Proteomes最新文献_第2页

Cell Surface Proteomics Reveals Hypoxia-Regulated Pathways in Cervical and Bladder Cancer. 细胞表面蛋白质组学揭示宫颈癌和膀胱癌的缺氧调节途径。

IF 3.6

Proteomes Pub Date : 2025-08-05 DOI: 10.3390/proteomes13030036

Faris Alanazi, Ammar Sharif, Melissa Kidd, Emma-Jayne Keevill, Vanesa Biolatti, Richard D Unwin, Peter Hoskin, Ananya Choudhury, Tim A D Smith, Conrado G Quiles

{"title":"Cell Surface Proteomics Reveals Hypoxia-Regulated Pathways in Cervical and Bladder Cancer.","authors":"Faris Alanazi, Ammar Sharif, Melissa Kidd, Emma-Jayne Keevill, Vanesa Biolatti, Richard D Unwin, Peter Hoskin, Ananya Choudhury, Tim A D Smith, Conrado G Quiles","doi":"10.3390/proteomes13030036","DOIUrl":"10.3390/proteomes13030036","url":null,"abstract":"Background Plasma membrane proteins (PMPs) play key roles in cell signalling, adhesion, and trafficking, and are attractive therapeutic targets in cancer due to their surface accessibility. However, their typically low abundance limits detection by conventional proteomic approaches.Methods: To improve PMP detection, we employed a surface proteomics workflow combining cell surface biotinylation and affinity purification prior to LC-MS/MS analysis in cervical (SiHa) and bladder (UMUC3) cancer cell lines cultured under normoxic (21% O2) or hypoxic (0.1% O2) conditions.Results: In SiHa cells, 43 hypoxia-upregulated proteins were identified exclusively in the biotin-enriched fraction, including ITGB2, ITGA7, AXL, MET, JAG2, and CAV1/CAV2. In UMUC3 cells, 32 unique upregulated PMPs were detected, including CD55, ADGRB1, SLC9A1, NECTIN3, and ACTG1. These proteins were not observed in corresponding whole-cell lysates and are associated with extracellular matrix remodelling, immune modulation, and ion transport. Biotinylation enhanced the detection of membrane-associated pathways such as ECM organisation, integrin signalling, and PI3K-Akt activation. Protein-protein interaction analysis revealed links between membrane receptors and intracellular stress regulators, including mitochondrial proteins.Conclusions: These findings demonstrate that surface biotinylation improves the sensitivity and selectivity of plasma membrane proteomics under hypoxia, revealing hypoxia-responsive proteins and pathways not captured by standard whole-cell analysis.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12371898/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144966548","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

Multiplex Targeted Proteomic Analysis of Cytokine Ratios for ICU Mortality in Severe COVID-19. 重症COVID-19重症监护病房死亡率细胞因子比值的多重靶向蛋白质组学分析

IF 3.6

Proteomes Pub Date : 2025-08-02 DOI: 10.3390/proteomes13030035

Rúben Araújo, Cristiana P Von Rekowski, Tiago A H Fonseca, Cecília R C Calado, Luís Ramalhete, Luís Bento

{"title":"Multiplex Targeted Proteomic Analysis of Cytokine Ratios for ICU Mortality in Severe COVID-19.","authors":"Rúben Araújo, Cristiana P Von Rekowski, Tiago A H Fonseca, Cecília R C Calado, Luís Ramalhete, Luís Bento","doi":"10.3390/proteomes13030035","DOIUrl":"10.3390/proteomes13030035","url":null,"abstract":"Background: Accurate and timely prediction of mortality in intensive care unit (ICU) patients, particularly those with COVID-19, remains clinically challenging due to complex immune responses. Proteomic cytokine profiling holds promise for refining mortality risk assessment.Methods: Serum samples from 89 ICU patients (55 discharged, 34 deceased) were analyzed using a multiplex 21-cytokine panel. Samples were stratified into three groups based on time from collection to outcome: ≤48 h (Group 1: Early), >48 h to ≤7 days (Group 2: Intermediate), and >7 days to ≤14 days (Group 3: Late). Cytokine levels, simple cytokine ratios, and previously unexplored complex ratios between pro- and anti-inflammatory cytokines were evaluated. Machine learning-based feature selection identified the most predictive ratios, with performance evaluated by area under the curve (AUC), sensitivity, and specificity.Results: Complex cytokine ratios demonstrated superior predictive accuracy compared to traditional severity markers (APACHE II, SAPS II, SOFA), individual cytokines, and simple ratios, effectively distinguishing discharged from deceased patients across all groups (AUC: 0.918-1.000; sensitivity: 0.826-1.000; specificity: 0.775-0.900).Conclusions: Multiplex cytokine profiling enhanced by computationally derived complex ratios may offer robust predictive capabilities for ICU mortality risk stratification, serving as a valuable tool for personalized prognosis in critical care.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12372026/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144966562","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

