Journal of proteomics最新文献

{"title":"Interspecific and intraspecific variability in venom composition of Naja naja and Naja kaouthia (Reptilia: Elapidae) populations from different habitats in Bangladesh.","authors":"Mohammad Abdul Wahed Chowdhury, Johannes Müller, Ibrahim Khalil Al Haidar, Md Mizanur Rahman, Mohammed Noman, Aniruddha Ghose, Abdullah Abu Sayeed, Robed Amin, Libia Sanz, Mohammad Abul Faiz, Ulrich Kuch, Juan J Calvete","doi":"10.1016/j.jprot.2025.105544","DOIUrl":"https://doi.org/10.1016/j.jprot.2025.105544","url":null,"abstract":"<p><p>The spectacled cobra (Naja naja) and monocled cobra (Naja kaouthia), widespread venomous snakes in South and Southeast Asia, occur in diverse habitats and cause neurotoxic envenoming. Despite reported venom variability of these two cobras across their range, no comparative study has been conducted from the interconnected but distinct habitats of Bangladesh. Using venomics and antivenomics, we analysed 26 individual venom samples of N. kaouthia and 17 of N. naja from Bangladesh across age groups and locations, respectively. Significant interspecific and intraspecific venom variability was observed, with geographically connected populations showing minimal divergence, while isolated populations (separated by river barriers or distinct ecosystems) exhibited pronounced compositional differences. Ontogenetic differences in venom composition between adult N. kaouthia and their juvenile offspring were detected. Commercially available Incepta polyvalent antivenom, produced against India's \"Big Four\" (including southern Indian N. naja), demonstrated poor efficacy against Bangladeshi cobra venoms. Collectively, our analyses demonstrate the existence of multi-dimensional variation in cobra venoms of Bangladesh that is influenced by biotic and abiotic factors. We emphasize the urgent need for region-specific antivenoms incorporating venom from ecologically distinct populations and age groups of both species across South Asia to improve snakebite treatment efficacy as well pre-clinical assessments to address biogeographic and ontogenetic venom diversity. SIGNIFICANCE: Snakebite envenoming is a major neglected tropical disease and a leading occupational health hazard especially for rural populations in many low-and middle-income countries. As differences in snake venom composition between and within species can greatly affect the clinical course of envenoming and the efficacy of treatment, detailed knowledge of this variability is highly important for public health planning and the development of better antidotes. In Bangladesh, the monocled cobra (Naja kaouthia) and the spectacled cobra (Naja naja) belong to the medically most important and most widely distributed common snake species, but data on the variability of their venoms in this country has been limited and its relation to climatic and other environmental factors remained unexplored. Here we report on the analysis of 43 individual venom samples from 26 N. kaouthia and 17 N. naja from different age groups and geographical localities in Bangladesh, using venomics and antivenomics methods. Our findings show that the venoms of these cobras are highly diverse qualitatively and quantitatively, with significant inter- and intraspecific, geographic and ontogenetic variability and differences in their reactivity with a commercial antivenom. The observed geographical variability appears to be influenced by climatic and other environmental variables of different habitats in Bangladesh. When designing impro","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":" ","pages":"105544"},"PeriodicalIF":2.8,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145238932","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":"Integration of proteomic and transcriptomic data of the venom and venom gland from Tityus jaimei.","authors":"Ana Escobar, Marcos H Salazar, Magdalena Hernández-Ortiz, Herlinda Clement, Sergio Encarnación, John Cleghorn, Hildaura Acosta, Gerardo Corzo","doi":"10.1016/j.jprot.2025.105543","DOIUrl":"https://doi.org/10.1016/j.jprot.2025.105543","url":null,"abstract":"<p><p>This work presents a comprehensive transcriptomic and proteomic analysis of the venom gland and venom of Tityus jaimei, a recently described scorpion species of medical relevance