a targeted assay comprising 240 peptides corresponding to 97 CHO-derived HCPs, RT shifts of several minutes resulted in truncated chromatographic peaks and peptide signal loss, even when wide scheduling windows were used. To overcome this limitation, a scout-triggered MRM (st-MRM) acquisition strategy based on event-driven monitoring was implemented.Results: This approach enabled robust peptide detection across diverse matrices within a single injection, without method re-optimization. Absolute quantification using stable isotope-labeled peptides spanned six orders of magnitude, with HCPs quantified down to 2.9 ppm in purified drug substances.Conclusion: Overall, st-MRM improves the robustness and transferability of highly multiplexed targeted proteomics workflows for HCP analysis.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"14 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12921893/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146259076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proteome-Wide Analysis of Functional Phosphosites in the FGFR Family of Proteins: Insights from Large-Scale Phosphoproteomic Analysis. FGFR蛋白家族中功能性磷酸化位点的蛋白质组分析：来自大规模磷酸化蛋白质组学分析的见解。

IF 3.6

Proteomes Pub Date : 2026-02-13 DOI: 10.3390/proteomes14010008

Akhina Palollathil, Althaf Mahin, Athira Perunelly Gopalakrishnan, Tejaswini R Poojari, Alimath Sambreena, Prathik Basthikoppa Shivamurthy, Rajesh Raju

{"title":"Proteome-Wide Analysis of Functional Phosphosites in the FGFR Family of Proteins: Insights from Large-Scale Phosphoproteomic Analysis.","authors":"Akhina Palollathil, Althaf Mahin, Athira Perunelly Gopalakrishnan, Tejaswini R Poojari, Alimath Sambreena, Prathik Basthikoppa Shivamurthy, Rajesh Raju","doi":"10.3390/proteomes14010008","DOIUrl":"10.3390/proteomes14010008","url":null,"abstract":"Background: Fibroblast growth factor receptors (FGFRs) play a crucial role in tissue homeostasis and organ development by regulating cellular processes, including proliferation, differentiation, and survival. Dysregulation of FGFRs contributes to developmental disorders and carcinogenesis. As membrane-bound receptors, they represent promising targets for therapeutic intervention and drug development.Methods: This study employed a systematic in silico analysis of publicly available phosphoproteomics datasets to provide a comprehensive overview of the phosphorylation regulatory network of the FGFR family.Results: We identified predominant phosphosites in FGFR1-4 that exhibited differential abundance across diverse experimental conditions, specifically, Y653 in FGFR1; S453, Y586, Y656, and Y657 in FGFR2; S444 and S445 in FGFR3; and S573 in FGFR4. Our analysis identified 32 and 89 significantly co-modulated phosphosites on other proteins with FGFR3 and FGFR4, respectively. Beyond the upstream kinases from the FGFR family, we also identified MAPK1 as a potential upstream kinase of FGFR4. Furthermore, disease enrichment analysis revealed that proteins co-modulated with FGFR3 were primarily involved in skeletal developmental disorders, such as brachydactyly, short toe, and syndactyly of fingers, whereas those associated with FGFR4 were linked to various cancers.Conclusions: Our findings highlight key disease-associated phosphosites within the FGFRs and offer a foundation for advancing phosphosite-focused therapeutic research.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"14 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12922108/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146259031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PTMs_Closed_Search: Multiple Post-Translational Modification Closed Search Using Reduced Search Space and Transferred FDR. PTMs_Closed_Search：使用缩减搜索空间和转移FDR的多重翻译后修改封闭搜索。

IF 3.6

Proteomes Pub Date : 2026-02-02 DOI: 10.3390/proteomes14010007

Yury Yu Strogov, Sergey A Spirin, Mark V Ivanov, Maria A Kulebyakina, Anastasia Yu Efimenko, Oleg I Klychnikov

