Estelle Maret, Kim Wiskott, Tobias Shipley, Federica Gilardi, Marc Augsburger, Aurelien Thomas, Tony Fracasso, Tatjana Sajic
{"title":"Activity-Based Proteome Profiling of Serum Serine Hydrolases: Application in Pediatric Abusive Head Trauma.","authors":"Estelle Maret, Kim Wiskott, Tobias Shipley, Federica Gilardi, Marc Augsburger, Aurelien Thomas, Tony Fracasso, Tatjana Sajic","doi":"10.1002/prca.202400022","DOIUrl":"10.1002/prca.202400022","url":null,"abstract":"<p><strong>Purpose: </strong>Traumatic brain injury (TBI), including pediatric abusive head trauma (AHT), is the leading cause of death and disability in children and young adults worldwide. The current understanding of trauma-induced molecular changes in the brain of human subjects with intracranial hemorrhage (ICH) remains inadequate and requires further investigation to improve the outcome and management of TBI in the clinic. Calcium-mediated damage at the site of brain injury has been shown to activate several catalytic enzymes.</p><p><strong>Experimental design: </strong>Serine hydrolases (SHs) are major catalytic enzymes involved in the biochemical pathways of blood coagulation, systemic inflammation, and neuronal signaling. Here, we investigated activity-based protein profiling (ABPP) coupled to liquid chromatography-mass spectrometry (LC-MS) by measuring the activity status of SH enzymes in the serum of infants with severe ICH as a consequence of AHT or atraumatic infants who died of sudden infant death syndrome (SIDS).</p><p><strong>Results: </strong>Our proof-of-principle study revealed significantly reduced physiological activity of dozens of metabolic SHs in the serum of infants with severe AHT compared to the SIDS group, with some of the enzymes being related to neurodevelopment and basic brain metabolism.</p><p><strong>Conclusions and clinical relevance: </strong>To our knowledge, this is the first study to investigate the ABPP of the SHs enzyme family to detect changes in their physiological activity in blood serum in severe TBI. We used antemortem (AM) serum from infants under the age of 2 years who were victims of AHT with a severe form of ICH. The analytical approach used in the proof-of-principle study shows reduced activities of serum serine lipases in AHT cases and could be further investigated in mild forms of AHT, which currently show 30% of misdiagnosed cases in clinics.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":" ","pages":"e202400022"},"PeriodicalIF":2.1,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142865203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jeong Min Cho, Minsang Kim, Jaeik Oh, Jung Hun Koh, Semin Cho, Yaerim Kim, Soojin Lee, Kwangsoo Kim, Yong Chul Kim, Seung Seok Han, Kwon-Wook Joo, Yon Su Kim, Hajeong Lee, Dong Ki Kim, Sehoon Park
{"title":"Causal Effects From Kidney Function to Plasma Proteome: Integrated Observational and Mendelian Randomization Analysis With >50,000 UK Biobank Participants.","authors":"Jeong Min Cho, Minsang Kim, Jaeik Oh, Jung Hun Koh, Semin Cho, Yaerim Kim, Soojin Lee, Kwangsoo Kim, Yong Chul Kim, Seung Seok Han, Kwon-Wook Joo, Yon Su Kim, Hajeong Lee, Dong Ki Kim, Sehoon Park","doi":"10.1002/prca.70002","DOIUrl":"https://doi.org/10.1002/prca.70002","url":null,"abstract":"<p><strong>Purpose: </strong>Chronic kidney disease (CKD) causes detrimental systemic effects, including inflammation or apoptosis, which lead to substantial morbidity and mortality. However, the causal effect of reduced kidney function on systemic proteomic signatures is incompletely understood.</p><p><strong>Methods: </strong>We performed an integrated Mendelian randomization (MR) and observational analyses to identify the causal association between kidney function and plasma protein levels, based on 1815 plasma protein profiles in 50,407 UK Biobank participants and the CKDGen Phase 4 genome-wide association study (GWAS) meta-analysis for the genetic instruments of eGFR.</p><p><strong>Results: </strong>The MR analysis revealed 383 plasma proteins causally associated with eGFR. Reduced kidney function was found to be causally associated with an increase in the plasma levels of 381 proteins, among which TNF and IGFBP4 were increased, while the level of two proteins, NPHS1 and SPOCK1, decreased. Apoptosis-related pathway was significantly enriched in the gene-set enrichment analysis. In network analysis, TNF was identified as a hub protein with multiple linkages to molecules included in the TNF-signaling pathways, involved in inflammation, fibrosis, and apoptosis.