Shotgun proteomics is widely used for comprehensive profiling of protein expression. However, this approach has inherent limitations in resolving “proteoforms”. Two-dimensional gel electrophoresis (2DE) has the potential to separate and visualize proteoforms effectively. To evaluate its utility, proteins extracted from soybean seed hypocotyls were analyzed by 2DE/LC-MS/MS. As a result, a total of 693 proteins were separated by 2DE, of which 302 were identified by LC-MS/MS. The dynamic range of protein abundance was approximately 102 to 104. This analysis revealed that the hypocotyls contain numerous proteoforms of proteins essential for seed physiology, including late embryogenesis abundant protein, glycinin, β-conglycinin, trypsin inhibitor, sucrose-binding protein, and glyceraldehyde-3-phosphate dehydrogenase. Furthermore, 2DE revealed that the expression of proteoforms of the major seed storage proteins, glycinin A2 and A3 subunits, and β-conglycinin β subunit in hypocotyls differed from that in cotyledons, suggesting distinct functional roles beyond nutrient storage during germination. Overall, the results demonstrate that 2DE is a valuable complementary technique to shotgun proteomics, providing proteoform-specific information that cannot be resolved by shotgun analysis alone.
Significance
Shotgun proteomics is widely used for comprehensive profiling of protein expression. However, this approach has inherent limitations when analyzing “proteoforms”. In the present study, we analyzed soybean seed hypocotyls using two-dimensional gel electrophoresis (2DE)-LC-MS/MS, demonstrating that 2DE is useful for effective proteoform analysis. 2DE provides proteoform-specific information that cannot be obtained from shotgun proteomics alone, making it a useful complementary method.
{"title":"Two-dimensional electrophoresis-based proteomics reveals soybean seed hypocotyl proteoforms","authors":"Jian-Zhong Tan , Hiroyuki Kagawa , Keiko Kizawa , Hisashi Hirano","doi":"10.1016/j.jprot.2026.105600","DOIUrl":"10.1016/j.jprot.2026.105600","url":null,"abstract":"<div><div>Shotgun proteomics is widely used for comprehensive profiling of protein expression. However, this approach has inherent limitations in resolving “proteoforms”. Two-dimensional gel electrophoresis (2DE) has the potential to separate and visualize proteoforms effectively. To evaluate its utility, proteins extracted from soybean seed hypocotyls were analyzed by 2DE/LC-MS/MS. As a result, a total of 693 proteins were separated by 2DE, of which 302 were identified by LC-MS/MS. The dynamic range of protein abundance was approximately 10<sup>2</sup> to 10<sup>4</sup>. This analysis revealed that the hypocotyls contain numerous proteoforms of proteins essential for seed physiology, including late embryogenesis abundant protein, glycinin, β-conglycinin, trypsin inhibitor, sucrose-binding protein, and glyceraldehyde-3-phosphate dehydrogenase. Furthermore, 2DE revealed that the expression of proteoforms of the major seed storage proteins, glycinin A2 and A3 subunits, and β-conglycinin β subunit in hypocotyls differed from that in cotyledons, suggesting distinct functional roles beyond nutrient storage during germination. Overall, the results demonstrate that 2DE is a valuable complementary technique to shotgun proteomics, providing proteoform-specific information that cannot be resolved by shotgun analysis alone.</div></div><div><h3>Significance</h3><div>Shotgun proteomics is widely used for comprehensive profiling of protein expression. However, this approach has inherent limitations when analyzing “proteoforms”. In the present study, we analyzed soybean seed hypocotyls using two-dimensional gel electrophoresis (2DE)-LC-MS/MS, demonstrating that 2DE is useful for effective proteoform analysis. 2DE provides proteoform-specific information that cannot be obtained from shotgun proteomics alone, making it a useful complementary method.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"326 ","pages":"Article 105600"},"PeriodicalIF":2.8,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146003749","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}
Ovarian granulosa cells (Gc) play a vital role in follicle maturation and successful ovulation. Omentin-1 (ITLN1) is an adipokine involved in energy metabolism and insulin resistance; its expression has been demonstrated in the ovary and varies depending on the degree of pig fatness. However, its effect on the global proteome of Gc has not been previously investigated. It was hypothesized that ITLN1 affects the abundance of proteins involved in key processes occurring in Gc in pigs. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of Gc identified 208 significantly differentially abundant proteins (DAPs) in the Large White pigs, with 99 proteins upregulated and 109 downregulated. In fatter Meishan pigs, 42 statistically significant DAPs were identified, including 25 upregulated and 17 downregulated proteins. The identified DAPs were associated with the estrogen signaling pathway, cell cycle and DNA replication, protein synthesis, transport and maturation, cytoskeleton dynamics, cell signaling, and hormonal regulation. Notably, the number and identity of DAPs differed markedly between the two breeds, suggesting that ITLN1-mediated effects are modulated by fatness and breed-specific metabolic status. To further illustrate the observed differences, selected proteins were also analyzed using Western blotting and ELISA, which were consistent with the LC-MS/MS findings. The results indicate that ITLN1 has a modulatory influence on the porcine Gc proteome, which is dependent on fat content. This highlights the important role of ITLN1 in regulating ovarian functions.
Significance
This study provides a comprehensive proteomic analysis of porcine granulosa cells (Gc) after treatment with omentin-1 (ITLN1) in pigs with different fat content (Large White < Meishan). The identified differentially abundant proteins (DAPs) are intricately linked to critical biological pathways, including estrogen signaling, cell cycle regulation, DNA replication, protein synthesis and transport, cytoskeleton organization, and hormonal regulation. These findings enhance our understanding of the molecular mechanisms underpinning ovarian follicle development and breed-related reproductive traits in pigs. The insights gained could inform future strategies to improve fertility and reproductive efficiency in swine production, as well as provide a valuable resource for comparative studies on ovarian biology across species.
