Pub Date : 2025-09-11DOI: 10.1016/j.jprot.2025.105526
Agyeya Pratap , Kadambot H.M. Siddique , Nicolas L. Taylor
Heat stress is a major threat to global wheat (Triticum aestivum 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 (r = 0.99) and Rubisco activase (r = 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.
Significance
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.
{"title":"Potential protein biomarkers for heat tolerance in wheat at seedling and ear peep stages","authors":"Agyeya Pratap , Kadambot H.M. Siddique , 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}
Pub Date : 2025-09-09DOI: 10.1016/j.jprot.2025.105527
Huixin Zuo , Linlin Huang , Mingming Huang , Xiao Ma , Chongxian Zheng , Benjamin W.B. Holman , Yimin Zhang , Xin Luo , Yanwei Mao
This research explored the role of peroxiredoxin 6 (Prdx6)-mediated non‑selenium glutathione peroxidase (NSGPx) activity in modulating the tenderization process of beef during post-mortem 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 longissimus lumborum muscles treated with hydrogen peroxide (H2O2), N-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 post-mortem 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 post-mortem. These results demonstrate that oxidative stress treatments modulate protein dynamics during aging, offering insights into strategies to enhance beef tenderness.
Significance
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 N-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 >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.
{"title":"Peroxiredoxin 6 (Prdx6) and oxidative stress in post-mortem beef tenderization: A proteomic perspective","authors":"Huixin Zuo , Linlin Huang , Mingming Huang , Xiao Ma , Chongxian Zheng , Benjamin W.B. Holman , Yimin Zhang , Xin Luo , 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 (H<sub>2</sub>O<sub>2</sub>), <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. H<sub>2</sub>O<sub>2</sub> 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 >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}
Pub Date : 2025-08-22DOI: 10.1016/j.jprot.2025.105525
Toby Lawrence , Michael Buckley
<div><div>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 <em>in silico</em> 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.</div></div><div><h3>Significance</h3><div>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 <em>in silico</em> PMFs from DNA-based sequences that greatly reduces search space and confidence matches to taxonomic interpretations of PMFs. This is a
{"title":"Sequence-driven species identification of ZooMS collagen peptide mass fingerprints","authors":"Toby Lawrence , Michael Buckley","doi":"10.1016/j.jprot.2025.105525","DOIUrl":"10.1016/j.jprot.2025.105525","url":null,"abstract":"<div><div>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 <em>in silico</em> 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.</div></div><div><h3>Significance</h3><div>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 <em>in silico</em> 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}
Pub Date : 2025-08-18DOI: 10.1016/j.jprot.2025.105519
K. Roger , I. Metatla , S. Ceccacci , K. Wahbi , L. Motté , C. Chhuon , I.C. Guerrera
Plasma is a complex biological fluid containing extracellular vesicles (EVs), residual platelets, and soluble proteins. While conventional plasma proteomics typically identifies hundreds of proteins, recent enrichment strategies have expanded coverage to thousands. It is still unclear whether these methods enrich preferentially different classes of protein and whether they allow for reliable quantification. Here, we compared three common advanced proteomic workflows—Proteograph (Seer), Mag-Net (ReSynBio), and ENRICHplus (PreOmics) as well as EV enrichment obtained by centrifugation. We explore the content in soluble proteins, EV cargo, and platelet-derived proteins after the enrichments. Quantification was evaluated comparing each method to neat plasma using protein coefficient of variation and point-biserial correlation.
We quantified an average of ∼4500 proteins with EV centrifugation, ∼4000 with Seer, ∼2800 with ENRICHplus, ∼2300 with Mag-Net, and ∼ 900 with neat plasma. Each method enriched distinct sets of protein signatures: EV preparations were enriched with EV markers such as CD81; ENRICHplus predominantly captured lipoproteins; and Proteograph was enriched for cytokines and hormones. Platelet protein intensity was directly correlated with total protein identifications but did not compromise quantification of low-abundance proteins. Across 50 healthy individuals, Proteograph consistently demonstrated reproducible enrichment and depletion patterns, with some reported exceptions.
Our results highlight the strengths and biases of different plasma enrichment strategies.
Significance
This study benchmarks corona formation strategies for enriching low-abundance plasma proteins, including those from platelets and EVs. While enabling deeper proteome coverage compared to depletion methods, these approaches also reshape the intensity landscape and reveal method-specific patterns in protein class enrichment and in quantification repeatability.