Molecular Remodeling of the Sperm Proteome Following Varicocele Sclero-Embolization: Implications for Semen Quality Improvement. 精索静脉曲张硬化栓塞后精子蛋白质组的分子重塑：对精液质量改善的影响。

IF 3.6

Proteomes Pub Date : 2025-07-15 DOI: 10.3390/proteomes13030034

Domenico Milardi, Edoardo Vergani, Francesca Mancini, Fiorella Di Nicuolo, Emanuela Teveroni, Emanuele Pierpaolo Vodola, Alessandro Oliva, Giuseppe Grande, Alessandro Cina, Roberto Iezzi, Michela Cicchinelli, Federica Iavarone, Silvia Baroni, Alberto Ferlin, Andrea Urbani, Alfredo Pontecorvi

{"title":"Molecular Remodeling of the Sperm Proteome Following Varicocele Sclero-Embolization: Implications for Semen Quality Improvement.","authors":"Domenico Milardi, Edoardo Vergani, Francesca Mancini, Fiorella Di Nicuolo, Emanuela Teveroni, Emanuele Pierpaolo Vodola, Alessandro Oliva, Giuseppe Grande, Alessandro Cina, Roberto Iezzi, Michela Cicchinelli, Federica Iavarone, Silvia Baroni, Alberto Ferlin, Andrea Urbani, Alfredo Pontecorvi","doi":"10.3390/proteomes13030034","DOIUrl":"10.3390/proteomes13030034","url":null,"abstract":"Background: Varicocele is a common condition involving the dilation of veins in the scrotum, often linked to male infertility and testicular dysfunction. This study aimed to elucidate the molecular effects of successful varicocele treatment on sperm proteomes following percutaneous sclero-embolization.Methods: High-resolution tandem mass spectrometry was performed for proteomic profiling of pooled sperm lysates from five patients exhibiting improved semen parameters before and after (3 and 6 months) varicocele sclero-embolization. Data were validated by Western blot analysis.Results: Seven proteins were found exclusively in varicocele patients before surgery-such as stathmin, IFT20, selenide, and ADAM21-linked to inflammation and oxidative stress. After sclero-embolization, 55 new proteins emerged, including antioxidant enzymes like selenoprotein P and GPX3. Thioredoxin (TXN) and peroxiredoxin (PRDX3) were upregulated, indicating restoration of key antioxidant pathways. Additionally, the downregulation of some histones and the autophagy-related protein ATG9A suggests a shift toward an improved chromatin organization and a healthier cellular environment post-treatment.Conclusions: Varicocele treatment that improves sperm quality and fertility parameters leads to significant proteome modulation. These changes include reduced oxidative stress and broadly restored sperm maturation. Despite the limited patient cohort analyzed, these preliminary findings provide valuable insights into how varicocele treatment might enhance male fertility and suggest potential biomarkers for improved male infertility treatment strategies.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12286009/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699304","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

Comprehensive Integrated Analyses of Proteins and Metabolites in Equine Seminal Plasma (Horses and Donkeys). 马和驴精浆中蛋白质和代谢物的综合综合分析。

