Journal of proteomics最新文献

{"title":"Ablation of ACSS2 drives alteration to cardiac and hepatic proteomic landscapes in a tissue- and sex-specific manner","authors":"Alexis M. Winters ,&nbsp;Jessica Wohlfahrt ,&nbsp;Tiara Wolf ,&nbsp;Ankita Sarkar ,&nbsp;Suraj J. Patel ,&nbsp;Jennifer Guergues ,&nbsp;Brant R. Burkhardt ,&nbsp;Stanley M. Stevens Jr.","doi":"10.1016/j.jprot.2026.105623","DOIUrl":"10.1016/j.jprot.2026.105623","url":null,"abstract":"<div><div>ACSS2 catalyzes the conversion of acetate into acetyl-CoA, linking nutrient availability to cellular processes such as lipid biosynthesis, energy production, and epigenetic regulation. Although ACSS2 has been studied under metabolically stressful conditions, its basal sex- and tissue-specific functions remain poorly defined. Here, we employed comprehensive proteomic characterization of the impact of global ACSS2 ablation in the liver and heart of adult male and female mice. Over 6000 proteins were identified per tissue, providing deep proteomic coverage. Despite the liver exhibiting greater baseline abundance of ACSS2, the most extensive remodeling occurred in the heart. Both tissues displayed marked sex differences, with males showing greater overall proteomic shifts, and minimal overlap in differentially abundant proteins occurring between males and females. Shared alterations across tissues converged on metabolic and immune regulation, whereas sex-specific changes implicated distinct structural and signaling pathways. Comparatively modest hepatic changes may reflect compensatory processes in the liver, in contrast to the strong inhibitory remodeling observed in the heart. These findings reveal a previously unrecognized degree of tissue- and sex-specificity in regulation by ACSS2, while also highlighting the importance of including female mice in proteomic studies, as male only approaches may overlook key sex-dependent adaptations.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"327 ","pages":"Article 105623"},"PeriodicalIF":2.8,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146154220","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":"Label-free proteomics revealed drought stress tolerance mechanisms in the sugar beet monosomic addition line M14","authors":"Xinyi Guo,&nbsp;Wenjing Qiu,&nbsp;Jiaming Zhu,&nbsp;Yingxiao He,&nbsp;Bing Yu","doi":"10.1016/j.jprot.2026.105608","DOIUrl":"10.1016/j.jprot.2026.105608","url":null,"abstract":"<div><div>Sugar beet M14 line is a diploid cultivated sugar beet (<em>Beta vulgaris</em> L.) that carries a monosomic addition of chromosome 9 from the wild white-flowered beet (<em>B. corolliflora</em> Zoss.), developed through distant hybridization. It exhibits enhanced salt and drought tolerance compared to the diploid cultivated beets. In this study, the M14 line exhibited superior water retention capacity under dehydration conditions compared with five major diploid cultivated varieties grown in northern China. Through integrated analysis of phenotype, photosynthetic parameters, physiological and biochemical indicators, and the expression of key drought-responsive genes, 3 days and 5 days of 20% PEG-6000 treatment were identified as two critical time points for the drought stress response of the M14 line. Through label-free quantitative proteomics, 903 and 526 DAPs were identified at 3 and 5 days, respectively. PPI network analysis further revealed key protein interaction modules in the M14 line under drought stress. Furthermore, qRT-PCR analysis of 12 key DAP-encoding genes revealed that their transcript levels generally corresponded to the protein expression trends. This study helped to produce molecular network maps of drought tolerance in the M14 line, uncovering the mechanisms underlying its drought tolerance.</div></div><div><h3>Significance</h3><div>The drought tolerance of the sugar beet M14 line and ive major diploid sugar beet varieties cultivated in northern China was evaluated, revealing that the M14 line showed the strongest drought resistance. This study uncovered the dynamic regulatory network responsible for drought tolerance in the M14 line at the proteomic level, highlighting the main response pathways and key functional proteins at 3 and 5 days after stress exposure. These results not only deepen our understanding of the molecular mechanisms behind the sugar beet drought tolerance but also identify important candidate proteins and key regulatory modules for molecular breeding drought-tolerant varieties.