血浆是一种复杂的生物液体，含有细胞外囊泡（EVs）、残留的血小板和可溶性蛋白质。虽然传统的血浆蛋白质组学通常识别数百种蛋白质，但最近的富集策略已将覆盖范围扩大到数千种。目前尚不清楚这些方法是否优先富集不同种类的蛋白质，以及它们是否允许可靠的定量。在这里，我们比较了三种常见的先进蛋白质组学工作流程- proteograph (Seer), magg - net （ReSynBio）和enrichment plus （PreOmics）以及通过离心获得的EV富集。我们研究了富集后可溶性蛋白、EV货物和血小板衍生蛋白的含量。用蛋白质变异系数和点双列相关性对每种方法与纯血浆的定量进行比较。我们用EV离心平均定量了~4500个蛋白，用Seer定量了~4000个，用enrichment定量了~2800个，用Mag-Net定量了~2300个，用纯等离子定量了 ~ 900个。每种方法都富集了不同的蛋白质特征集：EV制剂富集了EV标记物，如CD81；富集主要捕获脂蛋白；蛋白图富含细胞因子和激素。血小板蛋白强度与总蛋白鉴定直接相关，但不影响低丰度蛋白的定量。在50个健康个体中，Proteograph一致显示出可重复的富集和耗尽模式，有一些报道的例外。我们的结果突出了不同等离子体富集策略的优势和偏差。意义：本研究为富集低丰度血浆蛋白（包括来自血小板和ev的蛋白）的冠状形成策略提供了基准。与耗尽方法相比，这些方法能够实现更深的蛋白质组覆盖，同时也重塑了强度景观，并揭示了蛋白质类富集和定量可重复性的方法特异性模式。
{"title":"Mining the plasma proteome: Evaluation of enrichment methods for depth and reproducibility","authors":"K. Roger , I. Metatla , S. Ceccacci , K. Wahbi , L. Motté , C. Chhuon , I.C. Guerrera","doi":"10.1016/j.jprot.2025.105519","DOIUrl":"10.1016/j.jprot.2025.105519","url":null,"abstract":"<div><div>Plasma is a complex biological fluid containing extracellular vesicles (EVs), residual platelets, and soluble proteins. While conventional plasma proteomics typically identifies hundreds of proteins, recent enrichment strategies have expanded coverage to thousands. It is still unclear whether these methods enrich preferentially different classes of protein and whether they allow for reliable quantification. Here, we compared three common advanced proteomic workflows—Proteograph (Seer), Mag-Net (ReSynBio), and ENRICHplus (PreOmics) as well as EV enrichment obtained by centrifugation. We explore the content in soluble proteins, EV cargo, and platelet-derived proteins after the enrichments. Quantification was evaluated comparing each method to neat plasma using protein coefficient of variation and point-biserial correlation.</div><div>We quantified an average of ∼4500 proteins with EV centrifugation, ∼4000 with Seer, ∼2800 with ENRICHplus, ∼2300 with Mag-Net, and ∼ 900 with neat plasma. Each method enriched distinct sets of protein signatures: EV preparations were enriched with EV markers such as CD81; ENRICHplus predominantly captured lipoproteins; and Proteograph was enriched for cytokines and hormones. Platelet protein intensity was directly correlated with total protein identifications but did not compromise quantification of low-abundance proteins. Across 50 healthy individuals, Proteograph consistently demonstrated reproducible enrichment and depletion patterns, with some reported exceptions.</div><div>Our results highlight the strengths and biases of different plasma enrichment strategies.</div></div><div><h3>Significance</h3><div>This study benchmarks corona formation strategies for enriching low-abundance plasma proteins, including those from platelets and EVs. While enabling deeper proteome coverage compared to depletion methods, these approaches also reshape the intensity landscape and reveal method-specific patterns in protein class enrichment and in quantification repeatability.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105519"},"PeriodicalIF":2.8,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144883084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-18DOI: 10.1016/j.jprot.2025.105524
Zheng Fang , Yanjun Zhang , Xiaoxia Feng , Na Li , Liang Chen , Xianquan Zhan
Proteoforms represent the ultimate structural/functional forms of a gene product, defined by multiple factors, including amino acid sequences, post-translational modifications, spatial conformations, and interactions with other molecules. The human proteoform diversity significantly exceeds the number of human genes/transcripts, emphasizing the need for advanced analytical methods to characterize this complexity. Two-dimensional gel electrophoresis-liquid chromatography/mass spectrometry (2DE-LC/MS) and top-down MS (TD-MS) are complementary to detect, identify, and quantify the large-scale proteoforms. The emerging AI tools for structural biology such as AlphaFold 3 and D-I-TASSER will enable proteoformics to be high-throughput and precisely predict spatial conformations and molecular interactions. Integrating the large-scale experimental data derived from 2DE-LC/MS and TD-MS with AI-driven high-throughput structural analysis paves the way to deeply understand proteoform diversity and functionality. The combination of advanced 2DE-LC/MS, TD-MS, and AI-driven structural analysis represents a pivotal advancement in proteoformics. This integrated approach enables the comprehensive profiling of proteoforms, providing critical insights into their roles in health care. Such advancements hold promise for predictive, preventive, and personalized medicine, particularly through biomarker discovery and therapeutic target identification. Future developments in high-throughput capabilities and dynamic modeling are expected to address current challenges and further expand the applicability of proteoformics in biological and clinical research.