{"title":"The in vitro effect of omentin-1 on the global proteome of granulosa cells from normal weight Large White and fat Meishan pigs","authors":"Karolina Pich , Natalia Respekta-Długosz , Edyta Rytelewska , Bianka Świderska , Agata Malinowska , Nina Smolińska , Joëlle Dupont , Agnieszka Rak","doi":"10.1016/j.jprot.2026.105606","DOIUrl":"10.1016/j.jprot.2026.105606","url":null,"abstract":"<div><div>Ovarian granulosa cells (Gc) play a vital role in follicle maturation and successful ovulation. Omentin-1 (ITLN1) is an adipokine involved in energy metabolism and insulin resistance; its expression has been demonstrated in the ovary and varies depending on the degree of pig fatness. However, its effect on the global proteome of Gc has not been previously investigated. It was hypothesized that ITLN1 affects the abundance of proteins involved in key processes occurring in Gc in pigs. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of Gc identified 208 significantly differentially abundant proteins (DAPs) in the Large White pigs, with 99 proteins upregulated and 109 downregulated. In fatter Meishan pigs, 42 statistically significant DAPs were identified, including 25 upregulated and 17 downregulated proteins. The identified DAPs were associated with the estrogen signaling pathway, cell cycle and DNA replication, protein synthesis, transport and maturation, cytoskeleton dynamics, cell signaling, and hormonal regulation. Notably, the number and identity of DAPs differed markedly between the two breeds, suggesting that ITLN1-mediated effects are modulated by fatness and breed-specific metabolic status. To further illustrate the observed differences, selected proteins were also analyzed using Western blotting and ELISA, which were consistent with the LC-MS/MS findings. The results indicate that ITLN1 has a modulatory influence on the porcine Gc proteome, which is dependent on fat content. This highlights the important role of ITLN1 in regulating ovarian functions.</div></div><div><h3>Significance</h3><div>This study provides a comprehensive proteomic analysis of porcine granulosa cells (Gc) after treatment with omentin-1 (ITLN1) in pigs with different fat content (Large White < Meishan). The identified differentially abundant proteins (DAPs) are intricately linked to critical biological pathways, including estrogen signaling, cell cycle regulation, DNA replication, protein synthesis and transport, cytoskeleton organization, and hormonal regulation. These findings enhance our understanding of the molecular mechanisms underpinning ovarian follicle development and breed-related reproductive traits in pigs. The insights gained could inform future strategies to improve fertility and reproductive efficiency in swine production, as well as provide a valuable resource for comparative studies on ovarian biology across species.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"326 ","pages":"Article 105606"},"PeriodicalIF":2.8,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146030022","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}
Pub Date : 2026-04-20Epub Date: 2026-01-13DOI: 10.1016/j.jprot.2026.105602
Roberta Pena da Paschoa , Lucas Rodrigues Xavier , Caio Cezar Guedes Corrêa , Karina da Silva Vieira , Daniel Dastan Rezabala Pacheco , Lucas do Espirito Santo Gomes , Carlos Eduardo Assis da Silva , Laura Eliza de Oliveira Alves , Vitor Batista Pinto , Claudete Santa-Catarina , Vanildo Silveira
The induction of somatic embryogenesis is controlled by various genes and proteins involved in hormonal pathways and stress responses, which act as key regulators of in vitro cellular reprogramming. In this study, we employed a temporal proteomic approach to investigate the underlying molecular mechanisms governing sugarcane (Saccharum spp.) embryogenic callus formation in response to 2,4-dichlorophenoxyacetic acid (2,4-D) during induction. Proteomic profiling revealed 996 differentially accumulated proteins (DAPs) across at least one pairwise comparison among time points (0, 7, 14 and 21 days) during callus induction. These DAPs were classified into different clusters on the basis of their accumulation profile. Proteins involved in embryogenesis, histone epigenetic regulation, hormone responses and protein post-translational modification accumulate during callus induction. The predicted interactions between the TOPLESS protein and auxin response proteins (SKP1, CUL1 and CAND1) are associated with increased accumulation of the histone deacetylase HDT2 protein, a regulator of chromatin condensation, during embryogenic callus initiation. Moreover, proteomic analysis revealed a temporal reduction in methylation cycle enzymes during callus induction, whereas global DNA methylation showed only a slight, non-significant increase, suggesting that additional regulatory layers are present. The identified protein dynamics provide valuable targets for refining somatic embryogenesis protocols and advancing their biotechnological applications in sugarcane.
Significance
Genetic engineering and plant cloning usually involve the induction of embryogenic competence using 2,4-dichlorophenoxyacetic acid (2,4-D). This study presents protein-protein interaction (PPI) networks regulated during the induction of sugarcane callus using 2,4-D, in addition to the morphological aspects of the explant during the process. Proteomic analysis of time series shows the regulation of protein kinases and transcriptional regulators TOPLESS, CUL1, SKP1, CAND1, and ARGONAUTE kinases, revealing mechanisms of activation of induction and multiplication of embryogenic callus. Furthermore, the possible interaction between GH3.8 and SnRK/SAPK kinases suggests a link between hormonal responses.
