Journal of proteomics最新文献

{"title":"Spatial and development responses in the wheat leaf highlight the loss of chloroplast protein homeostasis during salt stress.","authors":"R W Samalka, N Wijeweera, Owen Duncan, A Harvey Millar","doi":"10.1016/j.jprot.2025.105438","DOIUrl":"https://doi.org/10.1016/j.jprot.2025.105438","url":null,"abstract":"<p><p>Salinity stress in wheat affects physiological and biochemical parameters in tissues that alter plant development and ultimately lower crop yield. Shoot tissues can accumulate high concentrations of sodium over time through the transpiration stream coming from the roots. This imposes physiological responses that align salt effects with the basipetal developmental gradient of the monocot leaf. The role of metabolic processes in generating and responding to these increases in sodium concentration over time was explored by linking changes in ion distributions to those of enzyme abundance from the base to the tip of leaves under salt stress. We found that enzymes for methionine synthesis and lipid degradation pathways increase, concomitantly with proteins in jasmonate synthesis, which are key players in plant stress-induced responses. Combining the use of Differential Abundance of Protein analysis and Weighted Correlation Network Analysis we have focused on identifying key protein hubs associated with responses to salt stress or salt susceptibility, shedding light on potential sites of salt sensitivity as targets for enhancing salt tolerance in wheat. We found chloroplast protein synthesis machinery, including the 30S and 50S ribosomal proteins, and plastid localised protein synthesis elongation factors, were significantly reduced in abundance and correlated with the altered K⁺/Na⁺ ratio along salt-stressed wheat leaves. Additionally, the plastid protease system including ATP-dependent caseinolytic protease and filamentous temperature-sensitive H proteases involved in chloroplast protein homeostasis, show decreased abundance with salt. The complex interplay of these processes in and across the leaf affects overall plant viability under salt stress mainly affecting the energy homeostasis in wheat shoot. Data are available via ProteomeXchange with identifier PXD059765. SIGNIFICANCE: Soil salinity is a major agricultural challenge that cause significant reduction in wheat yields, a staple crop vital for global food security. Despite extensive breeding efforts, developing salt-tolerant wheat remains challenging due to the complex, multi-genic nature of salinity tolerance. While numerous studies have explored molecular responses to salt stress making salt to control comparisons, there is little consensus on the primary points of metabolic disruptions that would determine the salt response in wheat. Our study addresses this gap by integrating proteomics with Weighted Coexpression Network Analysis (WCNA) to examine metabolic responses along the developmental gradient of wheat leaves. By exploiting the natural base-to-tip progression of leaf maturation under salt stress, we identify key protein groups linked to salt response. These findings provide new insights potential metabolic targets for enhancing wheat's resilience to salinity stress.</p>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":" ","pages":"105438"},"PeriodicalIF":2.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795220","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}

{"title":"iTRAQ-based quantitative proteomics reveals dysregulation of fibronectin 1 contributes to impaired endometrial decidualization in recurrent implantation failure","authors":"Jingying Wang ,&nbsp;Xuehan Zhao ,&nbsp;Jiaqi Wu ,&nbsp;Cong Wang ,&nbsp;Qin Wang ,&nbsp;Ying Fang ,&nbsp;Xiaokui Yang","doi":"10.1016/j.jprot.2025.105437","DOIUrl":"10.1016/j.jprot.2025.105437","url":null,"abstract":"<div><div>Recurrent implantation failure (RIF) poses challenges to successful embryo implantation. In this study, we utilized isobaric tags for relative and absolute quantification (iTRAQ) to profile endometrial protein abundance in RIF patients. Through functional and pathway analyses, ECM-related proteins including fibronectin 1 (FN1), collagen type I alpha 2 chain (COL1A2), and integrin beta-1 (ITGB1) were revealed to be associated with RIF. Correlation analysis identified TGF-β1 as an upstream regulator of FN1. Knockdown experiments showed TGF-β1 downregulation could inhibit FN1 expression to inhibit decidualization markers. Our findings suggest a mechanistic link between TGF-β1/FN1 axis dysregulation and impaired decidualization observed in RIF.