IF 3.6

Proteomes Pub Date : 2025-07-04 DOI: 10.3390/proteomes13030033

Xin Wen, Gerelchimeg Bou, Qianqian He, Qi Liu, Minna Yi, Hong Ren

{"title":"Comprehensive Integrated Analyses of Proteins and Metabolites in Equine Seminal Plasma (Horses and Donkeys).","authors":"Xin Wen, Gerelchimeg Bou, Qianqian He, Qi Liu, Minna Yi, Hong Ren","doi":"10.3390/proteomes13030033","DOIUrl":"10.3390/proteomes13030033","url":null,"abstract":"Background: The reproductive ability of equine species is a critical component of equine breeding programs, with sperm quality serving as a primary determinant of reproductive success. In this study, we perform an integrative analysis of proteomics and metabolomics in seminal plasma to identify proteins and metabolites associated with sperm quality and reproductive ability in equine species.Methods: We utilized the CEROS instrument to assess the morphology and motility of sperm samples from three horses and three donkeys. Additionally, we statistically analyzed the mating frequency and pregnancy rates in both species. Meanwhile, the 4D-DIA high-throughput proteomic and metabolomic profiling of seminal plasma samples from horses and donkeys revealed a complex landscape of proteins and metabolites.Results: Our findings reveal a certain degree of correlation between seminal plasma proteins and metabolites and sperm quality, as well as overall fertility. Notably, we found that the proteins B3GAT3, XYLT2, CHST14, HS2ST1, GLCE, and HSPG2 in the glycosaminoglycan biosynthesis signaling pathway; the metabolites D-glucose, 4-phosphopantetheine, and 4-hydroxyphenylpyruvic acid in the tyrosine metabolism, starch, and source metabolisms; and pantothenate CoA biosynthesis metabolism present unique characteristics in the seminal plasma of equine species.Conclusions: This comprehensive approach provides new insights into the molecular mechanisms underlying sperm quality and has identified potential proteins and metabolites that could be used to indicate reproduction ability. The findings from this study could be instrumental in developing novel strategies to enhance equine breeding practices and reproductive management. Future research will focus on exploring their potential for clinical application in the equine industry.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12285962/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699302","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

Proteomic Profiling Reveals Novel Molecular Insights into Dysregulated Proteins in Established Cases of Rheumatoid Arthritis. 蛋白质组学分析揭示了类风湿性关节炎病例中失调蛋白的新分子见解。

IF 3.6

Proteomes Pub Date : 2025-07-04 DOI: 10.3390/proteomes13030032

Afshan Masood, Hicham Benabdelkamel, Assim A Alfadda, Abdurhman S Alarfaj, Amina Fallata, Salini Scaria Joy, Maha Al Mogren, Anas M Abdel Rahman, Mohamed Siaj

{"title":"Proteomic Profiling Reveals Novel Molecular Insights into Dysregulated Proteins in Established Cases of Rheumatoid Arthritis.","authors":"Afshan Masood, Hicham Benabdelkamel, Assim A Alfadda, Abdurhman S Alarfaj, Amina Fallata, Salini Scaria Joy, Maha Al Mogren, Anas M Abdel Rahman, Mohamed Siaj","doi":"10.3390/proteomes13030032","DOIUrl":"10.3390/proteomes13030032","url":null,"abstract":"Background: Rheumatoid arthritis (RA) is a chronic autoimmune disorder that predominantly affects synovial joints, leading to inflammation, pain, and progressive joint damage. Despite therapeutic advancements, the molecular basis of established RA remains poorly defined. Methods: In this study, we conducted an untargeted plasma proteomic analysis using two-dimensional differential gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) in samples from RA patients and healthy controls in the discovery phase. Results: Significantly (ANOVA, p ≤ 0.05, fold change > 1.5) differentially abundant proteins (DAPs) were identified. Notably, upregulated proteins included mitochondrial dicarboxylate carrier, hemopexin, and 28S ribosomal protein S18c, while CCDC124, osteocalcin, apolipoproteins A-I and A-IV, and haptoglobin were downregulated. Receiver operating characteristic (ROC) analysis identified CCDC124, osteocalcin, and metallothionein-2 with high diagnostic potential (AUC = 0.98). Proteins with the highest selected frequency were quantitatively verified by multiple reaction monitoring (MRM) analysis in the validation cohort. Bioinformatic analysis using Ingenuity Pathway Analysis (IPA) revealed the underlying molecular pathways and key interaction networks involved STAT1, TNF, and CD40. These central nodes were associated with immune regulation, cell-to-cell signaling, and hematological system development. Conclusions: Our combined proteomic and bioinformatic approaches underscore the involvement of dysregulated immune pathways in RA pathogenesis and highlight potential diagnostic biomarkers. The utility of these markers needs to be evaluated in further studies and in a larger cohort of patients.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12286002/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699325","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