{"title":"Early regulatory networks driving somatic embryogenesis in Saccharum spp. L. revealed by time-resolved proteomics","authors":"Roberta Pena da Paschoa , Lucas Rodrigues Xavier , Caio Cezar Guedes Corrêa , Karina da Silva Vieira , Daniel Dastan Rezabala Pacheco , Lucas do Espirito Santo Gomes , Carlos Eduardo Assis da Silva , Laura Eliza de Oliveira Alves , Vitor Batista Pinto , Claudete Santa-Catarina , Vanildo Silveira","doi":"10.1016/j.jprot.2026.105602","DOIUrl":"10.1016/j.jprot.2026.105602","url":null,"abstract":"<div><div>The induction of somatic embryogenesis is controlled by various genes and proteins involved in hormonal pathways and stress responses, which act as key regulators of in vitro cellular reprogramming. In this study, we employed a temporal proteomic approach to investigate the underlying molecular mechanisms governing sugarcane (<em>Saccharum</em> spp.) embryogenic callus formation in response to 2,4-dichlorophenoxyacetic acid (2,4-D) during induction. Proteomic profiling revealed 996 differentially accumulated proteins (DAPs) across at least one pairwise comparison among time points (0, 7, 14 and 21 days) during callus induction. These DAPs were classified into different clusters on the basis of their accumulation profile. Proteins involved in embryogenesis, histone epigenetic regulation, hormone responses and protein post-translational modification accumulate during callus induction. The predicted interactions between the TOPLESS protein and auxin response proteins (SKP1, CUL1 and CAND1) are associated with increased accumulation of the histone deacetylase HDT2 protein, a regulator of chromatin condensation, during embryogenic callus initiation. Moreover, proteomic analysis revealed a temporal reduction in methylation cycle enzymes during callus induction, whereas global DNA methylation showed only a slight, non-significant increase, suggesting that additional regulatory layers are present. The identified protein dynamics provide valuable targets for refining somatic embryogenesis protocols and advancing their biotechnological applications in sugarcane.</div></div><div><h3>Significance</h3><div>Genetic engineering and plant cloning usually involve the induction of embryogenic competence using 2,4-dichlorophenoxyacetic acid (2,4-D). This study presents protein-protein interaction (PPI) networks regulated during the induction of sugarcane callus using 2,4-D, in addition to the morphological aspects of the explant during the process. Proteomic analysis of time series shows the regulation of protein kinases and transcriptional regulators TOPLESS, CUL1, SKP1, CAND1, and ARGONAUTE kinases, revealing mechanisms of activation of induction and multiplication of embryogenic callus. Furthermore, the possible interaction between GH3.8 and SnRK/SAPK kinases suggests a link between hormonal responses.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"326 ","pages":"Article 105602"},"PeriodicalIF":2.8,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145986725","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}
Pub Date : 2026-04-20Epub Date: 2026-01-20DOI: 10.1016/j.jprot.2026.105607
Marcella N. Melo-Braga , Gabriela C. Magalhães , Filipe A. Silva , Frank Kjeldsen , Martin R. Larsen , Robson A.S. Santos , Thiago Verano-Braga
Angiotensin-(1–7) [Ang-(1–7)] is a heptapeptide of the renin-angiotensin system (RAS) with antitumoral effects reported in various tumoral cell lines, including the human lung adenocarcinoma A549 lineage. While previous studies have shown that Ang-(1–7) modulates MAPK and PI3K-AKT signaling, the precise molecular mechanisms involved remain incompletely understood. To investigate the signaling events of Ang-(1–7) in lung cancer-derived cells, we employed an integrated proteomic and phosphoproteomic approach in A549 cells. We analyzed early (minutes) and late (hours) molecular responses to Ang-(1–7) treatment. The treatment resulted in time-dependent modulation of multiple signaling pathways, including significant alterations in the MAPK, PI3K-AKT, and mTOR pathways at both the protein and phosphorylation levels. Notably, widespread early dephosphorylation events were observed, similar to the effects seen with other RAS peptides with antitumoral effects. Additionally, Ang-(1–7) promoted a long-lasting nuclear accumulation (up to 24 h) of the transcription factor FOXO1 indicating its activation. FOXO1 is known to regulate genes involved in apoptosis, cell cycle arrest, and oxidative stress, suggesting a role in mediating the peptide's antitumoral effects. The study provides new insights into the molecular basis of Ang-(1–7)’s antitumoral activity in A549 cells and reinforce its therapeutic potential in lung cancer. Raw data are available via ProteomeXchange with identifier PXD066687.
Significance
This study provides the first comprehensive, time-resolved proteomic and phosphoproteomic analysis of Angiotensin-(1–7) signaling in the lung cancer cell line A549. By capturing both early and late molecular events in A549 cells, we reveal that Ang-(1–7) modulates critical pathways involved in tumor progression, including MAPK, PI3K-AKT, and mTOR signaling. Importantly, we demonstrate the nuclear accumulation of FOXO1, a key transcription factor associated with tumor suppression, as part of the Ang-(1–7) response in A549 cells.