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"327 ","pages":"Article 105608"},"PeriodicalIF":2.8,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146046663","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":"Comparative proteomics of amaranth and quinoa seeds reveals species-specific solubility traits of 11S globulins after Osborne and polarity-based extractions","authors":"Esaú Bojórquez-Velázquez ,&nbsp;Abraham M. Vidal-Limón ,&nbsp;Jesús Alejandro Zamora-Briseño ,&nbsp;Miriam L. Llamas-García ,&nbsp;Alberto Barrera-Pacheco ,&nbsp;Eduardo Espitia-Rangel ,&nbsp;Ana P. Barba de la Rosa","doi":"10.1016/j.jprot.2026.105621","DOIUrl":"10.1016/j.jprot.2026.105621","url":null,"abstract":"<div><div>Amaranth and quinoa are nutritious grains rich in essential amino acids, vitamins, and phytochemicals. The use of these emergent functional foods is still limited and their proteins are poorly characterized. Here, we compared amaranth and quinoa seeds by profiling their proteins using Osborne and polarity-based extraction methods and evaluating their relative protein content. The Osborne fractions and the two fractions generated by the polarity-based method (hydrophilic and hydrophobic) were quantified and analyzed by 1D-SDS-PAGE in the absence and presence of a reducing agent, as well as by diagonal electrophoresis. In addition, hydrophilic and hydrophobic proteins were analyzed by 2-DE, and the representative spots for each species were identified by LC-MS/MS. Both methods yield similar total protein amounts. The electrophoretic profiles showed differentiated patterns between the two seeds. All the extracts reflect the formation of high-molecular-mass aggregates because of interchain disulfide bonds. Intrachain disulfide bonds were also detected in 2S albumins. A differential behavior in the solubility of 11S globulins was observed across both species, and molecular modelling and molecular dynamics simulations were performed to explain this phenomenon. This study provides valuable insights into the structural differences between amaranth and quinoa proteins, which could help inform decisions about potential food applications.</div></div><div><h3>Significance</h3><div>This work addresses two main topics: the implementation of alternative methods for characterizing plant proteins and the detailed comparison of the protein profiles of amaranth and quinoa seeds using different electrophoretic approaches. The polarity-based method we propose represents an alternative to reduce sample handling and the number of extracts required for proteome characterization without sacrificing the protein yield. This study generated relevant information on the storage proteins of the two seeds analyzed, primarily 2S albumins, prolamins, and 11S globulins, to inform decision-making on their application in food technology.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"327 ","pages":"Article 105621"},"PeriodicalIF":2.8,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146137156","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-driven innovations in plant-based foods: Current advances, emerging technologies, and future perspectives","authors":"Fatma Boukid","doi":"10.1016/j.jprot.2026.105624","DOIUrl":"10.1016/j.jprot.2026.105624","url":null,"abstract":"<div><div>Despite rapid market growth, plant-based foods such as meat analogs, plant-based milk, yogurt alternatives, and fermented products still fall short of matching the sensory, structural, and nutritional qualities of animal-based counterparts, primarily due to simple ingredient substitution that fails to reproduce the molecular structure, interactions, and functional properties required for optimal texture, flavor, and nutritional performance. Proteomics, using advanced mass spectrometry (MS) and label-free quantification methods, provides an approach to analyze plant protein composition, structure, interactions, and modifications, enabling targeted functional improvements. This review describes how proteomic workflows inform formulation across three areas. First, protein compositional and structural characterization employs techniques such as liquid chromatography-tandem mass spectrometry (LC-MS/MS) and differential scanning calorimetry (DSC) coupled with MS to map protein composition and structural behavior, supporting decisions on protein sources, fractionation, and purification. Second, indirect proteomic methods coupled with other non-proteomic complementary tools are used to determine structure–function relationships induced by processing to examine processing-induced crosslinking, enzymatic modifications, and lipid–protein interactions that influence texture. Third, targeted MS methods, including selected reaction monitoring (SRM) and parallel reaction monitoring (PRM), are applied to profile off-flavor compounds and identify protein modification sites relevant to sensory and nutritional properties. By integrating proteomic data with processing strategies, this review outlines how proteomics can be used to examine key functional attributes related to texture, flavor, and nutritional quality in plant-based foods.