</div></div><div><h3>Significance</h3><div>Our study addresses the pressing issue of RIF, a significant obstacle in assisted reproductive technology. By employing isobaric tags for relative and absolute quantification (iTRAQ), we comprehensively analyzed endometrial protein abundance in RIF patients. Through functional and pathway enrichment analyses, we identified dysregulation in extracellular matrix (ECM)-related proteins, including FN1, COL1A2, and ITGB1, shedding light on their potential roles in implantation failure. Additionally, our correlation analysis revealed TGF-β1 as an upstream regulator of FN1, suggesting a novel regulatory axis involved in decidualization. Knockdown experiments further demonstrated the impact of TGF-β1 and FN1 on decidualization markers. This study contributes to a better understanding of the molecular mechanisms underlying RIF.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"316 ","pages":"Article 105437"},"PeriodicalIF":2.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143783648","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}

{"title":"Advancing tissue analysis: Integrating mass tags with mass spectrometry imaging and immunohistochemistry","authors":"Dandan Zhang ,&nbsp;Hairong Zhang ,&nbsp;Yuexin Yang ,&nbsp;Ying Jin ,&nbsp;Yingjie Chen ,&nbsp;Caisheng Wu","doi":"10.1016/j.jprot.2025.105436","DOIUrl":"10.1016/j.jprot.2025.105436","url":null,"abstract":"<div><div>In biological and biomedical research, it's a crucial task to detect or quantify proteins or proteomes accurately across multiple samples. Immunohistochemistry (IHC) and spatial proteomics based on mass spectrometry imaging (MSI) are used to detect proteins in tissue samples. IHC can detect precisely but has a limited throughput, whereas MSI can simultaneously visualize thousands of specific chemical components but hindered by detailed protein annotation. Thereby, the introduction of mass tags may be adopted to expand the potential for integrating MSI and IHC. By enriching optical information for IHC and enhancing MS signals, mass tags can boost the accuracy of qualitative, localization, and quantitative detection of specific proteins in tissue sections, thereby widening the scope of protein detection and annotation results. Consequently, more comprehensive information regarding biological processes and disease states can be obtained, which aids in understanding complex biological processes and disease mechanisms and provides additional perspectives for clinical diagnosis and treatment. In the current review, we aim to discuss the role of different mass tags (e.g., mass tags based on inorganic molecules and organic molecules) in the combined application of MSI and IHC.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"316 ","pages":"Article 105436"},"PeriodicalIF":2.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143780320","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}

{"title":"Proteomic insights into cell signaling and stress response mechanisms in Chaetoceros muelleri under nitrogen limitation","authors":"Damaristelma de Jesús-Campos ,&nbsp;Esaú Bojórquez-Velázquez ,&nbsp;Eliel Ruiz-May ,&nbsp;Diana Fimbres-Olivarría ,&nbsp;Corina Hayano-Kanashiro ,&nbsp;José Ángel Huerta-Ocampo","doi":"10.1016/j.jprot.2025.105435","DOIUrl":"10.1016/j.jprot.2025.105435","url":null,"abstract":"<div><div>Microalgae are often called “green factories” because they can perform photosynthesis, converting sunlight into biomass and high-value metabolites. Nitrogen concentration is a critical factor influencing protein accumulation. Unfortunately, nitrogen deprivation often negatively impacts biomass production. Understanding the relationship between nitrogen concentration and protein accumulation is crucial for harnessing the potential of microalgae in various industries and addressing environmental challenges. Here, we quantitatively compared the proteomic profiles of <em>Chaetoceros muelleri</em> diatom, grown in two Nitrogen-deficient conditions and control treatment by employing a Tandem Mass Tag-based quantitative proteomic approach. Proteins involved in photosynthesis were differentially accumulated under moderately nitrogen-deficient conditions. In contrast, proteins involved in cell signaling and protection mechanisms were differentially accumulated under severely nitrogen-limited conditions. Proteins associated with nitrogen metabolism, carbohydrate metabolism, and protein biosynthesis were differentially decreased in severely nitrogen-limited conditions, indicating differential response mechanisms of <em>C. muelleri</em> to varying nitrogen conditions. Our results show that <em>C. muelleri</em> employs distinct strategies in response to nitrogen limitation. These results provide valuable insights into the adaptive strategies of <em>C. muelleri</em> under nitrogen limitation, offering potential applications in optimizing microalgal cultures for the enhanced production of target metabolites in industrial bioreactors.