{"title":"PTMs_Closed_Search: Multiple Post-Translational Modification Closed Search Using Reduced Search Space and Transferred FDR.","authors":"Yury Yu Strogov, Sergey A Spirin, Mark V Ivanov, Maria A Kulebyakina, Anastasia Yu Efimenko, Oleg I Klychnikov","doi":"10.3390/proteomes14010007","DOIUrl":"10.3390/proteomes14010007","url":null,"abstract":"Background: Currently, post-translational modification (PTM) search in MS/MS data is performed using either open modification search (OMS) or closed search (CS) algorithms. The OMS method allows for the determination of many PTMs and unknown mass-shifts in one run. In contrast, closed search algorithms are more sensitive but limited in the number of PTMs that can be specified in one search. Methods: In this manuscript, we propose an optimized Python algorithm based on the IdentiPy search engine that performs an automated sequential search for each PTM based on previous annotations from public databases and customized protein lists. We also determined the sufficient size of the search space to increase the significance of false discovery rate (FDR) estimation. We modified the FDR calculation algorithm by implementing a spline approximation of the ratio of the modified decoys, and by calculating error propagation to filter out unstable data and determine the cutoff value. Results: The results of this pipeline for a test dataset were comparable to previously published data in terms of the number of unmodified peptides and proteins. Additionally, we identified 13 different types of peptide PTMs and achieved an increase in relative protein coverage. Our filtration method based on spline transferred FDR showed a superior number of identified peptides compared to separate FDR. Conclusions: Our developed pipeline can be used as a standalone application or as a module of multiple PTM search in data analysis platforms.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"14 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12921745/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146259100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evaluating the Impact of Two Different Diets on the Protein Profile of the Brain, Liver, and Intestine of the Barramundi. 评估两种不同饲料对澳洲鲈鱼脑、肝和肠蛋白质结构的影响。

IF 3.6

Proteomes Pub Date : 2026-01-29 DOI: 10.3390/proteomes14010006

Mohadeseh Montazeri Shatouri, Igor Pirozzi, Pinar Demir Soker, Zeshan Ali, Ardeshir Amirkhani, Paul A Haynes

{"title":"Evaluating the Impact of Two Different Diets on the Protein Profile of the Brain, Liver, and Intestine of the Barramundi.","authors":"Mohadeseh Montazeri Shatouri, Igor Pirozzi, Pinar Demir Soker, Zeshan Ali, Ardeshir Amirkhani, Paul A Haynes","doi":"10.3390/proteomes14010006","DOIUrl":"10.3390/proteomes14010006","url":null,"abstract":"Background: Commercial feed formulations are increasingly being evaluated for their nutritional impacts on aquaculture species, yet the molecular consequences of commonly used commercial diets remain underexplored.Methods: This study investigated the effects of two commercial diets, diet A (higher land animal protein) and diet B (higher fish meal content), on the protein profile in the brain, liver, and intestine of barramundi (Lates calcarifer). A 12-week feeding trial was conducted with controlled water quality, and proteomic profiling was performed using data-independent acquisition.Results: Differential analysis revealed consistent changes between diets across all tissues, with a higher percentage of differentially abundant proteins observed in between-diet comparisons (12.99% in brain, 12.73% in liver, and 16.59% in intestine) than within-diet controls (<8%), confirming a measurable dietary effect size. In total, 3901 proteins in the brain, 3660 in the liver, and 5025 in the intestine were quantified. Functional enrichment highlighted upregulation of ferroptosis pathways, downregulation of apelin signaling in the brain, and increased digestive proteases in the liver. ICP-MS confirmed elevated iron concentrations in the brain, liver, and intestine of fish fed on diet B.Conclusions: These findings demonstrate that molecular pathways linked to iron metabolism, digestion, and growth regulation are very sensitive to dietary composition, highlighting how proteomics can help identify subtle impacts of compositional differences in aquaculture feeding. Although physiological parameters did not differ significantly, the proteomic alterations observed across tissues likely indicate organ-specific metabolic adaptations to the differing nutrient availability between diets.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"14 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12921775/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146259038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrated Phosphoproteomics Identifies TGFβ-Dependent Phosphorylation Events Linking Kinase Signaling to Autophagy in Palatogenesis. 整合磷酸化蛋白质组学鉴定了tgf β依赖性磷酸化事件，将激酶信号传导与腭发育中的自噬联系起来。