</p><p><strong>Conclusions: </strong>In this proteo-genomic analysis, we identified 383 plasma proteins causally associated with eGFR, highlighting TNF-associated pathways as pathologically relevant processes in kidney disease progression, systemic inflammation, and organ fibrosis, warranting further investigation.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":" ","pages":"e70002"},"PeriodicalIF":2.1,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143524224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Eleni Skandalou, Mariell Rivedal, Hans-Peter Marti, Thea A S Halden, Trond Jenssen, Bjørn Egil Vikse, Anders Åsberg, Jessica Furriol
{"title":"Proteome of Renal Tubuli and Serum Differentiate Pre-Existing Type 2 Diabetes and Post-Transplant Diabetes in Kidney Transplant Recipients.","authors":"Eleni Skandalou, Mariell Rivedal, Hans-Peter Marti, Thea A S Halden, Trond Jenssen, Bjørn Egil Vikse, Anders Åsberg, Jessica Furriol","doi":"10.1002/prca.70000","DOIUrl":"https://doi.org/10.1002/prca.70000","url":null,"abstract":"<p><strong>Purpose: </strong>Diabetes mellitus (DM) is a major cause of end-stage kidney disease (ESKD), with kidney transplantation being the preferred treatment. However, post-transplant diabetes mellitus (PTDM) increases mortality and graft loss. While PTDM and Type 2 diabetes mellitus (T2DM) share risk factors, their mechanisms differ, particularly in diabetic nephropathy (DN). This study aimed to investigate the molecular differences in PTDM by mapping the proteomes of proximal tubuli and serum in normoglycemic (NG), pre-transplant T2DM, and PTDM patients one year post-transplantation. Experimental Design Proteomic analysis was performed on microdissected proximal tubular cells and serum samples from kidney transplant recipients categorized as NG, pre-transplant T2DM, or PTDM at one year post-transplantation. Mass spectrometry was used to identify differentially expressed proteins. Data analyses were performed using gene ontology databases and pathway analysis.</p><p><strong>Results: </strong>Proteomic analysis revealed key differences, including significant dysregulation of mitochondrial proteins and lipid metabolism pathways in PTDM patients compared to T2DM and NG groups. Additionally, we observed distinct serum patterns of cholesterol metabolism dysregulation in PTDM, highlighting a complex interplay between fatty acid metabolism, mitochondrial dysfunction and systemic lipid dysregulation that may drive renal injury in PTDM-related DN.</p><p><strong>Conclusions and clinical relevance: </strong>This pilot study is the first to perform proteomic analysis on both microdissected tubular cells and serum from post-transplant PTDM, pre-transplant T2DM and NG transplant recipients. The proteomic differences between PTDM and T2DM could help to develop targeted therapies and early diagnostic markers, ultimately improving transplant outcomes and patient management. Further research is needed to validate these findings and explore their therapeutic potential.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":" ","pages":"e70000"},"PeriodicalIF":2.1,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143483804","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Priyanaka Boettger, Hansjörg Schwertz, Herbert Platsch, Ursula Mueller-Werdan, Karl Werdan, Michael Buerke
{"title":"Intramural Administration of Translational Inhibitor Puromycin Upon Balloon Angioplasty Inhibits SMC Proliferation and Protein Synthesis-Vascular Proteome Profiling Analysis.","authors":"Priyanaka Boettger, Hansjörg Schwertz, Herbert Platsch, Ursula Mueller-Werdan, Karl Werdan, Michael Buerke","doi":"10.1002/prca.202400066","DOIUrl":"https://doi.org/10.1002/prca.202400066","url":null,"abstract":"<p><strong>Introduction: </strong>Percutaneous transluminal coronary angioplasty (PTCA) is an effective procedure to decrease the severity of stenotic coronary atherosclerotic lesions. However, its long-term success is limited by the formation of restenosis or neointima by increased proliferation of smooth muscle cells (SMCs) and synthesis of extracellular matrix. Polypeptide growth factors are potent SMC mitogens and are involved in SMC proliferation and extracellular matrix (ECM) synthesis. In this line, inhibition of de novo protein synthesis might be beneficial.