{"title":"Time-resolved proteomic and phosphoproteomic profiling of Angiotensin-(1–7) signaling in A549 cells","authors":"Marcella N. Melo-Braga , Gabriela C. Magalhães , Filipe A. Silva , Frank Kjeldsen , Martin R. Larsen , Robson A.S. Santos , Thiago Verano-Braga","doi":"10.1016/j.jprot.2026.105607","DOIUrl":"10.1016/j.jprot.2026.105607","url":null,"abstract":"<div><div>Angiotensin-(1–7) [Ang-(1–7)] is a heptapeptide of the renin-angiotensin system (RAS) with antitumoral effects reported in various tumoral cell lines, including the human lung adenocarcinoma A549 lineage. While previous studies have shown that Ang-(1–7) modulates MAPK and PI3K-AKT signaling, the precise molecular mechanisms involved remain incompletely understood. To investigate the signaling events of Ang-(1–7) in lung cancer-derived cells, we employed an integrated proteomic and phosphoproteomic approach in A549 cells. We analyzed early (minutes) and late (hours) molecular responses to Ang-(1–7) treatment. The treatment resulted in time-dependent modulation of multiple signaling pathways, including significant alterations in the MAPK, PI3K-AKT, and mTOR pathways at both the protein and phosphorylation levels. Notably, widespread early dephosphorylation events were observed, similar to the effects seen with other RAS peptides with antitumoral effects. Additionally, Ang-(1–7) promoted a long-lasting nuclear accumulation (up to 24 h) of the transcription factor FOXO1 indicating its activation. FOXO1 is known to regulate genes involved in apoptosis, cell cycle arrest, and oxidative stress, suggesting a role in mediating the peptide's antitumoral effects. The study provides new insights into the molecular basis of Ang-(1–7)’s antitumoral activity in A549 cells and reinforce its therapeutic potential in lung cancer. Raw data are available via ProteomeXchange with identifier <span><span>PXD066687</span><svg><path></path></svg></span>.</div></div><div><h3>Significance</h3><div>This study provides the first comprehensive, time-resolved proteomic and phosphoproteomic analysis of Angiotensin-(1–7) signaling in the lung cancer cell line A549. By capturing both early and late molecular events in A549 cells, we reveal that Ang-(1–7) modulates critical pathways involved in tumor progression, including MAPK, PI3K-AKT, and mTOR signaling. Importantly, we demonstrate the nuclear accumulation of FOXO1, a key transcription factor associated with tumor suppression, as part of the Ang-(1–7) response in A549 cells.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"326 ","pages":"Article 105607"},"PeriodicalIF":2.8,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146025908","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}
Pub Date : 2026-04-20Epub Date: 2026-01-22DOI: 10.1016/j.jprot.2026.105604
Jingxuan Hu , Yuan Zheng , Leyuan Li
As a direct readout of protein presence and abundance in complex microbiomes, metaproteomics has become central to uncovering functionality across diverse microbial ecosystems. Recent collaborative efforts within the research community have driven methodological advances, computational innovations, and diverse applications. With the advancing maturity of metaproteomics techniques, we highlight the Proteome-level Microbial Systems Ecology (ProMiSE) framework as a complementary framework for the next phase, providing a conceptual lens to interpret metaproteomics data with a bottom-up perspective that extends beyond functional profile and taxonomic composition to the quantitative assessment of system properties, processes, and dynamics. Building on existing metrics such as β-diversity and functional redundancy, future work can further develop quantitative approaches for resilience, exergy, and functional energy landscapes, thereby enabling a deeper systems-level understanding of microbiome dynamics and opening new avenues for the precise functional regulation of microbiomes.
Significance
This Perspective reviews the development of metaproteomics—particularly in the Journal of Proteomics—and envisions it as a transformative tool in microbial systems ecology, introducing the ProMiSE framework to integrate protein-resolved data with ecological theory and properties such as redundancy, resilience, and functional energy landscapes for the future of precise microbiome modulation.
{"title":"The untapped potential of metaproteomics in microbial systems ecology","authors":"Jingxuan Hu , Yuan Zheng , Leyuan Li","doi":"10.1016/j.jprot.2026.105604","DOIUrl":"10.1016/j.jprot.2026.105604","url":null,"abstract":"<div><div>As a direct readout of protein presence and abundance in complex microbiomes, metaproteomics has become central to uncovering functionality across diverse microbial ecosystems. Recent collaborative efforts within the research community have driven methodological advances, computational innovations, and diverse applications. With the advancing maturity of metaproteomics techniques, we highlight the Proteome-level Microbial Systems Ecology (ProMiSE) framework as a complementary framework for the next phase, providing a conceptual lens to interpret metaproteomics data with a bottom-up perspective that extends beyond functional profile and taxonomic composition to the quantitative assessment of system properties, processes, and dynamics. Building on existing metrics such as β-diversity and functional redundancy, future work can further develop quantitative approaches for resilience, exergy, and functional energy landscapes, thereby enabling a deeper systems-level understanding of microbiome dynamics and opening new avenues for the precise functional regulation of microbiomes.</div></div><div><h3>Significance</h3><div>This Perspective reviews the development of metaproteomics—particularly in the Journal of Proteomics—and envisions it as a transformative tool in microbial systems ecology, introducing the ProMiSE framework to integrate protein-resolved data with ecological theory and properties such as redundancy, resilience, and functional energy landscapes for the future of precise microbiome modulation.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"326 ","pages":"Article 105604"},"PeriodicalIF":2.8,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146041021","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}
Pub Date : 2026-03-19DOI: 10.1016/j.jprot.2026.105645
Heran Cao, Xiaohua Liu, Long Li, Shujuan Liu, Huihui Gao, Qian Dong, Hua Nie, Yan Li, Ye Gong, Tianqi Jin, Yang Wang, Weibing Qin, Wuzi Dong
The epididymis orchestrates sperm maturation through microenvironmental regulation and epididymosome-mediated cargo delivery. Despite emerging evidence implicating protein S-acylation in vesicular trafficking, its compartment-specific dynamics and functional implications in epididymal physiology remain poorly characterized. Here, we employed acyl-biotin exchange-based 4D proteomics to decode the S-acylation proteomic of porcine caput/cauda epididymidis and their exosomes. Comparative analysis identified 2780 and 2084 S-acylated proteins in caput and cauda tissues, respectively, with 317 upregulated and 579 downregulated S-acylated proteins in cauda versus caput. Functional enrichment revealed S-acylation-dependent regulation of signal transduction, vesicle trafficking, and immune pathways, particularly through lysosomal activity, AMPK signaling, and glutathione metabolism. Exosomal profiling demonstrated conserved S-acylated protein signatures between caput and cauda derived exosomes, with 114 S-acylated proteins shared among caput tissue and both exosomal populations, implicating long-distance transport of caput-specific cargoes. Validation identified 5 caput-enriched S-acylated proteins, including evolutionarily conserved OCLN, CDH1, PDZK1, BAG5, and SCRN1, which were detected in S-acylated forms within caput-derived exosomes and cauda exosomes, but absent in cauda tissue. This study reveals a potential role of S-acylation in mediating exosomal cargo trafficking during porcine epididymis. Our findings advance understanding of post-testicular sperm functionalization and highlight S-acylation as a potential therapeutic target for male infertility. SIGNIFICANCE: This study provides the comprehensive S-acylation proteomic atlas of the porcine epididymis and its exosomes, revealing how this reversible lipid modification spatiotemporally regulates exosome-mediated protein trafficking to support sperm maturation. We demonstrate that S-acylation governs key pathways including vesicle transport, immune regulation, and metabolic signaling in the epididymal microenvironment. Crucially, we identify a cohort of caput-enriched S-acylated proteins that are packaged into exosomes and transported distally to the cauda region, suggesting a previously unrecognized mechanism for long-distance intercellular communication. These findings establish S-acylation as a central regulator of epididymal function and offer molecular insights into post-testicular sperm maturation. The identified S-acylated proteins and associated pathways may serve as diagnostic biomarkers or therapeutic targets for male infertility, particularly in cases of defective sperm functionalization.