IF 3.6

Proteomes Pub Date : 2026-01-23 DOI: 10.3390/proteomes14010005

Xia Peng, Jing Chen, Xiaoyu Zheng, Xige Zhao, Yijia Wang, Xiaotong Wang, Juan Du

{"title":"Integrated Phosphoproteomics Identifies TGFβ-Dependent Phosphorylation Events Linking Kinase Signaling to Autophagy in Palatogenesis.","authors":"Xia Peng, Jing Chen, Xiaoyu Zheng, Xige Zhao, Yijia Wang, Xiaotong Wang, Juan Du","doi":"10.3390/proteomes14010005","DOIUrl":"10.3390/proteomes14010005","url":null,"abstract":"Background: Cleft palate (CP) is a prevalent craniofacial malformation, with the TGFβ pathway playing a critical role. Recent evidence links autophagy to regulating mouse embryonic palatal mesenchyme (MEPM) cells, but its interaction with TGFβ-activated phosphorylation cascades remains largely unknown. Here, we investigated the interplay between these pathways during palatogenesis.Methods: H&E and IHC analyses revealed increased expression of Beclin 1 and LC3 during the critical period of palatal shelf elevation and fusion (E13.5-E15.5). Bulk RNA sequencing (Bulk RNA-seq) further revealed enrichment of autophagy-related pathways and their interaction with TGFβ signaling. TMT-based phosphoproteomics was performed on TGFβ2-treated MEPM cells.Results: We identified 23,471 peptides and 3952 proteins, including 6339 phosphopeptides corresponding to 2195 phosphoproteins. Differential analysis found 477 phosphopeptides with increased abundance and 53 with decreased abundance, revealing the enrichment of seven serine (p-Ser) motifs (RxxS, SDxD, SDxE, SP, SxDE, SxEE, SxxxxD) and one threonine (p-Thr) motif (TP). Notably, kinase-substrate enrichment analysis identified CSNK2A as a previously unrecognized phosphorylation regulator, together with MAPKs and CDKs. Functional enrichment showed significant involvement of mTOR, MAPK, and autophagy/mitophagy pathways.Conclusions: Our findings revealed that TGFβ2 reshapes the MEPM phosphoproteome through Smad-independent pathway, expanding the palate-specific phospho-signaling atlas beyond the canonical Smad cascade.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"14 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12921946/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146259029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cross-Species Analysis of ABA-Induced Phosphosignaling Landscapes in Rice, Soybean, and Arabidopsis. aba诱导水稻、大豆和拟南芥磷酸化信号的跨物种分析。

IF 3.6

Proteomes Pub Date : 2026-01-20 DOI: 10.3390/proteomes14010004

Hinano Takase, Sotaro Katagiri, Takuma Ide, Aina Nagano, Haruki Sakurai, Hana Kokubo, Taiki Yanagisawa, Masanori Okamoto, Taishi Umezawa

{"title":"Cross-Species Analysis of ABA-Induced Phosphosignaling Landscapes in Rice, Soybean, and Arabidopsis.","authors":"Hinano Takase, Sotaro Katagiri, Takuma Ide, Aina Nagano, Haruki Sakurai, Hana Kokubo, Taiki Yanagisawa, Masanori Okamoto, Taishi Umezawa","doi":"10.3390/proteomes14010004","DOIUrl":"10.3390/proteomes14010004","url":null,"abstract":"Background: Abscisic acid (ABA) is a key phytohormone that regulates plant growth and stress responses through protein phosphorylation. While ABA-induced phosphosignaling has been extensively studied in Arabidopsis thaliana, its conservation and divergence across plant species remain unclear.Methods: Here, we performed phosphoproteomic analysis using LC-MS/MS in Arabidopsis, rice (Oryza sativa), and soybean (Glycine max) to compare ABA-responsive phosphorylation profiles among monocots, dicots, and legumes.Results: ABA treatments on Arabidopsis, rice, and soybean seedlings yielded approximately 24,604, 18,865, and 24,930 phosphopeptides, respectively. Comparative analyses revealed both conserved and species-specific ABA-responsive phosphoproteins.Conclusions: This work provides insights into the evolutionary diversification of ABA signaling and its potential applications in improving crop stress tolerance.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"14 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12922155/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146259067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Proteome of Dictyostelium discoideum Across Its Entire Life Cycle Reveals Sharp Transitions Between Developmental Stages. 盘状盘齿龙整个生命周期的蛋白质组揭示了发育阶段之间的急剧转变。

IF 3.6

Proteomes Pub Date : 2026-01-08 DOI: 10.3390/proteomes14010003

Sarena Banu, P V Anusha, Pedro Beltran-Alvarez, Mohammed M Idris, Katharina C Wollenberg Valero, Francisco Rivero

{"title":"The Proteome of Dictyostelium discoideum Across Its Entire Life Cycle Reveals Sharp Transitions Between Developmental Stages.","authors":"Sarena Banu, P V Anusha, Pedro Beltran-Alvarez, Mohammed M Idris, Katharina C Wollenberg Valero, Francisco Rivero","doi":"10.3390/proteomes14010003","DOIUrl":"10.3390/proteomes14010003","url":null,"abstract":"Background: Dictyostelium discoideum is widely used in developmental and evolutionary biology due to its ability to transition from a single cell to a multicellular organism in response to starvation. While transcriptome information across its life cycle is widely available, only early-stage data exist at the proteome level. This study characterizes and compares the proteomes of D. discoideum cells at the vegetative, aggregation, mound, culmination and fruiting body stages.Methods: Samples were collected from cells developing synchronously on nitrocellulose filters. Proteins were extracted and digested with trypsin, and peptides were analyzed by liquid chromatography-tandem mass spectrometry. Data were processed using Proteome Discoverer™ for protein identification and label-free quantification.Results: A total of 4502 proteins were identified, of which 1848 (41%) were present across all stages. Pairwise comparisons between adjacent stages revealed clear transitions, the largest ones occurring between the culmination and fruiting body and between the fruiting body and vegetative stage, involving 29% and 52% of proteins, respectively. Hierarchical clustering assigned proteins to one of nine clusters, each displaying a distinct pattern of abundances across the life cycle.Conclusions: This study presents the first complete developmental proteomic time series for D. discoideum, revealing changes that contribute to multicellularity, cellular differentiation and morphogenesis.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"14 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12821622/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146012177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Beyond Repression: ArsR Functions as a Global Activator of Metabolic and Redox Responses in Escherichia coli. 超越抑制：ArsR在大肠杆菌中作为代谢和氧化还原反应的全局激活因子。