</p><p><strong>Methods: </strong>We examined the effects of different concentrations of translational inhibitor puromycin on SMC proliferation and apoptosis, in vitro. Further, we examined the effects of local administration of puromycin in a rabbit balloon injury model of the iliac artery.</p><p><strong>Results: </strong>Injection of puromycin or its vehicle was performed with an infusion-balloon catheter directly into the vessel wall during angioplasty. PTA in the vehicle group resulted in neointima formation 3 weeks after the vascular intervention. In contrast, puromycin treatment resulted in a significant reduction of intima-media ratio. We observed decreased elastin and collagen III synthesis in puromycin-treated animals. With proteomics, we could demonstrate reduced protein expression of lamin, vimentin, alpha-1 antitrypsin, alpha-actin allowing puromycin treatment. In in vitro experiments, puromycin decreased SMCs proliferation (i.e., BrdU incorporation) following FCS stimulation.</p><p><strong>Perspective: </strong>Based on the data from our animal experiments, aministration of puromycin directly into the vessel wall during angioplasty may be effective in preventing or reducing restenosis in humans.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":" ","pages":"e202400066"},"PeriodicalIF":2.1,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143493442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"dRama: Differential Ramachandran Plot as a Tool to Analyze Subtle Changes in Protein Secondary Structure.","authors":"Piotr Batys, Leszek Krzemień, Jakub Barbasz","doi":"10.1002/prca.202400087","DOIUrl":"10.1002/prca.202400087","url":null,"abstract":"<p><p>Determination of the changes in protein structure is crucial for a better understanding of their function and properties, which is highly important in identifying the causes of the disease, new drug development, and clinical applications. The Ramachandran plot, displaying the set of torsional angles, phi (Φ) and psi (Ψ), of the protein backbone, serves as a popular and convenient tool for secondary structure analysis and interpretation. However, identifying subtle changes in protein structure is often hindered in traditional Ramachandran plot, especially with the large amount of data generated by molecular dynamics (MD) simulations. In this paper, we proposed a useful and efficient tool, that is, differential Ramachandran plot (dRama), which enables to compare protein structures and extract the differences, providing a highly readable graphical representation. dRama is available at: https://github.com/MaksWolf44/dRama.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":" ","pages":"e202400087"},"PeriodicalIF":2.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142710816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"ECMHA-PP: A Breast Cancer Prognosis Prediction Model Based on Energy-Constrained Multi-Head Self-Attention.","authors":"Fan Zhang, Chaoyang Liu, Xinhong Zhang","doi":"10.1002/prca.202400035","DOIUrl":"10.1002/prca.202400035","url":null,"abstract":"<p><strong>Purpose: </strong>Breast cancer is a significant threat to women's health. Precise prognosis prediction for breast cancer can help doctors implement more rational treatment strategies. Artificial intelligence can assist doctors in decision-making and enhance prediction accuracy.</p><p><strong>Experimental design: </strong>In this paper, a deep learning model ECMHA-PP (Energy Constrained Multi-Head Self-Attention based Prognosis Prediction) is proposed to predict the prognosis of breast cancer. ECMHA-PP utilizes patients' clinical data and extracts features through a cross-position mix and a channel mix multi-layer perceptron. Then, it incorporates an energy-constrained multi-head self-attention layer to improve feature extraction capability. The source code of ECMHA-PP has been hosted on GitHub and is available at https://github.com/xiaoliu166370/ECMHA-PP.</p><p><strong>Results: </strong>To evaluate our proposed method, prognostic prediction experiments were performed on the METABRIC dataset, yielding outstanding results with an average accuracy of 93.0% and an average area under the curve of 0.974. To further validate the model's performance, we conducted tests on another independent dataset, BRCA, achieving an accuracy of 87.6%.