Significance
Proteoformics is the future of proteomics, whose two main complementary analytical approaches are 2DE-LC/MS and TD-MS. The AI-driven large-cale structural analysis enables to high-throughput and precisely analyze spatial conformations and molecular interactions of proteoforms, which helps to deeply understand proteoform diversity and functionality. Proteoformics holds transformative potential to uncover biomarkers, guide targeted therapies, and advance predictive diagnosis in the context of personalized medicine.
{"title":"Proteoformics: Current status and future perspectives","authors":"Zheng Fang , Yanjun Zhang , Xiaoxia Feng , Na Li , Liang Chen , Xianquan Zhan","doi":"10.1016/j.jprot.2025.105524","DOIUrl":"10.1016/j.jprot.2025.105524","url":null,"abstract":"<div><div>Proteoforms represent the ultimate structural/functional forms of a gene product, defined by multiple factors, including amino acid sequences, post-translational modifications, spatial conformations, and interactions with other molecules. The human proteoform diversity significantly exceeds the number of human genes/transcripts, emphasizing the need for advanced analytical methods to characterize this complexity. Two-dimensional gel electrophoresis-liquid chromatography/mass spectrometry (2DE-LC/MS) and top-down MS (TD-MS) are complementary to detect, identify, and quantify the large-scale proteoforms. The emerging AI tools for structural biology such as AlphaFold 3 and D-I-TASSER will enable proteoformics to be high-throughput and precisely predict spatial conformations and molecular interactions. Integrating the large-scale experimental data derived from 2DE-LC/MS and TD-MS with AI-driven high-throughput structural analysis paves the way to deeply understand proteoform diversity and functionality. The combination of advanced 2DE-LC/MS, TD-MS, and AI-driven structural analysis represents a pivotal advancement in proteoformics. This integrated approach enables the comprehensive profiling of proteoforms, providing critical insights into their roles in health care. Such advancements hold promise for predictive, preventive, and personalized medicine, particularly through biomarker discovery and therapeutic target identification. Future developments in high-throughput capabilities and dynamic modeling are expected to address current challenges and further expand the applicability of proteoformics in biological and clinical research.</div></div><div><h3>Significance</h3><div>Proteoformics is the future of proteomics, whose two main complementary analytical approaches are 2DE-LC/MS and TD-MS. The AI-driven large-cale structural analysis enables to high-throughput and precisely analyze spatial conformations and molecular interactions of proteoforms, which helps to deeply understand proteoform diversity and functionality. Proteoformics holds transformative potential to uncover biomarkers, guide targeted therapies, and advance predictive diagnosis in the context of personalized medicine.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105524"},"PeriodicalIF":2.8,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144894990","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-18DOI: 10.1016/j.jprot.2025.105523
Maritza G. Verdugo-Molinares , Marco Ku-Centurion , Laura Cortes-Sanabria , Yadira O. Lugo-Melchor , Emilie Pinault , Luis Evangelista , Cesar O. Ramos-Garcia , Pierre Marquet , Zesergio Melo
Chronic kidney disease is a multifactorial entity characterized by decreased glomerular filtration rate (GFR). The last stage of the disease requires renal replacement therapy or kidney transplantation. As a disease with no treatment at earlier stages, and few biomarkers available, proteomics represent an excellent tool searching for new more efficient biomarkers. Urinary extracellular vesicles are an important source of information for kidney alterations, and their collection is not invasive. In this exploratory study, we worked on urine samples collected from patients at Centro Medico Nacional de Occidente in Guadalajara, Jalisco, and isolated urinary extracellular vesicles (uEVs) by ultracentrifugation. Our objective was to compare the Proteomic Profile of uEVs between Mexican patients with normal kidney function, end-stage renal disease, or kidney transplantation. High resolution mass spectrometry analysis reveals alterations in end-stage renal disease regarding the energy metabolism, cytoskeleton organization and cell motility. Proteomic alterations in transplant patients point towards the conservation of fibrotic process. Important proteins such as cystatins can be proposed as candidates for kidney transplant monitoring, while Gelsolin, a protein with an important role in assessing podocyte damage, stands out as a probable marker of chronic kidney disease. Data are available via ProteomeXchange with identifier PXD065380.