in Panama and Costa Rica. High-throughput RNA sequencing (RNA-seq) and tandem mass spectrometry (MS/MS) enabled the identification of a diverse repertoire of venom proteins. Notably, this is the first report of proteins belonging to the nucleotide pyrophosphatase/phosphodiesterase and knottins families in the venom proteome of a scorpion from the genus Tityus. In addition, several known venom protein families were identified, including hyaluronidases, voltage-gated sodium and potassium channel toxins, lipolysis-activating peptides (LVPs), cysteine-rich secretory proteins (CRISPs), metalloproteinases, peptidylglycine alpha-hydroxylating monooxygenases (PHMs), serine proteases, alpha-amylases, single insulin-like growth factor-binding domain proteins, non-disulfide-bridged peptides (NDBPs), chitinases, cyclotide trypsin inhibitors, and calcin-like peptides. The identification of 16 distinct families in the venom of Tityus jaimei offers novel insights into its composition and the diversity of Tityus venoms in Central America. Finally, the use of IA to protein domain search for protein annotation. SIGNIFICANCE T JAIMEI: In this work, we present a comprehensive transcriptomic and proteomic analysis of the venom gland and venom of Tityus jaimei, a recently described scorpion species of medical relevance in Panama and Costa Rica. Notably, we report for the first time proteins belonging to the nucleotide pyrophosphatase/phosphodiesterase and knottins families in the venom proteome of a scorpion from the genus Tityus. In addition, several known venom protein families were identified, including hyaluronidases, voltage-gated sodium and potassium channel toxins, lipolysis-activating peptides (LVPs), cysteine-rich secretory proteins (CRISPs), metalloproteinases, peptidylglycine alpha-hydroxylating monooxygenases (PHMs), serine proteases, alpha-amylases, single insulin-like growth factor-binding domain proteins, non-disulfide-bridged peptides (NDBPs), chitinases, cyclotide trypsin inhibitors, and calcin-like peptides. The identification of 16 distinct families in the venom of Tityus jaimei offers novel insights into its composition and the diversity of Tityus venoms in Central America.</p>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":" ","pages":"105543"},"PeriodicalIF":2.8,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145232912","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":"Extruded Limnospira platensis with enzyme supplementation shifts the broiler muscle proteome toward enhanced energy metabolism pathways.","authors":"Maria Pinheiro Spínola, Dina Rešetar Maslov, Ivana Rubić, Mónica Mendes da Costa, Vladimir Mrljak, Madalena Lordelo, André Martinho de Almeida, José António Mestre Prates","doi":"10.1016/j.jprot.2025.105541","DOIUrl":"https://doi.org/10.1016/j.jprot.2025.105541","url":null,"abstract":"<p><p>Limnospira platensis (Spirulina) is known for its nutritional and bioactive profile, but its high-level dietary inclusion effects in broilers, particularly post-extrusion and enzyme pre-treatment, remain underexplored. We investigated how 15 %L. platensis raw (MA), extruded (MAE) or extruded with pancreatin (0.20 %) and lysozyme (0.01 %) (MAEM) affects the pectoralis major proteome of Ross 308 broilers. Birds were fed until day 35, then muscle proteins were prepared by filter-aided sample preparation, TMT 6-plex labelling and analysed by LC-MS/MS. Statistical analysis identified 26 differentially abundant proteins (p < 0.05, ≥ 2 peptides). MAEM samples clustered separately, showing increased abundance of NDUFA10 (Complex I; + 1.30-fold), COX5B (Complex IV; + 1.25-fold) and glycogen phosphorylase (+ 1.40-fold). Enrichment analysis revealed up-regulation of ATP synthesis, oxidative phosphorylation and glycogen catabolism in L. platensis groups, whereas control diets featured proteins linked to fatty-acid β-oxidation and myofibrillar assembly. These results indicate that extrusion combined with enzyme treatment enhances nutrient bioavailability and shifts the broiler muscle proteome toward energy-metabolism pathways without compromising performance. Data are available via ProteomeXchange (PXD064230). SIGNIFICANCE: The incorporation of Spirulina (Limnospira platensis) as a sustainable alternative to conventional feed ingredients