</div></div><div><h3>Significance</h3><div>This review highlights the pivotal role of proteomics in advancing next-generation plant-based foods. Proteomic analysis enables an in-depth understanding of plant protein structure, composition, interactions, and bioactivity, providing critical insights for the development of functionally enhanced and consumer-acceptable alternatives. By integrating proteomics with AI, machine learning, multi-omics approaches, and cutting-edge analytical tools such as spatial proteomics and mass spectrometry imaging, the review demonstrates how protein functionality, flavor, texture, nutrition, and allergenicity can be optimized. Furthermore, it emphasizes the potential of proteomics to accelerate innovation in personalized nutrition, support sustainable and circular food systems, improve food safety, and reduce waste by valorizing plant-based by-products. This work serves as a roadmap for researchers and industry stakeholders seeking to leverage proteomics to design novel, high-quality, and sustainable plant-based protein products.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"327 ","pages":"Article 105624"},"PeriodicalIF":2.8,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146154196","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":"Comparative peptidomics of four wasp venoms reveals extensive peptide diversity, proteolytic patterns, and predicted bioactivities.","authors":"Kai Wang, Jiangtao Qiao, Loïc Quinton, Gauthier Eppe, Xianbin Meng, Guozhong Huang, Eric Haubruge, Hongcheng Zhang","doi":"10.1016/j.jprot.2026.105676","DOIUrl":"https://doi.org/10.1016/j.jprot.2026.105676","url":null,"abstract":"<p><p>Wasp venoms possess complex compositions and diverse bioactivities, making them potential pharmacological sources. In this study, venoms from four wasp species (Vespa mandarinia, V. velutina, V. basalis, and Provespa barthelemyi) were collected by electrical stimulation and analyzed using liquid chromatography-tandem mass spectrometry. A total of 681 peptides were identified, nearly 90% of which had not been previously reported. Comparative analyses revealed pronounced species-specific signatures at both peptide and peptide family levels. Sequence-based analyses indicated that peptide release is consistent with targeted proteolytic cleavage patterns, exhibiting features resembling known substrate preferences of metalloproteases and serine proteases, rather than stochastic degradation. Bioinformatic predictions identified 291 peptides with potential bioactive properties spanning multiple functional categories, with angiotensin-converting enzyme (ACE) and dipeptidyl peptidase IV (DPP4) inhibitory activities being the most prominently represented. Among these, eight ACE inhibitory peptides and seventeen DPP4 inhibitory peptides were prioritized as candidates based on predicted safety profiles, and sequence-based analysis further identified ten putative cryptides. Overall, this study establishes the first comparative peptidomic dataset across four wasp venoms, providing insights into peptide diversity, inferred generation patterns, and predicted activities. SIGNIFICANCE: Venoms are rich sources of biologically active molecules and have historically provided templates for clinically used therapeutics. Although major protein toxins have been extensively characterized, the endogenous low-molecular-weight peptide fraction remains comparatively underexplored, particularly in social wasps, and systematic comparative resources remain limited. Venom peptidomic datasets inherently contain multiple layers of biological information, including diversification patterns, peptide origin, and potential bioactivity, yet these aspects are often interpreted independently. By integrating these dimensions, this study establishes a multi-level analytical framework for extracting biological insights and function-related information from venom peptidomes. The identification of consistent cleavage patterns suggests a degree of regulation in peptide generation, shifting the interpretation of venom peptides from degradation by-products toward biologically organized repertoires. Moreover, candidate prioritization illustrates how peptidomic datasets can generate experimentally testable functional hypotheses rather than serving solely as descriptive catalogs. The resulting dataset serves as a reference resource for cumulative comparative analyses. The analytical framework presented here also provides a transferable strategy for functional peptide discovery in other complex secretions.