Significance
Chronic Kidney disease is a growing public health burden, increasing each year, and favored by major chronic diseases such as diabetes and hypertension. Although Mexico is one of the countries with the highest incidence of chronic kidney disease, proteomics studies involving Mexican patients had not yet been conducted. uEVs are features of particular interest to study the disease and discover biomarkers. We characterized the uEVs proteomic profile in Mexican patients, providing new insights into the pathogenesis of chronic kidney disease and kidney transplantation disorders. We identified promising biomarker candidates for transplant monitoring, and one as an early indicator of ESRD progression. uEVs may serve as a non-invasive platform for renal disease investigation, potentially offering non-invasive biomarkers for patient monitoring as well as mechanistic insights for future research into kidney pathophysiology.
{"title":"Potential kidney biomarkers in urinary extracellular vesicles from end stage renal disease and post-transplant patients","authors":"Maritza G. Verdugo-Molinares , Marco Ku-Centurion , Laura Cortes-Sanabria , Yadira O. Lugo-Melchor , Emilie Pinault , Luis Evangelista , Cesar O. Ramos-Garcia , Pierre Marquet , Zesergio Melo","doi":"10.1016/j.jprot.2025.105523","DOIUrl":"10.1016/j.jprot.2025.105523","url":null,"abstract":"<div><div>Chronic kidney disease is a multifactorial entity characterized by decreased glomerular filtration rate (GFR). The last stage of the disease requires renal replacement therapy or kidney transplantation. As a disease with no treatment at earlier stages, and few biomarkers available, proteomics represent an excellent tool searching for new more efficient biomarkers. Urinary extracellular vesicles are an important source of information for kidney alterations, and their collection is not invasive. In this exploratory study, we worked on urine samples collected from patients at Centro Medico Nacional de Occidente in Guadalajara, Jalisco, and isolated urinary extracellular vesicles (uEVs) by ultracentrifugation. Our objective was to compare the Proteomic Profile of uEVs between Mexican patients with normal kidney function, end-stage renal disease, or kidney transplantation. High resolution mass spectrometry analysis reveals alterations in end-stage renal disease regarding the energy metabolism, cytoskeleton organization and cell motility. Proteomic alterations in transplant patients point towards the conservation of fibrotic process. Important proteins such as cystatins can be proposed as candidates for kidney transplant monitoring, while Gelsolin, a protein with an important role in assessing podocyte damage, stands out as a probable marker of chronic kidney disease. Data are available via ProteomeXchange with identifier PXD065380.</div></div><div><h3>Significance</h3><div>Chronic Kidney disease is a growing public health burden, increasing each year, and favored by major chronic diseases such as diabetes and hypertension. Although Mexico is one of the countries with the highest incidence of chronic kidney disease, proteomics studies involving Mexican patients had not yet been conducted. uEVs are features of particular interest to study the disease and discover biomarkers. We characterized the uEVs proteomic profile in Mexican patients, providing new insights into the pathogenesis of chronic kidney disease and kidney transplantation disorders. We identified promising biomarker candidates for transplant monitoring, and one as an early indicator of ESRD progression. uEVs may serve as a non-invasive platform for renal disease investigation, potentially offering non-invasive biomarkers for patient monitoring as well as mechanistic insights for future research into kidney pathophysiology.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105523"},"PeriodicalIF":2.8,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144886149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-12DOI: 10.1016/j.jprot.2025.105522
Sergio Encarnación-Guevara , Jeovanis Gil
Lysine acetylation, once viewed primarily as a histone mark, is now recognized as a widespread regulator of protein function. Recent breakthroughs in chemical labeling, isotopic tagging workflows, and data-independent acquisition mass spectrometry enable precise, site-specific quantification of acetylation stoichiometry. This quantitative “acetylomics” approach reveals a “rheostat” model, where most acetylation sites exhibit low occupancy, acting as subtle modulators, while a subset of highly acetylated lysines (e.g., p53 C-terminus, AKT1, histones) serve as pivotal regulatory switches in gene expression, metabolism, and cell fate. Site-specific occupancy changes (e.g., p53, PKM2) increasingly serve as robust biomarkers for cancer diagnosis, prognosis, and therapeutic monitoring, often surpassing mRNA or total protein levels. Quantitative acetylation data now guide the development of targeted epigenetic therapies, including HDAC and p300/CBP inhibitors. Beyond oncology, acetylomics can pinpoint metabolic bottlenecks in heart failure, epigenetic deficits in neurodegenerative conditions, and inflammatory signaling nodes. With advances in high-throughput workflows, FFPE and liquid biopsy compatibility, and microfluidic platforms, acetylation stoichiometry is poised for clinical translation. We highlight both the promise and challenges of this emerging dimension of precision medicine, emphasizing the need for integrated multi-omics approaches and robust clinical validation to fully realize the potential of quantitative acetylomics in disease diagnosis and therapy.