is gaining attention in poultry nutrition. However, its specific effects on broiler's muscle proteome, as well as the impact of higher Spirulina inclusion levels on animal performance, remain largely unexplored. Herein, we investigated how extruded L. platensis, with and without enzyme supplementation, influences muscle protein expression. Results revealed a metabolic shift toward enhanced mitochondrial ATP production and glycogen metabolism when L. platensis was incorporated into the diets, suggesting improved energy efficiency and nutrient utilisation. These findings provide valuable insight into the biological mechanisms underlying muscle development in broilers fed microalgae-based diets. More broadly, they highlight the potential of combining pre-treated microalga ingredients as a strategy to optimise animal performance and health in the framework of poultry production.</p>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":" ","pages":"105541"},"PeriodicalIF":2.8,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145206672","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":"Molecular signature of early obesity-associated insulin resistance: Adipocyte-derived extracellular vesicle proteins reveal stage-specific candidates for metabolic dysfunction","authors":"Jaime Delgadillo-Velázquez ,&nbsp;Esaú Bojórquez-Velázquez ,&nbsp;Eliel Ruiz-May ,&nbsp;Elizabeth Carvajal-Millan ,&nbsp;Magdalena Aguirre-García ,&nbsp;Efraín Alday-Noriega ,&nbsp;José Ángel Huerta-Ocampo ,&nbsp;Humberto Astiazaran-Garcia","doi":"10.1016/j.jprot.2025.105540","DOIUrl":"10.1016/j.jprot.2025.105540","url":null,"abstract":"<div><div>Visceral obesity is closely related to insulin resistance (IR), a key process in developing metabolic diseases. Adipocyte-derived extracellular vesicles (AdEVs) have emerged as mediators of intercellular communication, carrying signals reflecting adipose tissue's functional state. This study aimed to perform a comparative proteomic analysis of AdEVs to propose a molecular fingerprint of specific biomarker candidates for IR in early-onset obesity. AdEVs were isolated from epididymal adipocytes of 16-week-old male Wistar rats on a high-fat diet (HFD) and controls and analyzed by mass spectrometry coupled to a multi-software protein identification bioinformatics strategy. For relative quantification using the label-free method, more than 1200 proteins were identified, with 431 being overrepresented and unique to HFD, associated explicitly with energy metabolism, cellular stress, and insulin signaling. Based on biological plausibility, and/or the best log2FC and <em>p</em>-value scores, six proteins were proposed as part of the IR molecular fingerprint: Atp5f1b, Anxa6, Myo1c, GLUT4, Anxa5, and Aoc3. Phosphoproteomic analysis revealed key modifications in phosphorylated proteins such as CaATPase (S663), PLIN (S130), and PPM1H (S260,265). The results suggest that AdEVs reflect early mitochondrial alterations related to IR, which could be employed as potential non-invasive biomarker candidates for metabolic dysfunction and follow-up in early overweight or obesity.</div><div>Significance</div><div>In this study, we demonstrate that adipocyte-derived extracellular vesicles (AdEVs) encapsulate a stage-resolved molecular signature that reflects key pathophysiological events underlying the early development of insulin resistance in obesity. These vesicles carry proteins linked to lipotoxicity, mitochondrial and endoplasmic reticulum stress, and impaired vesicular trafficking, offering mechanistic insight into how local adipocyte dysfunction may trigger systemic metabolic impairment. This EV-based proteomic fingerprint advances our understanding of insulin resistance pathogenesis and identifies potential biomarker candidates for early metabolic risk stratification.