</div></div><div><h3>Biological significance</h3><div>The marine diatom <em>Chaetoceros muelleri</em> accumulates lipids and carbohydrates under low nitrogen conditions without affecting its biomass. Response to nitrogen limitation in <em>C. muelleri</em> was examined by isobaric labelling-based proteomics. We identified changes mainly focused on photosynthesis pathways, cell signaling and protection mechanisms, nitrogen and carbohydrate metabolism, as well as protein biosynthesis. Our results indicate that <em>C. muelleri</em> activate unique strategies in response to different nitrogen concentrations, and this differential response represents a key factor for inducing metabolite accumulation without affecting biomass production.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"316 ","pages":"Article 105435"},"PeriodicalIF":2.8,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692595","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}

{"title":"Serum N-glycoproteomics characterization of differential N-glycosylation in schizophrenia","authors":"Ming Bi ,&nbsp;Yun Chen ,&nbsp;Zhixin Tian","doi":"10.1016/j.jprot.2025.105434","DOIUrl":"10.1016/j.jprot.2025.105434","url":null,"abstract":"<div><div>Glycosylation plays a crucial role in neurotransmission and signaling in schizophrenia; however, comprehensive characterization at the glycoproteome level is still lacking. Here we report our site- and structure-specific quantitative N-glycoproteomics characterization of differential N-glycosylation in the sera of schizophrenia patients at the molecular level of intact N-glycopeptide, where comprehensive qualitative (N-glycosite, monosaccharide composition and sequence structures of N-glycans) and quantitative (fold change) information are obtained. With tandem mass tag labeling, liquid chromatography tandem mass spectrometry analysis and site- and structure-specific DB search using GPSeeker, 7855 intact N-glycopeptides were identified corresponding to 1914 peptide backbones, 1997 N-glycosites and 1671 N-glycoprotein; where 1088 intact N-glycopeptides were differentially expressed in the sera of schizophrenia patients (relative to healthy control) with fold change of no less than 1.5. Function annotation of the corresponding N-glycoproteins was carried out. Neurodegeneration and complement pathway were enriched. These findings provide a comprehensive site- and structure-specific picture of aberrant N-glycosylation in schizophrenia and may foster further function and mechanism studies.</div></div><div><h3>Significance</h3><div>Schizophrenia, as a complex mental disorder, is affecting an increasing number of individuals globally, yet clinical research has struggled to clearly elucidate its pathogenesis. Current diagnostic and treatment approaches largely depend on patient symptoms and behavior, which lack precision. N-glycoproteomics offers a new dimension of understanding by exploring how schizophrenia alters protein glycosylation patterns in the body. Investigating N-glycoproteins not only contributes to the identification of novel early diagnostic biomarkers but also enhances our knowledge of disease pathogenesis. These molecular insights could pave the way for more accurate diagnostic tools and targeted therapies.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"316 ","pages":"Article 105434"},"PeriodicalIF":2.8,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143673874","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}

{"title":"Proteomic insights into the molecular mechanism of anlotinib inhibition in TP53-mutated non-small cell lung cancer","authors":"Jie-Mei Jiang ,&nbsp;Zi-Wei Cheng ,&nbsp;Li Zhang ,&nbsp;Ting-Fei Tan ,&nbsp;Teng Zhang ,&nbsp;Han-Bing Shi ,&nbsp;Kai-Feng Hou ,&nbsp;Quan Xia","doi":"10.1016/j.jprot.2025.105433","DOIUrl":"10.1016/j.jprot.2025.105433","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Objective&lt;/h3&gt;&lt;div&gt;Tumor protein 53 (TP53) is the commonly mutated gene in non-small cell lung cancer (NSCLC) that is associated with poor prognosis, and anlotinib exerts inhibitory effects on TP53-mutated NSCLC. The aim of this study was to investigate the inhibitory effect of anlotinib on TP53-mutated NSCLC and its possible mechanism.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;div&gt;The growth ability of TP53-mutated NSCLC cells were tested by Cell counting kit-8 assay. Proteins in TP53-mutated NSCLC cells treated with anlotinib were analyzed using label-free liquid chromatography-mass spectrometry. Differentially represented proteins were analyzed by KEGG, GO, and PPIs. TP53 pathway related proteins were verified using western blotting.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Results&lt;/h3&gt;&lt;div&gt;The cell viability was significantly reduced in TP53-mutated NSCLC cell as opposed to TP53 wild cell by anlotinib treatment. 