SDS Depletion from Intact Membrane Proteins by KCl Precipitation Ahead of Mass Spectrometry Analysis. 质谱分析前用KCl沉淀法去除完整膜蛋白的SDS。

IF 3.6

Proteomes Pub Date : 2025-07-02 DOI: 10.3390/proteomes13030030

Tania Iranpour, Mapenzi Mirimba, Chloe Shenouda, Adam Lynch, Alan A Doucette

{"title":"SDS Depletion from Intact Membrane Proteins by KCl Precipitation Ahead of Mass Spectrometry Analysis.","authors":"Tania Iranpour, Mapenzi Mirimba, Chloe Shenouda, Adam Lynch, Alan A Doucette","doi":"10.3390/proteomes13030030","DOIUrl":"10.3390/proteomes13030030","url":null,"abstract":"Background: Membrane proteins are preferentially solubilized with sodium dodecyl sulfate (SDS), which necessitates a purification protocol to deplete the surfactant prior to mass spectrometry analysis. However, maintaining solubility of intact membrane proteins is challenged in an SDS-free environment. SDS precipitation with potassium salts (KCl) offers a potentially viable workflow to deplete SDS and permit proteoform analysis. The purpose of this study is to devise a robust detergent-based protocol applicable for processing and analysis of intact membrane-associated proteoforms.Methods: The precipitation conditions impacting SDS removal from spinach chloroplasts and liver membrane proteome preparations were evaluated, capitalizing on optimization of pH (highly basic), addition of MS-compatible solubilizing additives (urea) and adjustment of the KCl to SDS ratio to maximize recovery and purity.Results: Characterization of the SDS-solubilized, KCl-precipitated spinach membrane preparation revealed multiple charge envelope MS spectra displaying high signal to noise, free of SDS adducts. Precipitation at pH 12 or with urea improved protein recovery and purity. Bottom-up analysis identified 1826 distinct liver protein groups from four independent SDS precipitation conditions. While precipitation at pH 8 without urea revealed a greater number of protein identifications by mass spectrometry, precipitation under highly basic conditions (pH 12) with urea provided higher membrane protein recovery and achieved the greatest number (732 of 1056) and largest percentage (69.3%) of membrane proteins identified in the SDS removal workflow.Conclusion: This workflow provides new opportunities for MS-based proteoform analysis by capitalizing on the benefits of SDS for protein extraction while maintaining high solubility and purity of intact proteins though KCl precipitation of the surfactant.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12286100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699326","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

Comparative Label-Based Proteomics of Venoms from Echis ocellatus, Naja nigricollis, and Bitis arietans. 比较标记-基于蛋白质组学的ecis ocellatus， Naja nigricollis和Bitis arieans毒液。

IF 3.6

Proteomes Pub Date : 2025-07-02 DOI: 10.3390/proteomes13030031

Abdulbaki Alfa-Ibrahim Adio, Samuel Odo Uko, Jiddah Muhammad Lawal, Ibrahim Malami, Nafiu Lawal, Amina Jega Yusuf Jega, Bilyaminu Abubakar, Muhammad Bashir Bello, Kasimu Ghandi Ibrahim, Murtala Bello Abubakar, Abdussamad Muhammad Abdussamad, Mujtaba Sulaiman Abubakar, Mustapha Umar Imam