</p>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":" ","pages":"105676"},"PeriodicalIF":2.8,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147839405","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":"Cosine similarity analysis of venom proteomes of Indian cobras, Naja naja and Naja kaouthia reveals significant interspecies and geographic variations.","authors":"Sneha Bansode, Kruti Modi, Sana Ziya, Ankit Goel, Mahesh Kulkarni, Nishigandha Naik","doi":"10.1016/j.jprot.2026.105665","DOIUrl":"https://doi.org/10.1016/j.jprot.2026.105665","url":null,"abstract":"<p><p>The Indian cobra (genus Naja) is one of the 'Big Fours' responsible for dreaded snakebite incidents in India. Immediate anti-snake venom (ASV) treatment is the only solution for cobra envenomation. Currently available ASVs are not efficacious nationwide, probably due to geographical variations in venom. The lack of precise information on venom variation is the foremost hurdle to ASV improvement. Hence, mapping of geographical variation in snake venom proteome is of utmost importance. Here, we report mass spectrometry-based proteomic analysis of the venom of Naja naja and Naja kaouthia, collected in the wild from seven regions in India. For the first time, the proteomes of N. kaouthia venom from two Northeastern States of India, Assam and Mizoram, have been characterized. More than 65 proteins from the 12 major protein families were detected in venom samples from all locations. The identification of unique proteins enabled us to understand the variation in venom. In all the venom samples, most of the unique proteins belonged to two families: 3FTX and PLA2. N. kaouthia venom from Assam and Mizoram contained unique proteins in the SVMP and SVSP families. In N. naja only one unique SVMP is seen in the venom from Chandigarh. Cosine similarity analysis revealed an interesting and distinctive similarity between samples from western and northeastern regions. Similarity analysis of proteomic profiles demonstrated the use of machine learning to solve the snakebite problem. SIGNIFICANCE: This study highlights the importance of understanding the geographic variation in the venom of Indian cobras (Naja naja and Naja kaouthia) to improve anti-snake venom (ASV) treatments. The current ASVs are not effective across all regions in India due to differences in venom composition. By mapping the venom proteome from different regions, a unique set of proteins was identified. This knowledge is crucial for developing more effective ASVs that can save lives by providing targeted treatment for cobra envenomation.</p>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":" ","pages":"105665"},"PeriodicalIF":2.8,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147839392","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":"Machine learning-enhanced plasma proteomics discriminates pancreatic cancer-associated diabetes from type 2 diabetes mellitus.","authors":"Lucas Cardoso Lazari, Carlos Del Cistia Donnarumma, Luiz Henrique Gomes Matheus, Renata D'Alpino Peixoto, Mozânia Reis de Matos, Hellen Paula Valerio, Livia Rosa-Fernandes, Sueli M Oba-Shinjo, Marcel Cerqueira César Machado, Marcel Autran Cesar Machado, Suely K N Marie, Maria Lucia Correa-Giannella, Giuseppe Palmisano","doi":"10.1016/j.jprot.2026.105663","DOIUrl":"10.1016/j.jprot.2026.105663","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Pancreatic ductal adenocarcinoma (PDAC) is frequently preceded by new-onset diabetes mellitus (NODM), yet differentiating PDAC-associated DM from type 2 diabetes (T2D) remains clinically challenging. We investigated whether plasma proteomic profiling combined with machine learning could discriminate these conditions. Plasma samples from individuals with PDAC (with and without DM), long-standing T2D, and controls were analyzed by MALDI-TOF mass spectrometry. Spectral features were processed through a nested cross-validation framework to prevent data leakage, and model interpretability was explored using SHAP values. In parallel, low-molecular-weight proteins were characterized by GeLC-MS followed by LC-MS/MS and differential abundance analysis. Machine learning models distinguished PDAC-associated DM from T2D with a balanced accuracy of 85%. Proteomic analyses identified distinct signatures in PDAC- associated DM, including downregulation of erythrocyte-related proteins and PPBP, and upregulation of acute-phase reactants such as FGA, CP, and SERPINA3. Treatment-naïve cases displayed increased circulating epithelial and keratin-associated proteins, which were attenuated after therapy, suggesting dynamic tumor-related remodeling. These findings demonstrate that integrating MALDI-TOF profiling with machine learning can capture plasma signatures associated with PDAC-associated DM. Although