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"322 ","pages":"Article 105540"},"PeriodicalIF":2.8,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145206649","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 proteomic analysis of residual proteins in waterlogged ancient leather","authors":"Lijie Tang ,&nbsp;Hailiang Yang ,&nbsp;Zhijiang Wu ,&nbsp;Liping Bao ,&nbsp;Yang Zhou ,&nbsp;Huabing Wang","doi":"10.1016/j.jprot.2025.105537","DOIUrl":"10.1016/j.jprot.2025.105537","url":null,"abstract":"<div><div>Leather artifacts hold significant historical and cultural value in human civilization. During long-term preservation, ancient relics, especially waterlogged leather artifacts, are susceptible to protein degradation. Therefore, analyses of the structure and protein composition of these ancient relics are crucial for their effective conservation. However, comprehensive research in this field is scarce and urgently needed. In this study, systematic investigations of the structures of fresh vegetable-tanned leather, dried leather artifacts, and waterlogged leather artifacts were performed from multiple perspectives. Compared with fresh vegetable-tanned leather and dry leather artifacts, the deterioration of waterlogged leather artifacts resulted in a darkened color, increased brittleness, and reduced fiber structure. Infrared analyses revealed that the characteristic peaks of the amide II and III bands were nearly absent in waterlogged leather artifacts. The species of the leather artifacts were analyzed using enzyme-linked immunosorbent assay (ELISA). Furthermore, comparative proteomic analysis revealed a markedly reduced repertoire of protein species in waterlogged leather artifacts compared with fresh vegetable-tanned leather. In particular, the number of peptides derived from type I collagen and other structural proteins was substantially diminished. This loss of collagen- and structure-related peptides, together with extensive fiber disintegration, underlies the pronounced morphological deterioration observed in waterlogged leather. By integrating species identification through ELISA with proteomic profiling, we establish a strategy that enables rapid, sensitive, and specific characterization of leather proteins.</div></div><div><h3>Significance</h3><div>This study integrated stereomicroscopy, scanning electron microscopy (SEM), and fourier transform infrared spectroscopy (FTIR) to systematically characterize morphological and microstructural differences between fresh vegetable-tanned leather and archaeological waterlogged leather artifacts. To further unravel residual proteins, comparative proteomic profiling was implemented to identify compositional shifts in collagenous proteins resulting from prolonged waterlogged burial conditions. A multidisciplinary approach was used to assess the characteristics of waterlogged leather artifacts.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"322 ","pages":"Article 105537"},"PeriodicalIF":2.8,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145137764","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":"Structural dynamics of the TPS/TPP complex in Saccharomyces cerevisiae: Insights from cross-linking mass spectrometry and computational modeling","authors":"Renata M. Santos ,&nbsp;Viviane A. Bastos ,&nbsp;Felipe F.M. Bagatelli ,&nbsp;Richard H. Valente ,&nbsp;Louise U. Kurt ,&nbsp;Diogo B. Lima ,&nbsp;Carla C. Oliveira ,&nbsp;Fabio C.S. Nogueira ,&nbsp;Elis C.A. Eleutherio ,&nbsp;Paulo C. Carvalho ,&nbsp;Francisco Gomes-Neto","doi":"10.1016/j.jprot.2025.105535","DOIUrl":"10.1016/j.jprot.2025.105535","url":null,"abstract":"<div><div>Trehalose, a ubiquitous disaccharide, plays a vital role in cell viability, including pathogenic fungi, making its synthetic pathway a key target for antifungal drug design. The structural details of the trehalose-phosphate synthase (TPS)/trehalose-phosphate phosphatase (TPP) complex, which is responsible for synthesizing trehalose, have remained elusive. Information on the structure and topology of the TPS/TPP complex remains scarce, significantly limiting the mechanistic understanding of trehalose synthesis. This study presents the first overview of the interactions within the <em>Saccharomyces cerevisiae</em> TPS/TPP complex following a 40 °C heat shock, analyzed by cross-linking mass spectrometry (XL-MS) and computational modeling. Our cross-linking data corroborate the UniProt-available AlphaFold models for isolated subunits. Intrinsically disordered regions are suggested for the regulatory subunits, while cross-linking analysis highlights the disordered N-terminus of Tsl1 as an important region in assembling the TPS/TPP complex. Finally, the phosphorylation prediction indicates that Tps3-disordered regions at the N-terminus and the phosphatase-like domains are preferentially phosphorylated, triggering the inhibition of Tps2 activity and halting T6P accumulation. These insights enhance our understanding of the structural dynamics and flexibility of the TPS/TPP complex, opening new avenues for potential therapeutic applications with diminished or no toxicity to humans.