附睾通过微环境调控和附睾小体介导的货物输送来协调精子成熟。尽管新出现的证据表明蛋白质s -酰化在囊泡运输中，但其在附睾生理中的室特异性动力学和功能意义仍然缺乏表征。本研究采用基于酰基生物素交换的4D蛋白质组学方法解码猪附睾头尾及其外泌体的s -酰化蛋白质组学。通过对比分析，在头端和尾端组织中分别鉴定出2780和2084个 s -酰化蛋白，尾端与头端相比，s -酰化蛋白上调317个，下调579个。功能富集揭示了s -酰化依赖的信号转导、囊泡运输和免疫途径的调节，特别是通过溶酶体活性、AMPK信号传导和谷胱甘肽代谢。外泌体分析显示，在头形组织和尾形衍生的外泌体之间存在保守的s -酰化蛋白特征，其中114个 s -酰化蛋白在头形组织和两个外泌体群体中共享，这暗示了头形特异性货物的远距离运输。验证鉴定了5个富含帽状体的s -酰化蛋白，包括进化上保守的OCLN、CDH1、PDZK1、BAG5和SCRN1，这些蛋白在帽状体衍生的外泌体和尾状外泌体中以s -酰化形式存在，但在尾状组织中不存在。这项研究揭示了s -酰化在猪附睾过程中介导外泌体货物运输中的潜在作用。我们的研究结果促进了对睾丸后精子功能化的理解，并强调s -酰化是男性不育症的潜在治疗靶点。意义：本研究提供了猪附睾及其外泌体的s -酰化蛋白质组学图谱，揭示了这种可逆的脂质修饰如何在时空上调节外泌体介导的蛋白质运输，以支持精子成熟。我们证明s -酰化控制着附睾微环境中的关键途径，包括囊泡运输、免疫调节和代谢信号。至关重要的是，我们确定了一组富含帽状蛋白的s -酰化蛋白，它们被包装成外泌体并向远端运输到尾区，这表明了一种以前未被认识到的远距离细胞间通信机制。这些发现确立了s -酰化是附睾功能的中枢调节因子，并为睾丸后精子成熟提供了分子视角。鉴定出的s酰化蛋白和相关途径可作为男性不育的诊断生物标志物或治疗靶点，特别是在精子功能缺陷的情况下。
{"title":"Comprehensive S-acylation profiling of the porcine epididymis and exosomes reveals a role in cargo sorting and long-distance trafficking.","authors":"Heran Cao, Xiaohua Liu, Long Li, Shujuan Liu, Huihui Gao, Qian Dong, Hua Nie, Yan Li, Ye Gong, Tianqi Jin, Yang Wang, Weibing Qin, Wuzi Dong","doi":"10.1016/j.jprot.2026.105645","DOIUrl":"https://doi.org/10.1016/j.jprot.2026.105645","url":null,"abstract":"<p><p>The epididymis orchestrates sperm maturation through microenvironmental regulation and epididymosome-mediated cargo delivery. Despite emerging evidence implicating protein S-acylation in vesicular trafficking, its compartment-specific dynamics and functional implications in epididymal physiology remain poorly characterized. Here, we employed acyl-biotin exchange-based 4D proteomics to decode the S-acylation proteomic of porcine caput/cauda epididymidis and their exosomes. Comparative analysis identified 2780 and 2084 S-acylated proteins in caput and cauda tissues, respectively, with 317 upregulated and 579 downregulated S-acylated proteins in cauda versus caput. Functional enrichment revealed S-acylation-dependent regulation of signal transduction, vesicle trafficking, and immune pathways, particularly through lysosomal activity, AMPK signaling, and glutathione metabolism. Exosomal profiling demonstrated conserved S-acylated protein signatures between caput and cauda derived exosomes, with 114 S-acylated proteins shared among caput tissue and both exosomal populations, implicating long-distance transport of caput-specific cargoes. Validation identified 5 caput-enriched S-acylated proteins, including evolutionarily conserved OCLN, CDH1, PDZK1, BAG5, and SCRN1, which were detected in S-acylated forms within caput-derived exosomes and cauda exosomes, but absent in cauda tissue. This study reveals a potential role of S-acylation in mediating exosomal cargo trafficking during porcine epididymis. Our findings advance understanding of post-testicular sperm functionalization and highlight S-acylation as a potential therapeutic target for male infertility. SIGNIFICANCE: This study provides the comprehensive S-acylation proteomic atlas of the porcine epididymis and its exosomes, revealing how this reversible lipid modification spatiotemporally regulates exosome-mediated protein trafficking to support sperm maturation. We demonstrate that S-acylation governs key pathways including vesicle transport, immune regulation, and metabolic signaling in the epididymal microenvironment. Crucially, we identify a cohort of caput-enriched S-acylated proteins that are packaged into exosomes and transported distally to the cauda region, suggesting a previously unrecognized mechanism for long-distance intercellular communication. These findings establish S-acylation as a central regulator of epididymal function and offer molecular insights into post-testicular sperm maturation. The identified S-acylated proteins and associated pathways may serve as diagnostic biomarkers or therapeutic targets for male infertility, particularly in cases of defective sperm functionalization.</p>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":" ","pages":"105645"},"PeriodicalIF":2.8,"publicationDate":"2026-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147494118","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}
Pub Date : 2026-03-18DOI: 10.1016/j.jprot.2026.105644
Erika Keiko Martinez Vargas, Alvija Šalaševičienė, Per Ertbjerg
The global shift toward plant-based diets has increased the demand for sustainable and nutritionally equivalent alternatives to animal meat. High-moisture extrusion (HME) technology enables the transformation of plant proteins into fibrous, meat-like textures; however, the molecular changes induced by this process remain largely understudied. Peptidomics, a large-scale mass-spectrometry-based analysis of peptides, offers a promising approach to investigate protein modifications, digestibility, and bioactive peptide generation in plant-based meat analogs (PBMAs). Particular attention is given to LC-MS/MS workflows, acquisition strategies (data-dependent and data-independent acquisition), and sample preparation challenges associated with complex processed food matrices. This review summarizes current advances in the application of peptidomics to HME-derived matrices and highlights knowledge gaps that limit the current understanding of extrusion-induced molecular transformations. Integrating peptidomics into the design of PBMAs can benefit product optimization for both texture and nutritional functionality. SIGNIFICANCE: Understanding how high-moisture extrusion (HME) alters plant protein structure and digestibility is crucial for advancing nutritionally equivalent and sustainable alternatives to animal meat. This review synthesizes current evidence on the use of