126 differentially represented proteins (37 upregulated and 89 downregulated) were found between the anlotinib and control groups in TP53-mutated NSCLC cell. Bioinformatics analyses revealed that the differentially represented proteins were primarily involved in catalytic activity, cellular processes, and metabolite interconversion. PANTHER Classification System found that anlotinib mainly impacted the p53 signaling pathway, De novo purine biosynthesis and Integrin signaling. KEGG enrichment and PPI networks of the differentially represented proteins revealed cyclin-dependent kinase 1 (CDK1) and mitogen-activated protein kinase kinase 3 (MAP2K3) as the core protein, which are related to the p53 signaling pathway. Western blotting also revealed that anlotinib significantly suppressed the expression of CDK1 and MAP2K3 in TP53-mutated NSCLC cells, that indicated the possible mechanism may involve the MAP2K3/p53/CDK1 pathway.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Conclusions&lt;/h3&gt;&lt;div&gt;Our findings showed that anlotinib selectively inhibited the growth of TP53-mutated NSCLC cells and downregulated the expression levels of CDK1 and MAP2K3. The MAP2K3/p53/CDK1 pathway may be the molecular mechanism underlying anlotinib's efficacy in TP53-mutated NSCLC.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Statement of significance&lt;/h3&gt;&lt;div&gt;Tumor protein 53 (TP53) is the commonly mutated gene in non-small cell lung cancer (NSCLC) that is associated with poor prognosis, and anlotinib exerts inhibitory effects on TP53-mutated NSCLC. However, the action mechanism of anlotinib in the treatment of TP53-mutated NSCLC remains unclear.&lt;/div&gt;&lt;div&gt;In this study, we used label-free quantitative proteomics to reveal the molecular mechanism of anlotinib inhibition in TP53-mutated NSCLC. We found that anlotinib significantly inhibited the growth of TP53-mutated NSCLC cells and downregulated the expression levels of CDK1 and MAP2K3. The MAP2K3/p53/CDK1 pathway may be the molecular mechanism underlying anlotinib's efficacy in TP53-mutated NSCLC.&lt;/div&gt;&lt;div&gt;Our study promotes the use of anti-angiogenic drugs in TP53-mutated NSCLC. I","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"316 ","pages":"Article 105433"},"PeriodicalIF":2.8,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143670232","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}

{"title":"Proteomics of Sternaspis chinensis to understand phosphate biomineralization in annelids","authors":"Meiling Ge ,&nbsp;Anning Mou ,&nbsp;Xinlong Li ,&nbsp;Xuying Hu ,&nbsp;Yue Dong ,&nbsp;Zhong Li ,&nbsp;Xuelei Zhang ,&nbsp;Qinzeng Xu","doi":"10.1016/j.jprot.2025.105431","DOIUrl":"10.1016/j.jprot.2025.105431","url":null,"abstract":"<div><div>Organisms with phosphate hard tissues contribute to the evolutionary history of life and global biogeochemical cycles. The annelid Sternaspidae is an important group of phosphate-mineralizing organisms, known for its unique amorphous phosphate ventro-caudal shield. However, the molecular mechanisms underlying the formation of their phosphate shields remain unclear. In this study, we identified shield matrix proteins (ShiMPs) from <em>Sternaspis chinensis</em> (SC group with hard shield) and <em>Sternaspis liui</em> syn (SL group with soft shield) using liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 1360 ShiMPs were identified, with 237 differentially expressed proteins between the two morphologies. The differential expression of collagen, extracellular matrix proteins with new EGF-VWA domains, and calcium-binding proteins in different morphological shields suggested that they may be associated with the variation in shield phenotypes. Furthermore, the phenoloxidase innate immune cascade pathway was found to be upregulated in the SL group. Compared with other biomineral proteins, sternaspid shields lacked typical chitin-related proteins but were rich in collagen proteins containing EGF domains, suggesting that collagen may serve as a scaffold for amorphous phosphate deposition. This study provided a molecular dataset for the formation of sternaspid shields and revealed the molecular regulatory features of different shield morphologies.</div></div><div><h3>Significance</h3><div>Phosphate is one of the important types of biominerals in invertebrates. However, the molecular mechanisms underlying its formation in these organisms remain poorly understood, and no studies have yet explored phosphate biomineralization in annelids. In this study, we performed proteomic analysis of matrix proteins in the phosphate shields of the annelid Sternaspidae to provide new insights into phosphate biomineralization in this group. Comparative analysis of the matrix proteins in different morphological shields from <em>Sternaspis chinensis</em> revealed the regulation of collagen, extracellular matrix proteins, calcium-binding proteins, and immune-related proteins. By comparing with other biominerals, we proposed that collagen may serve as a scaffold for amorphous phosphate deposition in sternaspid shields. This study advances our understanding of phosphate biomineralization in annelids and provides a foundation for future research on the formation mechanisms of phosphate biominerals in invertebrates.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"316 ","pages":"Article 105431"},"PeriodicalIF":2.8,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143637185","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}