IF 3.6

Proteomes Pub Date : 2026-01-04 DOI: 10.3390/proteomes14010001

Brett Sather, James Larson, Kian Hutt Vater, Jade Westrum, Timothy R McDermott, Brian Bothner

{"title":"Beyond Repression: ArsR Functions as a Global Activator of Metabolic and Redox Responses in Escherichia coli.","authors":"Brett Sather, James Larson, Kian Hutt Vater, Jade Westrum, Timothy R McDermott, Brian Bothner","doi":"10.3390/proteomes14010001","DOIUrl":"10.3390/proteomes14010001","url":null,"abstract":"Background: The arsenic-responsive repressor, ArsR, has long been understood as a canonical regulator of the arsRBC operon, which confers resistance to arsenic stress. However, recent studies suggest a broader regulatory scope for ArsR. Here, we investigated the proteomic landscape of Escherichia coli strains with and without ArsR to elucidate ArsR as an activator in both non-stressing and arsenic-stressing conditions.Methods: Using mass-spectrometry-based shotgun proteomics and statistical analyses, we characterized the differential abundance of proteins across AW3110 (ΔarsRBC), AW3110 complemented with arsR, and wild-type K-12 strains under control and arsenite-stressed conditions.Results: Our study shows that ArsR influences proteomic networks beyond the ars operon, integrating metabolic and redox responses crucial for cellular adaptation and survival. This suggests that ArsR has a significant role in gut microbiome metabolomic profiles in response to arsenite. Proteins involved in alanine, lactaldehyde, arginine, thioredoxin, and proline pathways were significantly elevated in strains where ArsR was detected, both with and without arsenite. We identified proteins exhibiting an \"ArsR-dependent\" activation pattern, highlighting ArsR's potential role in redox balance and energy metabolism.Conclusions: These findings challenge the classical view of ArsR as a repressor and position it as a pleiotropic regulator, including broad activation.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"14 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12821715/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146012164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proteomics and Bioinformatics Profiles of Human Mesothelial Cell Line MeT-5A. 人间皮细胞系MeT-5A的蛋白质组学和生物信息学分析。

IF 3.6

Proteomes Pub Date : 2026-01-04 DOI: 10.3390/proteomes14010002

Rachel L Watkin, Avedis A Kazanjian, Jennifer R Damicis, Elizabeth Yohannes

{"title":"Proteomics and Bioinformatics Profiles of Human Mesothelial Cell Line MeT-5A.","authors":"Rachel L Watkin, Avedis A Kazanjian, Jennifer R Damicis, Elizabeth Yohannes","doi":"10.3390/proteomes14010002","DOIUrl":"10.3390/proteomes14010002","url":null,"abstract":"Background: Despite existing proteomics studies of other cell types, a comprehensive proteome of mesothelial cells has not been characterized. This study establishes a crucial baseline proteome for mesothelial cells to better understand their fundamental bioprocesses in healthy and injured states. Methods: Using mass spectrometry-based shotgun proteomics, we characterized the cellular fraction (CF) and conditioned medium (CM) proteomes of mesothelial cell line MeT-5A. The datasets were analyzed for Gene Ontology (GO) terms and canonical pathway enrichments to identify biological themes. Results: Our analysis identified 5087 protein groups, including 1532 shared proteins, 3122 unique to the CF and 433 exclusive to the CM. GO annotation revealed distinct functional enrichment profiles, reflecting the differing roles of intracellular and secreted proteins. While intracellular proteins were linked to core cellular functions, the extracellular proteome was enriched for signaling and cell-to-cell interaction pathways. The proteins shared by both compartments provided an integrated view of the molecular coordination between the cellular and extracellular environments. Conclusions: This study provides the first comprehensive baseline proteome for mesothelial cells and their secreted medium, offering a vital resource for future investigations into the mesothelium, particularly in the context of disease or injury.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"14 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12821629/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146012195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0