peptidomics to elucidate the molecular transformations and peptide release dynamics occurring during extrusion and subsequent digestion of plant-based meat analogs (PBMAs). Specifically, it addresses current gaps in the peptidomics literature regarding extrusion-processed plant proteins, method selection for complex food matrices, and the linkage between peptide profiles, processing conditions, and digestibility outcomes. By integrating principles of protein chemistry, digestion modeling, and emerging computational tools, the review positions peptidomics as a bridge between processing parameters, structural organization, and nutritional functionality. This mechanistic perspective deepens our understanding of extrusion-induced modifications and establishes a conceptual framework for designing PBMAs with optimized texture, digestibility, and bioactive potential, thereby expanding the predictive and hypothesis-driven application of proteomic sciences to sustainable food innovation.
{"title":"Peptidomics assessment of plant-based meat analogs produced by high-moisture extrusion: Analytical strategies, challenges, and future perspectives.","authors":"Erika Keiko Martinez Vargas, Alvija Šalaševičienė, Per Ertbjerg","doi":"10.1016/j.jprot.2026.105644","DOIUrl":"https://doi.org/10.1016/j.jprot.2026.105644","url":null,"abstract":"<p><p>The global shift toward plant-based diets has increased the demand for sustainable and nutritionally equivalent alternatives to animal meat. High-moisture extrusion (HME) technology enables the transformation of plant proteins into fibrous, meat-like textures; however, the molecular changes induced by this process remain largely understudied. Peptidomics, a large-scale mass-spectrometry-based analysis of peptides, offers a promising approach to investigate protein modifications, digestibility, and bioactive peptide generation in plant-based meat analogs (PBMAs). Particular attention is given to LC-MS/MS workflows, acquisition strategies (data-dependent and data-independent acquisition), and sample preparation challenges associated with complex processed food matrices. This review summarizes current advances in the application of peptidomics to HME-derived matrices and highlights knowledge gaps that limit the current understanding of extrusion-induced molecular transformations. Integrating peptidomics into the design of PBMAs can benefit product optimization for both texture and nutritional functionality. SIGNIFICANCE: Understanding how high-moisture extrusion (HME) alters plant protein structure and digestibility is crucial for advancing nutritionally equivalent and sustainable alternatives to animal meat. This review synthesizes current evidence on the use of peptidomics to elucidate the molecular transformations and peptide release dynamics occurring during extrusion and subsequent digestion of plant-based meat analogs (PBMAs). Specifically, it addresses current gaps in the peptidomics literature regarding extrusion-processed plant proteins, method selection for complex food matrices, and the linkage between peptide profiles, processing conditions, and digestibility outcomes. By integrating principles of protein chemistry, digestion modeling, and emerging computational tools, the review positions peptidomics as a bridge between processing parameters, structural organization, and nutritional functionality. This mechanistic perspective deepens our understanding of extrusion-induced modifications and establishes a conceptual framework for designing PBMAs with optimized texture, digestibility, and bioactive potential, thereby expanding the predictive and hypothesis-driven application of proteomic sciences to sustainable food innovation.</p>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":" ","pages":"105644"},"PeriodicalIF":2.8,"publicationDate":"2026-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147490994","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}
Pub Date : 2026-03-15Epub Date: 2025-12-24DOI: 10.1016/j.jprot.2025.105587
Gustavo Zanete Alencar , Dalton Muller Pessôa Filho , Karina Oliveira Santos , Anderson Geremias Macedo , Henrique Basso Vitti , Guilherme Neves Gasparino , Larissa Tercília Grizzo Thomassian , Murilo Henrique Faria , Ana Carolina Magalhães
Blood flow restriction (BFR) has been applied as alternative strategy to reproduce the effects of conventional high-load intensity training (HI) while training with low-loads (LI). Therefore, the aim of this research was to evaluate the salivary proteomic and metabolic responses to different resistance training in young adults.Ten participants were selected and underwent to training with LI (30 %1RM – one repetition maximum) plus BFR vs. HI (70 %1RM) without BFR, at 48 h-interval. Stimulated saliva was collected before and immediately after the sessions, while breath-by-breath oxygen uptake (VO2) was measured during and after each session. Arterial blood samples for lactate concentration measurement (in EqO2[La]) were taken at 1st minute of resting between each exercise. For HI, there was an increase in two actin cytoplasmic isoforms and two immunoglobulin isoforms and a decrease of six hemoglobin isoforms. For LI-BFR, there was an increase in two hemoglobin isoforms, and the same immunoglobulin isoforms (t-test, p < 0.05). No differences were significant between HI and LI + BRF training regarding the total energy demand (in mlO2), absolute oxygen values (mlO2) for oxidative response (VO2ON), glycolytic (EqO2[La]), and oxygen debt (VO2OFF) (p > 0.05). Both HI and LI + BFR protocols modulated immune system activity and exhibited divergent hemoglobin patterns.