</div></div><div><h3>Significance</h3><div>This research contributes to a comprehensive structural understanding of the TPS/TPP complex in <em>Saccharomyces cerevisiae</em>, a key enzymatic system involved in trehalose synthesis. Trehalose is essential in cellular viability and stress adaptation, particularly in pathogenic fungi, making its biosynthetic pathway a promising target for antifungal drug development. By integrating cross-linking mass spectrometry (XL-MS) and computational modeling, this study uncovers critical interactions and dynamic features of the TPS/TPP complex, including the involvement of intrinsically disordered regions in its regulatory subunits possibly contributing to complex assembly and regulation under heat shock conditions. Furthermore, the phosphorylation predictions shed light on how disordered regions on Tps3 would participate in modulating Tps2 activity to regulate trehalose-phosphate levels, offering insights into the complex's functional dynamics. This work fills a crucial knowledge gap in understanding trehalose biosynthesis and paves the way for novel antifungal strategies with reduced toxicity to human cells.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"322 ","pages":"Article 105535"},"PeriodicalIF":2.8,"publicationDate":"2025-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145131242","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":"Anisomelic acid promotes proteasomal degradation of HPV16 E6 via E3 ligase recruitment: A mass spectrometry-based interactome study","authors":"Michael Santos Silva ,&nbsp;Leila S. Coelho-Rato ,&nbsp;Navid Delshad ,&nbsp;Tatiana Tarkhova ,&nbsp;Joakim Edman ,&nbsp;Preethy Paul ,&nbsp;Annika Meinander ,&nbsp;John E. Eriksson","doi":"10.1016/j.jprot.2025.105536","DOIUrl":"10.1016/j.jprot.2025.105536","url":null,"abstract":"<div><div>Human papillomavirus (HPV) is a major driver of cervical and other epithelial cancers, with the viral oncoprotein E6 playing a central role in tumorigenesis by promoting degradation of the tumor suppressor p53. While prophylactic vaccines prevent infection, there remains a critical need for therapeutic strategies that eliminate established HPV-positive cells. Here, we identify anisomelic acid (AA), a natural diterpenoid, as a novel pharmacological principle that selectively induces the degradation of HPV16 E6. Using cellular thermal shift assay, we demonstrate that AA directly interacts with E6, likely triggering a conformational change that promotes its ubiquitination. Proteomic analysis of the E6 interactome in AA-treated cells revealed consistent enrichment of E3 ubiquitin ligases, including E6AP, UBR4, CDC20, and TRIP12, as well as proteasomal subunits. To our knowledge, this represents the first comprehensive proteomics framework of the HPV16 E6 interactome under small-molecule treatment conditions. These findings support a model in which AA facilitates proteasome-mediated elimination of E6, and the dataset itself provides a timely and valuable resource for HPV biology and therapeutic development.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"322 ","pages":"Article 105536"},"PeriodicalIF":2.8,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145086449","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":"Potential protein biomarkers for heat tolerance in wheat at seedling and ear peep stages","authors":"Agyeya Pratap ,&nbsp;Kadambot H.M. Siddique ,&nbsp;Nicolas L. Taylor","doi":"10.1016/j.jprot.2025.105526","DOIUrl":"10.1016/j.jprot.2025.105526","url":null,"abstract":"<div><div>Heat stress is a major threat to global wheat (<em>Triticum aestivum</em> L.) production, adversely affecting crop yields and grain quality. Understanding wheat's heat tolerance mechanisms is crucial for developing resilient cultivars. This study used targeted proteomics to validate heat-induced changes to protein abundances in seedling and flag leaves of heat-tolerant (Vixen-T) and heat-sensitive (HD2329-S) wheat genotypes. Proteomics samples were collected on days 1, 3 and 5 of heat exposure (32/16 °C day/night for 3 hours per day over 5 days) and day 12 post-recovery. Flag leaf gas exchange was studied under heat treatment during ear peep and significant genotype × heat treatment interactions were observed for all traits. Significant protein abundance changes occurred under heat stress for 15 and 14 proteins at the seedling and ear peep stages, respectively. Two key proteins—DM2 domain-containing protein (<em>r =</em> 0.99) and Rubisco activase (<em>r =</em> 0.96)—showed consistent responses across both developmental stages. Redox homeostasis and protein chaperone pathways emerged as major contributors to wheat heat tolerance. These findings highlight critical protein biomarkers that can support breeding efforts to develop heat-tolerant wheat varieties, offering valuable strategies for sustaining wheat productivity under climate change.</div></div><div><h3>Significance</h3><div>This study identifies and validates novel protein biomarkers associated with heat tolerance in wheat. These proteins were discovered in our previous study in the flag leaves of four genotypes with contrasting heat responses (tolerant: RAJ3765, HD2932; susceptible: HD2329, HD2733) under short-term heat stress at the ear peep stage. These biomarkers were further validated in two genotypes (tolerant: Vixen; susceptible: HD2329) under short-term heat stress at both seedling and ear peep stages. The validated protein isoforms span key biological processes, including photosynthesis, redox regulation, chromatin remodelling, protein folding, and carbohydrate and secondary metabolism. This panel of protein biomarkers offers a novel molecular framework for breeding heat-tolerant wheat, providing a strategic avenue, utilising targeted proteomics, to sustain yield under rising temperatures.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"322 ","pages":"Article 105526"},"PeriodicalIF":2.8,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058669","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":"Peroxiredoxin 6 (Prdx6) and oxidative stress in post-mortem beef tenderization: A proteomic perspective","authors":"Huixin Zuo ,&nbsp;Linlin Huang ,&nbsp;Mingming Huang ,&nbsp;Xiao Ma ,&nbsp;Chongxian Zheng ,&nbsp;Benjamin W.B. Holman ,&nbsp;Yimin Zhang ,&nbsp;Xin Luo ,&nbsp;Yanwei Mao","doi":"10.1016/j.jprot.2025.105527","DOIUrl":"10.1016/j.jprot.2025.105527","url":null,"abstract":"<div><div>This research explored the role of peroxiredoxin 6 (Prdx6)-mediated non‑selenium glutathione peroxidase (NSGPx) activity in modulating the tenderization process of beef during <em>post-mortem</em> aging, extending up to 168 h. Shear force, NSGPx activity, differential protein abundance, heat shock proteins (HSP70, HSP27), and troponin-T levels were analyzed in beef <em>longissimus lumborum</em> muscles treated with hydrogen peroxide (H₂O₂), <em>N</em>-acetylcysteine (NAC), mercaptosuccinic acid (MA), or saline (Control). MA treatment inhibited NSGPx activity and accelerated tenderization compared to NAC. Proteomics revealed that proteins differentially abundant between 0 and 24 h <em>post-mortem</em> were linked to cytoskeleton, extracellular matrix, amino acid metabolism, and apoptosis pathways.MA upregulated HSP70 abundance, oxidative stress, and troponin-T breakdown. H₂O₂ upregulated HSP70 and HSP27 abundance only within 6–12 h <em>post-mortem</em>. These results demonstrate that oxidative stress treatments modulate protein dynamics during aging, offering insights into strategies to enhance beef tenderness.</div></div><div><h3>Significance</h3><div>This study highlights peroxiredoxin 6 (Prdx6) as a crucial regulatory element that affects oxidative stress-associated pathways involved in the meat tenderization process during post-mortem beef aging. We demonstrate that inhibiting Prdx6's on‑selenium glutathione peroxidase (NSGPx) enzymatic activity with mercaptosuccinic acid (MA) increases HSP70 abundance and accelerates troponin-T proteolysis through enhanced oxidative stress and calcium signaling pathways. Conversely, antioxidant <em>N</em>-acetylcysteine (NAC) delays tenderization by preserving cytoskeletal integrity. Our TMT-based proteomics further identifies 35 core proteins linking extracellular matrix remodeling, amino acid metabolism, and apoptosis to tenderness modulation. These findings provide the first mechanistic evidence that targeted manipulation of Prdx6 activity can optimize beef aging efficiency. For the meat industry, MA treatment offers a science-driven strategy to reduce tenderization time by &gt;20 % within 24–72 h post-mortem, lowering processing costs while maintaining quality. This work also establishes HSP70 and troponin-T degradation as novel biomarkers for real-time monitoring of oxidative stress in meat processing systems.