exploratory, this approach supports further validation in prospective cohorts aimed at improving PDAC risk stratification among individuals with NODM. SIGNIFICANCE: Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy with a dismal 5-year survival rate, primarily due to late-stage diagnosis. The frequent occurrence of new-onset diabetes mellitus (NODM) as a paraneoplastic syndrome offers a critical window for early detection. However, the clinical challenge of distinguishing PDAC-associated diabetes (PDAC-DM) from type 2 diabetes mellitus (T2D) has hindered the implementation of effective screening strategies. This study addresses this significant clinical problem by leveraging a multi-faceted proteomics approach. We demonstrate that the integration of MALDI-TOF mass spectrometry peptide profiling with machine learning algorithms can accurately discriminate PDAC-DM from T2D with 85% accuracy. Furthermore, we used LC-MS/MS to identify specific low molecular weight proteins that are differentially regulated between these conditions, providing a molecular basis for the observed discrimination. Our work is significant as it presents a novel, high-throughput pipeline for biomarker discovery that combines the scalability of MALDI-TOF with the analytical power of LC-MS/MS and machine learning. The identified plasma signatures hold strong translational potential to improve risk stratification in patients with NODM, ultimately enabling earlier diagnosis of PDAC and improving patient survival prospects. This research directly contributes to the field of","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":" ","pages":"105663"},"PeriodicalIF":2.8,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147816517","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":"Functional and protein interaction analysis of Nop7 in trypanosomatid parasites.","authors":"Tomás Nepomuceno-Mejía, Laila Espinosa-Renteria, Aldo Yael Miranda-Muñoz, Emmanuel Torres-Morales, Juan Felipe Osorio-Méndez, Luis Enrique Florencio-Martínez, Santiago Martínez-Calvillo","doi":"10.1016/j.jprot.2026.105675","DOIUrl":"https://doi.org/10.1016/j.jprot.2026.105675","url":null,"abstract":"<p><p>Nucleolar protein 7 (Nop7), also known as PES1 or Pescadillo, is a conserved factor essential for ribosome biogenesis, cell cycle progression, proliferation, and nucleolar organization in yeast and metazoans. Its dysregulation has been linked to multiple human diseases. Here, we characterize Nop7 in Trypanosoma brucei and Leishmania major, microorganisms that possess atypical ribosomes whose 28S-type ribosomal RNA is multifragmented. In silico analyses indicates that trypanosomatids Nop7 exhibits putative structural adaptations that may support specialized protein-protein interactions. A PTP-tagged version of Nop7 localize to the nucleolus throughout cell cycle in both species. To define the Nop7 interactome, we performed tandem affinity purifications coupled with mass spectrometry, revealing extensive association with numerous transient trans-acting factors, including Erb1 and Ytm1, which together with Nop7 form a heterotrimeric complex (PeBow in mammals) essential for 60S ribosome subunit maturation. Comparative proteomic allowed us to identify several nucleolar proteins that represent potential parasite-specific factors needed for ribosome production. RNAi-mediated depletion of Nop7 in T. brucei impaired growth, disrupted morphology, and altered DNA content, underscoring its critical role in cell cycle progression and survival. Collectively, our findings provide the first proteomic map of Nop7-associated factors in trypanosomatids, revealing new candidates for future functional and therapeutic studies.</p>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":" ","pages":"105675"},"PeriodicalIF":2.8,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147816573","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":"Barley protein: From agricultural staple to sustainable protein solution","authors":"Fatma Boukid","doi":"10.1016/j.jprot.2026.105603","DOIUrl":"10.1016/j.jprot.2026.105603","url":null,"abstract":"<div><div>Barley protein is a multifunctional, sustainable plant-based ingredient with potential in food, nutraceutical, and industrial applications. This review synthesizes current knowledge on barley protein, emphasizing how proteomics and processing methods influence its composition, digestibility, and functional properties. Proteomic analyses reveal the distribution of major protein fractions, albumins, globulins, hordeins, and glutelins and their bioactive peptides, which exhibit antioxidant, antihypertensive, antidiabetic, and appetite-regulating activities. Protein concentrates and isolates offer improved digestibility and functional quality, though lysine remains limiting. Advanced techniques, including enzymatic hydrolysis, ultrasound-assisted extraction, and post-processing modifications, are evaluated for their impact on protein structure and functionality. Barley protein's potential applications in novel foods, micro- and nano-encapsulation, and targeted bioactive delivery are highlighted. By integrating proteomics insights with nutritional and technological perspectives, this work underscores the role of barley proteins in sustainable food systems.