</p><p><strong>Conclusions and clinical relevance: </strong>In comparison with other widely used advanced methods, ECMHA-PP demonstrated higher comprehensive performance, making it a reliable prognostic prediction model for breast cancer. Given its robust feature extraction and prediction capabilities.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":" ","pages":"e202400035"},"PeriodicalIF":2.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142771714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Understanding LC/MS-Based Metabolomics: A Detailed Reference for Natural Product Analysis.","authors":"Jyotirmay Sarkar, Rajveer Singh, Shivani Chandel","doi":"10.1002/prca.202400048","DOIUrl":"10.1002/prca.202400048","url":null,"abstract":"<p><p>Liquid chromatography, when used in conjunction with mass spectrometry (LC/MS), is a powerful tool for conducting accurate and reproducible investigations of numerous metabolites in natural products (NPs). LC/MS has gained prominence in metabolomic research due to its high throughput, the availability of multiple ionization techniques and its ability to provide comprehensive metabolite coverage. This unique method can significantly influence various scientific domains. This review offers a comprehensive overview of the current state of LC/MS-based metabolomics in the investigation of NPs. This review provides a thorough overview of the state of the art in LC/MS-based metabolomics for the investigation of NPs. It covers the principles of LC/MS, various aspects of LC/MS-based metabolomics such as sample preparation, LC modes, method development, ionization techniques and data pre-processing. Moreover, it presents the applications of LC/MS-based metabolomics in numerous fields of NPs research such as including biomarker discovery, the agricultural research, food analysis, the study of marine NPs and microbiological research. Additionally, this review discusses the challenges and limitations of LC/MS-based metabolomics, as well as emerging trends and developments in this field.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":" ","pages":"e202400048"},"PeriodicalIF":2.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142546981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Advancements in Single-Cell Proteomics and Mass Spectrometry-Based Techniques for Unmasking Cellular Diversity in Triple Negative Breast Cancer.","authors":"Lakshmi Vineela Nalla, Aarika Kanukolanu, Madhuri Yeduvaka, Siva Nageswara Rao Gajula","doi":"10.1002/prca.202400101","DOIUrl":"10.1002/prca.202400101","url":null,"abstract":"<p><strong>Background: </strong>Triple-negative breast cancer (TNBC) is an aggressive and complex subtype of breast cancer characterized by a lack of targeted treatment options. Intratumoral heterogeneity significantly drives disease progression and complicates therapeutic responses, necessitating advanced analytical approaches to understand its underlying biology. This review aims to explore the advancements in single-cell proteomics and their application in uncovering cellular diversity in TNBC. It highlights innovations in sample preparation, mass spectrometry-based techniques, and the potential for integrating proteomics into multi-omics platforms.</p><p><strong>Methods: </strong>The review discusses the combination of improved sample preparation methods and cutting-edge mass spectrometry techniques in single-cell proteomics. It emphasizes the challenges associated with protein analysis, such as the inability to amplify proteins akin to transcripts, and examines strategies to overcome these limitations.</p><p><strong>Results: </strong>Single-cell proteomics provides a direct link to phenotype and cell behavior, complementing transcriptomic approaches and offering new insights into the mechanisms driving TNBC. The integration of advanced techniques has enabled deeper exploration of cellular heterogeneity and disease mechanisms.</p><p><strong>Conclusion: </strong>Despite the challenges, single-cell proteomics holds immense potential to evolve into a high-throughput and scalable multi-omics platform. Addressing existing hurdles will enable deeper biological insights, ultimately enhancing the diagnosis and treatment of TNBC.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":" ","pages":"e202400101"},"PeriodicalIF":2.