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"322 ","pages":"Article 105527"},"PeriodicalIF":2.8,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145040422","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":"Sequence-driven species identification of ZooMS collagen peptide mass fingerprints","authors":"Toby Lawrence ,&nbsp;Michael Buckley","doi":"10.1016/j.jprot.2025.105525","DOIUrl":"10.1016/j.jprot.2025.105525","url":null,"abstract":"&lt;div&gt;&lt;div&gt;Developments in biomolecular species identification of animal tissues have been ongoing for decades, with collagen peptide mass fingerprinting becoming increasingly used in recent years. However, establishing confidence in the species biomarkers within these fingerprints requires sequence assignment, usually done via LC-ESI-MS/MS-based approaches and correlation with sequence databases. This study develops an approach that allows collagen fingerprints to be matched to sequence databases directly. To do so we create theoretical spectra from &lt;em&gt;in silico&lt;/em&gt; digests of publicly available sequences that are then filtered by previously collected proteomic sequence data. These inform on the likely number of collagen post translational modifications, vastly reducing the number of peaks in the theoretical spectra and so making overlapping peptide signals as well as false positives less likely. We retrieved a database containing 211 mammals and tested this approach with spectra of 29 modern reference species and 98 archaeological examples of 10 different families, some for which the taxa were represented in the sequence database, and others that were not. This approach was found to be at least 93 % accurate for predicting the correct family in both modern and archaeological spectra, and capable of species-level identification in some cases. This sequence-driven analysis allows rapid comparison across whole spectra, rather than small sets of markers for a particular taxon, which removes human error from manual identification and ensures that the selected markers derive from the protein of interest, unlike machine-learning methods.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Significance&lt;/h3&gt;&lt;div&gt;Species identification using collagen peptide mass fingerprinting is a MALDI-based mass spectrometric method becoming increasingly popular, largely because of its reliance on the dominant protein in the most enduring of biological tissues, bone and tooth dentine. This endurance has great significance to fields such as bioarchaeology and palaeontology, but also applies to processed foodstuffs, for which proteomics-based species identification has been ongoing for decades. However, with this increase in demand, there are greater explorations into a wider range of vertebrate species under investigation, making biomarker selection more challenging. Although the use of DNA-based gene sequence information has been a cornerstone for probability-based proteomic inferences, their use in fingerprint analysis for species identification has remained indirect, where tools such as Mascot's PMF search application may be suitable for protein identification but often struggle with such species-level inferences. Here we introduce a means to create post-translational modification rules based on observation in LC-MS/MS data to generate improved &lt;em&gt;in silico&lt;/em&gt; PMFs from DNA-based sequences that greatly reduces search space and confidence matches to taxonomic interpretations of PMFs. This is a","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105525"},"PeriodicalIF":2.8,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144920402","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}