{"title":"Comparative Label-Based Proteomics of Venoms from Echis ocellatus, Naja nigricollis, and Bitis arietans.","authors":"Abdulbaki Alfa-Ibrahim Adio, Samuel Odo Uko, Jiddah Muhammad Lawal, Ibrahim Malami, Nafiu Lawal, Amina Jega Yusuf Jega, Bilyaminu Abubakar, Muhammad Bashir Bello, Kasimu Ghandi Ibrahim, Murtala Bello Abubakar, Abdussamad Muhammad Abdussamad, Mujtaba Sulaiman Abubakar, Mustapha Umar Imam","doi":"10.3390/proteomes13030031","DOIUrl":"10.3390/proteomes13030031","url":null,"abstract":"Background: Snake envenomation is a major public health issue in Nigeria, primarily due to bites from Echis ocellatus, Naja nigricollis, and Bitis arietans. Understanding their venom composition is essential for effective antivenom development. This study characterizes and compares the venom proteomes of these snakes using iTRAQ-based proteomics, focusing on key toxin families and their relative abundances. Methods: Venom samples were ethically collected from adult snakes, pooled by species, lyophilized, and stored for proteomic analysis. Proteins were extracted, digested with trypsin, and labeled with iTRAQ. Peptides were analyzed via mass spectrometry, and data were processed using Mascot and IQuant for protein identification and quantification. Results:E. ocellatus and B. arietans venoms had similar profiles, rich in C-type lectins, serine proteases, and phospholipase A2s. These comprised 17%, 11%, and 5% in E. ocellatus and 47%, 10%, and 7% in B. arietans, with metalloproteinases dominating both (53% and 47%). In N. nigricollis, three-finger toxins (9%) were most abundant, followed by metalloproteinases (3%). All species shared four core protein families, with N. nigricollis also containing four uncharacterized proteins. Conclusions: This study highlights venom compositional differences, advancing snake venom biology and informing targeted antivenom development.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12286013/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699301","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 Protein Extraction Techniques for Elucidating Proteomic Changes in Yeast Deletion Strains. 酵母缺失菌株蛋白质组学变化的蛋白质提取技术评价。

IF 3.6

Proteomes Pub Date : 2025-07-01 DOI: 10.3390/proteomes13030028

Valentina Rossio, Joao A Paulo

{"title":"Evaluating Protein Extraction Techniques for Elucidating Proteomic Changes in Yeast Deletion Strains.","authors":"Valentina Rossio, Joao A Paulo","doi":"10.3390/proteomes13030028","DOIUrl":"10.3390/proteomes13030028","url":null,"abstract":"Background: Alterations in protein abundance profiles in yeast deletion strains are frequently utilized to gain insights into cellular functions and regulatory networks, most of which are conserved in higher eukaryotes.Methods: This study investigates the impact of protein extraction methodologies on the whole proteome analysis of S. cerevisiae, comparing detergent-based lysis versus mechanical lysis with silica beads. We evaluated the proteomic profiles of wild-type and two yeast deletion strains, siz1Δ and nfi1Δ (siz2Δ), which are SUMO E3 ligases. Combining isobaric TMTpro-labeling with mass spectrometry using real-time search MS3, we profiled over 4700 proteins, covering approximately 80% of the yeast proteome.Results: Hierarchical clustering and principal component analyses revealed that the choice of protein extraction method significantly influenced the proteomic data, overshadowing the genetic variances among these strains. Notably, the detergent-based lysis showed superior performance in extracting proteins compared to mechanical lysis. Despite minimal proteomic alterations among strains, we observed consistent changes regardless of the lysis strategy in proteins such as Ino1, Rep1, Rep2, Snz1, and Fdh1 in both SUMO E3 ligase deletion strains, implying potential redundant mechanisms of control for these proteins.Conclusion: These findings underscore the importance of method selection at each step of sample preparation in proteomic studies and enhance our comprehension of cellular adaptations to genetic perturbations.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12286038/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699303","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

Proteoform Patterns in Hepatocellular Carcinoma Tissues: Aspects of Oncomarkers. 肝细胞癌组织中的蛋白质形态模式：肿瘤标志物的方面。