{"title":"Skin mucus and blood plasma as non-lethal sources of malnutrition protein biomarkers in meagre (Argyrosomus regius)","authors":"Joana Oliveira ,&nbsp;Cláudia Raposo de Magalhães ,&nbsp;Denise Schrama ,&nbsp;Pedro M. Rodrigues ,&nbsp;Marisa Barata ,&nbsp;Florbela Soares ,&nbsp;Pedro Pousão-Ferreira ,&nbsp;Aires Oliva-Teles ,&nbsp;Ana Couto","doi":"10.1016/j.jprot.2025.105432","DOIUrl":"10.1016/j.jprot.2025.105432","url":null,"abstract":"<div><div>Developing dietary formulations for aquaculture that meet nutritional requirements is essential to production, as nutrition is key for fish growth and health. However, novel dietary formulations may induce malnutrition, which is complex to evaluate and often requires animal sacrifice. Therefore, finding reliable non-lethal biomarkers to diagnose malnutrition in fish is important. This study aimed to obtain vital information on potential non-lethal biomarkers from blood plasma and skin mucus to assess the fish's nutritional status using meagre (<em>Argyrosomus regius</em>) juveniles. For that purpose, a nutritional challenge was performed with fish fed a fish meal (FM) and fish-oil (FO) based control diet (55.1 % FM; 11 % FO, CTRL), a challenging diet (15 % FM; 7 % FO, CD), and a highly challenging diet (5 % FM; 5 % FO, ED), which, despite being nutritionally complete, may pose digestive and physiological challenges to carnivorous species. Diets significantly affected blood parameters, except for leukocyte counts, peroxidase activity, and immunoglobulin levels. Overall, blood parameters showed potential as non-lethal biomarkers to accurately identify signs of malnutrition. Meagre's plasma and skin mucus proteomes provided crucial information on the species' reaction to malnutrition, and 29 proteins connected to various physiological functions such as metabolism, development and immunity showed potential as non-lethal biomarkers.</div></div><div><h3>Significance</h3><div>The significance of this study lies in the establishment of potential non-lethal biomarkers for diagnosing malnutrition in fish. The results demonstrate that immunological, haematological, and biochemical parameters measured in fish blood can reveal signs of nutritional deficiencies. The findings further highlight that the proteomes of plasma and skin mucus provide valuable information about the fish's nutritional status. Notably, 29 proteins identified in this study, associated with various physiological functions, exhibit biomarker potential and warrant consideration in future research in the field of aquaculture nutrition. Moreover, the research provides critical insights into the proteome of meagre (<em>Argyrosomus regius</em>), enhancing our understanding of the species and contributing to the future improvement of its aquaculture production.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"316 ","pages":"Article 105432"},"PeriodicalIF":2.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143627963","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}

{"title":"The dawn of the revolution that will allow us to precisely describe how microbiomes function","authors":"Jean Armengaud","doi":"10.1016/j.jprot.2025.105430","DOIUrl":"10.1016/j.jprot.2025.105430","url":null,"abstract":"&lt;div&gt;&lt;div&gt;The community of microorganisms inhabiting a specific environment, such as the human gut - including bacteria, fungi, archaea, viruses, protozoa, and others - is known as the microbiota. A holobiont, in turn, refers to an integrated ecological unit where microbial communities function and interact with their host, thus is a more integrative concept. To understand the processes involved, the diversity of microorganisms present must be identified and their molecular components quantified, especially proteins. Indeed, proteins – through their roles as catalytic units, structural components, and signaling molecules – are the main drivers of biological processes. Metagenomics has significantly expanded what we know about the genetic material present in microbiota, revealing their functional potential; metabolomics delivers an overall snapshot of the metabolites produced by the community. But metaproteomics offers a complementary approach to explore microbiome and holobiont functionality by focusing on the active proteins and