</div></div><div><h3>Significance</h3><div>This review synthesizes current knowledge on barley protein composition, emphasizing insights gained from proteomic analyses. By characterizing protein fractions, bioactive peptides, and allergenic determinants, proteomics enables a deeper understanding of barley's functional, nutritional, and health-related properties. The work highlights how extraction and processing influence protein quality and bioactivity, informing strategies for the development of novel plant-based foods. These insights provide a foundation for future research and industrial applications, advancing barley as a sustainable and functional protein source in human nutrition.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"326 ","pages":"Article 105603"},"PeriodicalIF":2.8,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146003744","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":"Sputum proteomics and phosphoproteomics for improving chronic obstructive pulmonary disease knowledge","authors":"Fei Long ,&nbsp;Xiaoyin Zeng ,&nbsp;Fengyan Wang ,&nbsp;Xufei Wang ,&nbsp;Weijuan Shi ,&nbsp;Yanting Lan ,&nbsp;Jiahao Cheng ,&nbsp;Chen Zhu ,&nbsp;Yiqi Yang ,&nbsp;Jing Xiao ,&nbsp;Longbo Hu ,&nbsp;Long Tan ,&nbsp;Yuqiong Yang ,&nbsp;Rongchang Chen ,&nbsp;Zhenyu Liang ,&nbsp;Tao Peng ,&nbsp;Shaohua Lu","doi":"10.1016/j.jprot.2026.105605","DOIUrl":"10.1016/j.jprot.2026.105605","url":null,"abstract":"<div><div>Analysis of proteins and other molecular components in induced sputum provides critical insights for the diagnosis, pathological assessment, and therapeutic monitoring of respiratory diseases. In this study, we collected three distinct types of induced sputum samples from patients with chronic obstructive pulmonary disease (COPD) and subjected them to proteomic and phosphoproteomic analysis using three different enzymatic digestion methods. We found that raw sputum samples yielded a higher number of uniquely identified proteins and phosphoproteins (1313 proteins and 1603 phosphorylation sites, corresponding to 782 phosphoproteins) and provided a more comprehensive characterization of COPD pathology. Furthermore, compared to in-gel digestion and in-solution digestion, the filter-aided sample preparation method increased protein identification by approximately 30% and yielded the highest number of unique protein identifications. Our study is the first to demonstrate that raw induced sputum can serve as a viable alternative source for liquid biopsy in respiratory diseases. We have also established the first methodological framework and dataset for proteomic and phosphoproteomic analysis of raw induced sputum, generating a preliminary map of the COPD sputum proteome and phosphoproteome. This novel proteomic and phosphoproteomic approach has untangled biologically relevant pathways in respiratory physiology, highlighting potential avenues for future research.</div></div><div><h3>Significance</h3><div>In this study, we aimed to investigate the feasibility of establishing and evaluating proteomic research methods using sputum samples from patients with chronic obstructive pulmonary disease (COPD). The ultimate goal was to develop analytical approaches suitable for sputum proteomics and phosphoproteomics and to preliminarily map the sputum proteome and phosphoproteome in COPD. It was found that raw sputum samples more comprehensively reflect the disease characteristics of COPD and are therefore more suitable for proteomic and phosphoproteomic studies of COPD. Among three mainstream enzymatic digestion methods, the Filter-Aided Sample Preparation (FASP) method demonstrated superior identification rates and was deemed most suitable for processing raw sputum samples. Furthermore, this study reports for the first time a draft map of the proteome and phosphoproteome of COPD sputum. This research provides valuable insights into sputum proteomic analysis and offers a useful resource for the study of respiratory diseases.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"326 ","pages":"Article 105605"},"PeriodicalIF":2.8,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146018988","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}