Significance
The current study, which identified protein from saliva samples, a non-invasive method, and analyzed physiological markers, enabled the comparison of different resistance exercise protocols. Although no significant differences were observed in the metabolic responses to each protocol, which highlights the potential of LI + BRF to reproduce a high-intensity training stimulus, the changes in salivary protein profiles indicate specific functional adaptations that may become evident over time.
{"title":"Salivary proteomics and metabolic responses to resistance training with and without blood flow restriction in young adults","authors":"Gustavo Zanete Alencar , Dalton Muller Pessôa Filho , Karina Oliveira Santos , Anderson Geremias Macedo , Henrique Basso Vitti , Guilherme Neves Gasparino , Larissa Tercília Grizzo Thomassian , Murilo Henrique Faria , Ana Carolina Magalhães","doi":"10.1016/j.jprot.2025.105587","DOIUrl":"10.1016/j.jprot.2025.105587","url":null,"abstract":"<div><div>Blood flow restriction (BFR) has been applied as alternative strategy to reproduce the effects of conventional high-load intensity training (HI) while training with low-loads (LI). Therefore, the aim of this research was to evaluate the salivary proteomic and metabolic responses to different resistance training in young adults.Ten participants were selected and underwent to training with LI (30 %1RM – one repetition maximum) plus BFR vs. HI (70 %1RM) without BFR, at 48 h-interval. Stimulated saliva was collected before and immediately after the sessions, while breath-by-breath oxygen uptake (VO<sub>2</sub>) was measured during and after each session. Arterial blood samples for lactate concentration measurement (in EqO<sub>2[La]</sub>) were taken at 1<sup>st</sup> minute of resting between each exercise. For HI, there was an increase in two actin cytoplasmic isoforms and two immunoglobulin isoforms and a decrease of six hemoglobin isoforms. For LI-BFR, there was an increase in two hemoglobin isoforms, and the same immunoglobulin isoforms (<em>t</em>-test, <em>p</em> < 0.05). No differences were significant between HI and LI + BRF training regarding the total energy demand (in mlO<sub>2</sub>), absolute oxygen values (mlO<sub>2</sub>) for oxidative response (VO<sub>2ON</sub>), glycolytic (EqO<sub>2[La]</sub>), and oxygen debt (VO<sub>2OFF</sub>) (<em>p</em> > 0.05). Both HI and LI + BFR protocols modulated immune system activity and exhibited divergent hemoglobin patterns.</div></div><div><h3>Significance</h3><div>The current study, which identified protein from saliva samples, a non-invasive method, and analyzed physiological markers, enabled the comparison of different resistance exercise protocols. Although no significant differences were observed in the metabolic responses to each protocol, which highlights the potential of LI + BRF to reproduce a high-intensity training stimulus, the changes in salivary protein profiles indicate specific functional adaptations that may become evident over time.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"325 ","pages":"Article 105587"},"PeriodicalIF":2.8,"publicationDate":"2026-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145843898","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}
Pub Date : 2026-03-15Epub Date: 2025-12-26DOI: 10.1016/j.jprot.2025.105588
Ana Luiza T. Silva , Bianca C.S.C. de Barros , Joanderson P.C. da Silva , Isabel S. Carvalho , Marcelo L. Santoro , Alison F.A. Chaves , Solange M.T. Serrano
Snakebite envenomation is a critical yet underexplored public health issue, particularly in tropical and subtropical regions. Bothrops jararaca venom induces severe local and systemic effects, including pulmonary injury, however, the molecular mechanisms underlying lung tissue damage remain poorly understood. This study employed label- free quantitative proteomics to map protein alterations in the lung tissue in a mouse model of envenomation. Using Data-Dependent Acquisition (DDA) and Data-Independent Acquisition (DIA) approaches combined with different sample preparation methods, we provide a comprehensive proteomic profile of venom-induced pulmonary damage. Our findings reveal significant changes in proteins involved in inflammatory responses, extracellular matrix remodeling, oxidative stress, and blood coagulation. Comparative analyses highlight the superior performance of DIA over DDA, with DIA offering deeper proteome coverage, enhanced detection of low-abundance proteins, and improved resolution of venom-induced alterations. This benchmark study underscores the potential of DIA as a robust tool for elucidating complex, systemic, mammalian molecular responses to animal toxins. By bridging the gap between proteomic methodologies and pathophysiological insights, our findings contribute to a deeper understanding of viperid snake venom-induced lung injury and give insights for improved clinical management strategies.