functional pathways from each taxon. Significant recent advances in high-resolution tandem mass spectrometry have greatly expanded the catalog of peptide sequences accessible in each sample, creating the conditions for unprecedented taxonomical profiling, while also providing more accurate biomass quantification, more detailed protein characterization, and a greater capacity to monitor abundance and distinguish host biomarkers. By integrating artificial intelligence into the metaproteomics pipeline, extended datasets can now be efficiently mined to gain a more comprehensive functional view of complex biological systems, paving the way for next-generation metaproteomics. In this perspective, I discuss the transformative potential of this methodology. We are on the cusp of a remarkable omic revolution that promises to uncover the intricate workings of microbiomes by producing a vast array of new knowledge with multiple applications.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Significance&lt;/h3&gt;&lt;div&gt;Metaproteomics provides a powerful lens to investigate microbiome and holobiont functionality by identifying and quantifying active proteins and functional pathways within each taxon. Recent breakthroughs in high-resolution tandem mass spectrometry have dramatically expanded the repertoire of peptide sequences detectable per sample. This progress enables unprecedented taxonomic resolution for microbial identification, more precise biomass quantification, comprehensive protein characterization, abundance monitoring, and the unique identification of host biomarkers. In this commentary, I delve into the distinctive features that make metaproteomics a transformative tool. I discuss the recent advancements in tandem mass spectrometry and argue that the primary challenge in analyzing complex samples is shifting from data acquisition to data interpretation. With the integration of artificial intelligence, I believe next-generation metaproteomics is poised to b","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"316 ","pages":"Article 105430"},"PeriodicalIF":2.8,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143621266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomics reveals genetic mechanisms of cold resistance in Hezuo pig liver tissue","authors":"Yali Zhang ,&nbsp;Xiaoli Gao ,&nbsp;Chao Liu ,&nbsp;Qiaoli Yang ,&nbsp;Xiaoyu Huang ,&nbsp;Yajuan Li ,&nbsp;Shuangbao Gun","doi":"10.1016/j.jprot.2025.105420","DOIUrl":"10.1016/j.jprot.2025.105420","url":null,"abstract":"<div><div>Cold stress poses a significant challenge to pig farming in northern China, leading to reduced productivity and, in severe cases, even mortality. However, the mechanisms underlying cold resistance in pigs are not well understood. To explore the genetic mechanism of cold resistance in pigs under low-temperature conditions, the cold-tolerant Hezuo pig was selected as a model. DIA proteomics analysis was performed on liver tissues from Hezuo pigs after 24 h of exposure to low-temperature treatments. The results showed that approximately 149 differential abundance proteins (DAPs) were detected (95 up-regulated and 54 down-regulated). GO analysis showed that these DAPs were mainly associated with lipid metabolism, vesicle fusion, and membrane function. KEGG analysis showed that these DAPs were primarily enriched in lipid metabolism-related pathways such as cholesterol metabolism and vitamin digestion and absorption. Comprehensive analysis identified APOA4, APOA2, SREBF2, ATP23, STX2, USO1, ETFA, RAB11FIP1, ETNPPL, and SGMS1 as potential key proteins involved in cold resistance mechanisms. The mRNA expression of the genes for two key candidate proteins (<em>APOA4</em> and <em>SREBF2</em>), which are involved in lipid metabolism, was analyzed using qRT-PCR, revealing a significant up-regulation after low-temperature treatment. These findings provide significant insights into the mechanisms of cold resistance in animals and may serve as candidate markers for further studies on cold tolerance.</div></div><div><h3>Significance</h3><div>Cold resistance is one of the key traits in pigs and involves multiple complex coordinated regulatory mechanisms. However, its genetic mechanisms are not completely understood. In this study, a DIA proteomics approach was used to identify proteins and pathways associated with cold resistance in the liver of low-temperature-treated Hezuo pigs. These findings offer novel candidate proteins and key pathways for investigating the molecular mechanisms of cold resistance in Hezuo pigs, providing a base for further elucidating the mechanisms of cold tolerance in pigs.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"316 ","pages":"Article 105420"},"PeriodicalIF":2.8,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143597247","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}