IF 3.6

Proteomes Pub Date : 2025-07-01 DOI: 10.3390/proteomes13030027

Elena Zorina, Natalia Ronzhina, Olga Legina, Nikolai Klopov, Victor Zgoda, Stanislav Naryzhny

{"title":"Proteoform Patterns in Hepatocellular Carcinoma Tissues: Aspects of Oncomarkers.","authors":"Elena Zorina, Natalia Ronzhina, Olga Legina, Nikolai Klopov, Victor Zgoda, Stanislav Naryzhny","doi":"10.3390/proteomes13030027","DOIUrl":"10.3390/proteomes13030027","url":null,"abstract":"Background: Human proteins exist in numerous modifications-proteoforms-which are promising targets for biomarker studies. In this study, we aimed to generate comparative proteomics data, including proteoform patterns, from hepatocellular carcinoma (HCC) and nonmalignant liver tissues.Methods: To investigate protein profiles and proteoform patterns, we employed a panoramic, integrative top-down proteomics approach: two-dimensional gel electrophoresis (2DE) coupled with liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS).Results: We visualized over 2500 proteoform patterns per sample type, enabling the identification of distinct protein signatures and common patterns differentiating nonmalignant and malignant liver cells. Among these, 1270 protein patterns were uniformly observed across all samples. Additionally, 38 proteins-including pyruvate kinase PKM (KPYM), annexin A2 (ANXA2), and others-exhibited pronounced differences in proteoform patterns between nonmalignant and malignant tissues.Conclusions: Most proteoform patterns of the same protein were highly similar, with the dominant peak corresponding to theoretical (unmodified) protein parameters. However, certain proteins displayed altered proteoform patterns and additional proteoforms in cancer compared to controls. These proteins were prioritized for further characterization.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12285994/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699306","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

Alterations in Tear Proteomes of Adults with Pre-Diabetes and Type 2 Diabetes Mellitus but Without Diabetic Retinopathy. 成人糖尿病前期和2型糖尿病但无糖尿病视网膜病变的泪液蛋白质组的改变

IF 3.6

Proteomes Pub Date : 2025-07-01 DOI: 10.3390/proteomes13030029

Guoting Qin, Cecilia Chao, Shara Duong, Jennyffer Smith, Hong Lin, Wendy W Harrison, Chengzhi Cai

{"title":"Alterations in Tear Proteomes of Adults with Pre-Diabetes and Type 2 Diabetes Mellitus but Without Diabetic Retinopathy.","authors":"Guoting Qin, Cecilia Chao, Shara Duong, Jennyffer Smith, Hong Lin, Wendy W Harrison, Chengzhi Cai","doi":"10.3390/proteomes13030029","DOIUrl":"10.3390/proteomes13030029","url":null,"abstract":"Background: Type 2 diabetes mellitus (T2DM) is an epidemic chronic disease that affects millions of people worldwide. This study aims to explore the impact of T2DM on the tear proteome, specifically investigating whether alterations occur before the development of diabetic retinopathy.Methods: Flush tear samples were collected from healthy subjects and subjects with preDM and T2DM. Tear proteins were processed and analyzed by mass spectrometry-based shotgun proteomics using a data-independent acquisition parallel acquisition serial fragmentation (diaPASEF) approach. Machine learning algorithms, including random forest, lasso regression, and support vector machine, and statistical tools were used to identify potential biomarkers.Results: Machine learning models identified 17 proteins with high importance in classification. Among these, five proteins (cystatin-S, S100-A11, submaxillary gland androgen-regulated protein 3B, immunoglobulin lambda variable 3-25, and lambda constant 3) exhibited differential abundance across these three groups. No correlations were identified between proteins and clinical assessments of the ocular surface. Notably, the 17 important proteins showed superior prediction accuracy in distinguishing all three groups (healthy, preDM, and T2DM) compared to the five proteins that were statistically significant.Conclusions: Alterations in the tear proteome profile were observed in adults with preDM and T2DM before the clinical diagnosis of ocular abnormality, including retinopathy.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12286239/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699300","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