Significance
Bothrops snakebites remain a major neglected health problem, causing severe local and systemic complications. While the impact of viperid venoms on muscle and kidney tissues is well documented, the effects on the lungs — an organ critically involved in systemic envenomation outcomes — remain poorly understood. Our study provides the first comprehensive proteomic characterization of lung responses to B. jararaca venom in a murine model, revealing alterations in pathways related to inflammation, extracellular matrix remodeling, oxidative stress, and coagulation. These molecular insights fill an important knowledge gap by showing that proteomic disturbances occur even in the absence of overt lung pathology, highlighting the lungs as a key systemic target of envenomation. Moreover, by demonstrating that antivenom administration mitigates many of these changes, our findings underscore both the therapeutic efficacy of antivenom and the need to better understand its broader systemic footprint. This work advances both toxinology and proteomics by linking molecular-level disturbances to clinically relevant systemic outcomes.
{"title":"Assessing systemic effects of Bothrops jararaca venom in the lungs in a mouse model by label-free proteomics using DDA and DIA","authors":"Ana Luiza T. Silva , Bianca C.S.C. de Barros , Joanderson P.C. da Silva , Isabel S. Carvalho , Marcelo L. Santoro , Alison F.A. Chaves , Solange M.T. Serrano","doi":"10.1016/j.jprot.2025.105588","DOIUrl":"10.1016/j.jprot.2025.105588","url":null,"abstract":"<div><div>Snakebite envenomation is a critical yet underexplored public health issue, particularly in tropical and subtropical regions. <em>Bothrops jararaca</em> venom induces severe local and systemic effects, including pulmonary injury, however, the molecular mechanisms underlying lung tissue damage remain poorly understood. This study employed label- free quantitative proteomics to map protein alterations in the lung tissue in a mouse model of envenomation. Using Data-Dependent Acquisition (DDA) and Data-Independent Acquisition (DIA) approaches combined with different sample preparation methods, we provide a comprehensive proteomic profile of venom-induced pulmonary damage. Our findings reveal significant changes in proteins involved in inflammatory responses, extracellular matrix remodeling, oxidative stress, and blood coagulation. Comparative analyses highlight the superior performance of DIA over DDA, with DIA offering deeper proteome coverage, enhanced detection of low-abundance proteins, and improved resolution of venom-induced alterations. This benchmark study underscores the potential of DIA as a robust tool for elucidating complex, systemic, mammalian molecular responses to animal toxins. By bridging the gap between proteomic methodologies and pathophysiological insights, our findings contribute to a deeper understanding of viperid snake venom-induced lung injury and give insights for improved clinical management strategies.</div></div><div><h3>Significance</h3><div><em>Bothrops</em> snakebites remain a major neglected health problem, causing severe local and systemic complications. While the impact of viperid venoms on muscle and kidney tissues is well documented, the effects on the lungs — an organ critically involved in systemic envenomation outcomes — remain poorly understood. Our study provides the first comprehensive proteomic characterization of lung responses to <em>B. jararaca</em> venom in a murine model, revealing alterations in pathways related to inflammation, extracellular matrix remodeling, oxidative stress, and coagulation. These molecular insights fill an important knowledge gap by showing that proteomic disturbances occur even in the absence of overt lung pathology, highlighting the lungs as a key systemic target of envenomation. Moreover, by demonstrating that antivenom administration mitigates many of these changes, our findings underscore both the therapeutic efficacy of antivenom and the need to better understand its broader systemic footprint. This work advances both toxinology and proteomics by linking molecular-level disturbances to clinically relevant systemic outcomes.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"325 ","pages":"Article 105588"},"PeriodicalIF":2.8,"publicationDate":"2026-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145850154","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}
Pub Date : 2026-03-15Epub Date: 2025-12-31DOI: 10.1016/j.jprot.2025.105597
Murilo Salardani , Alison F.A. Chaves , Leonardo Cardili , Miyuki Uno , Solange M.T. Serrano , Roger Chammas , André Zelanis
Melanoma is an aggressive skin cancer with a high metastatic potential, influenced by both genetic and environmental factors. Proteases play a key role in shaping the tumor microenvironment and enabling transformed cells to actively colonize distant sites (metastasis). We performed proteomic mapping of protease cleavage sites in formalin-fixed paraffin-embedded tissue samples and profiled potentially active proteases in samples from melanoma patients with distinct prognostic outcomes. Although protein abundance alone did not indicate potential markers of disease progression, the observed cleaved fragments may serve for monitoring potentially active proteases in patient samples in targeted proteomics analysis. The findings provide valuable insights into melanoma biology and potential therapeutic prospects.
{"title":"Combining information on degradomics and gene expression data in prospecting metastatic melanoma proteolytic signatures","authors":"Murilo Salardani , Alison F.A. Chaves , Leonardo Cardili , Miyuki Uno , Solange M.T. Serrano , Roger Chammas , André Zelanis","doi":"10.1016/j.jprot.2025.105597","DOIUrl":"10.1016/j.jprot.2025.105597","url":null,"abstract":"<div><div>Melanoma is an aggressive skin cancer with a high metastatic potential, influenced by both genetic and environmental factors. Proteases play a key role in shaping the tumor microenvironment and enabling transformed cells to actively colonize distant sites (metastasis). We performed proteomic mapping of protease cleavage sites in formalin-fixed paraffin-embedded tissue samples and profiled potentially active proteases in samples from melanoma patients with distinct prognostic outcomes. Although protein abundance alone did not indicate potential markers of disease progression, the observed cleaved fragments may serve for monitoring potentially active proteases in patient samples in targeted proteomics analysis. The findings provide valuable insights into melanoma biology and potential therapeutic prospects.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"325 ","pages":"Article 105597"},"PeriodicalIF":2.8,"publicationDate":"2026-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145892564","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}
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