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726282/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142682556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Proteomic Analysis of Fibroblasts Exposed to Resin Composite Release.","authors":"Yohann Flottes, Elisabeth Dursun","doi":"10.1002/prca.202400049","DOIUrl":"10.1002/prca.202400049","url":null,"abstract":"<p><strong>Objective: </strong>To investigate the potential effects of products released by a resin composite on the proteome of human gingival fibroblasts.</p><p><strong>Methods: </strong>Fifteen resin composite cylinders of a Bis-GMA-based resin composite (Tetric EvoCeram, Ivoclar) were made and placed in a culture medium for 24 h. Then, 30 mL of this medium was placed for 72 h in contact with human gingival fibroblasts and a second control group consisted of cells placed in culture medium only. Afterward, cells were collected, washed, and their proteins extracted. Three two-dimensional electrophoresis were performed per condition. Image analysis of the gels was carried out to highlight the differential protein spots. These spots were then analyzed by an ESI/qTOF mass spectrometer. Finally, specific databases provided protein identification, their interactions, and the pathways where they are implicated.</p><p><strong>Results: </strong>Delta2D software allowed the detection of 21 spots of different proteins. The MASCOT identified 28 proteins. Five proteins from four spots were upregulated, 23 proteins from 17 spots were downregulated. The UniProt database showed that all these proteins were involved in cellular architecture, structural modifications and quality control of proteins, cellular homeostasis, and metabolic pathways. The STRING database revealed the interactions between the regulated proteins. The GO enrichment analysis showed that 19 pathways were affected.</p><p><strong>Significance: </strong>The products released from the resin composite tested led to changes in the fibroblast proteome. Under the conditions of this study, resin composite released products can cause early adverse effects on cells, but without complete inhibition of their cellular functions.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":" ","pages":"e202400049"},"PeriodicalIF":2.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142473127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ling-Ling Jiao, Hui-Lin Dong, Yan-Hua Qin, Jun Zhu, Peng-Lin Wu, Jing Liu, Yi Cao, Chang-Jian Wu, Yuan Zhang, Fan Cao, Feng Li, Huai-Yuan Zhu
{"title":"Comparisons of Whole Saliva and Cell Free Saliva by DIA-Based Proteome Profiling.","authors":"Ling-Ling Jiao, Hui-Lin Dong, Yan-Hua Qin, Jun Zhu, Peng-Lin Wu, Jing Liu, Yi Cao, Chang-Jian Wu, Yuan Zhang, Fan Cao, Feng Li, Huai-Yuan Zhu","doi":"10.1002/prca.202400031","DOIUrl":"10.1002/prca.202400031","url":null,"abstract":"<p><strong>Background: </strong>Saliva has emerged as a promising diagnostic resource due to its accessibility, noninvasiveness, and repeatability, enabling early disease detection and timely intervention. However, current studies often overlook the distinction between whole saliva (WS) and cell-free saliva (CFS). Objective This study aims to compare the proteomic profiles of WS and CFS.</p><p><strong>Method and result: </strong>The saliva was detected with and without low-abundance protein enrichment using nanoparticles, employing DIA-MS technology. Our findings reveal a substantial enhancement in the detectability of low-abundance proteins in saliva with utilization of nanoparticles, enabling identification of 12%-15% low-abundance proteins previously undetectable in WS or CFS. In total, 3817 saliva proteins were identified, with 3413 found in WS and 2340 in CFS. More interestingly, we found that it was not the similarity of the samples that did the clustering, but rather it depended more on the different detection methods and sample types. And the predominant functions of the identified proteins in WS were related to oxidative phosphorylation and neurodegenerations, whereas those in CFS were primarily associated with nitrogen and glycosaminoglycan metabolism. And both exhibited functions in immune response and proteasome.</p><p><strong>Conclusion: </strong>This study represents the first comparison of WS and CFS, providing valuable experimental evidence for guiding the selection of research subjects in future saliva omics studies.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":" ","pages":"e202400031"},"PeriodicalIF":2.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726274/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142818982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}