Significance
Understanding the extent of acetylation occupancy in proteins, beyond simply determining presence or absence of acetylation, has profound implications for biology and medicine. This review emphasizes the importance of acetylation stoichiometry, connecting advanced proteomic technologies with translational science. We emphasize that quantifying site occupancy reveals which acetylation events truly modulate enzyme function. For instance, it can identify which acetylation events truly modulate enzyme activity or gene expression. Additionally, it can highlight molecular changes in diseases like cancer that are not apparent through qualitative analyses. These quantitative insights pave the way for clinical innovations, including novel biomarkers that stratify patients based on their acetylation profiles and targeted therapies that modulate acetylation levels. In summary, this work highlights the evolving landscape of protein acetylation research over the past two decades and its increasing influence on translational proteomics, celebrating milestones achieved by the global research community.
赖氨酸乙酰化，曾经主要被认为是一个组蛋白标记，现在被认为是一个广泛的蛋白质功能调节。最近在化学标记、同位素标记工作流程和数据独立采集质谱方面的突破使乙酰化化学计量学的精确、特定位点的量化成为可能。这种定量的“乙酰组学”方法揭示了一种“变阻器”模型，其中大多数乙酰化位点表现出低占用，作为微妙的调节剂，而高度乙酰化的赖氨酸子集（例如p53 c -端，AKT1，组蛋白）在基因表达，代谢和细胞命运中起关键的调节开关作用。位点特异性占用变化（如p53、PKM2）越来越多地作为癌症诊断、预后和治疗监测的强有力的生物标志物，通常超过mRNA或总蛋白水平。定量乙酰化数据现在指导靶向表观遗传治疗的发展，包括HDAC和p300/CBP抑制剂。除了肿瘤学，乙酰组学还可以精确定位心力衰竭的代谢瓶颈、神经退行性疾病的表观遗传缺陷和炎症信号节点。随着高通量工作流程、FFPE和液体活检相容性以及微流体平台的进步，乙酰化化学计量学已准备好用于临床翻译。我们强调了精准医学这一新兴维度的前景和挑战，强调需要整合多组学方法和强大的临床验证，以充分发挥定量乙酰组学在疾病诊断和治疗中的潜力。理解乙酰化在蛋白质中的占据程度，不仅仅是简单地确定乙酰化的存在与否，对生物学和医学具有深远的意义。这篇综述强调了乙酰化化学计量学的重要性，将先进的蛋白质组学技术与转化科学联系起来。我们强调，量化位点占用揭示哪些乙酰化事件真正调节酶的功能。例如，它可以识别哪些乙酰化事件真正调节酶活性或基因表达。此外，它还可以通过定性分析来突出癌症等疾病中不明显的分子变化。这些定量的见解为临床创新铺平了道路，包括基于乙酰化谱对患者进行分层的新型生物标志物和调节乙酰化水平的靶向治疗。总之，这项工作突出了过去二十年来蛋白质乙酰化研究的发展前景及其对翻译蛋白质组学的日益增长的影响，庆祝了全球研究界取得的里程碑。
{"title":"Expanding the landscape of lysine acetylation stoichiometry and clinical impact","authors":"Sergio Encarnación-Guevara , Jeovanis Gil","doi":"10.1016/j.jprot.2025.105522","DOIUrl":"10.1016/j.jprot.2025.105522","url":null,"abstract":"<div><div>Lysine acetylation, once viewed primarily as a histone mark, is now recognized as a widespread regulator of protein function. Recent breakthroughs in chemical labeling, isotopic tagging workflows, and data-independent acquisition mass spectrometry enable precise, site-specific quantification of acetylation stoichiometry. This quantitative “acetylomics” approach reveals a “rheostat” model, where most acetylation sites exhibit low occupancy, acting as subtle modulators, while a subset of highly acetylated lysines (e.g., p53 C-terminus, AKT1, histones) serve as pivotal regulatory switches in gene expression, metabolism, and cell fate. Site-specific occupancy changes (e.g., p53, PKM2) increasingly serve as robust biomarkers for cancer diagnosis, prognosis, and therapeutic monitoring, often surpassing mRNA or total protein levels. Quantitative acetylation data now guide the development of targeted epigenetic therapies, including HDAC and p300/CBP inhibitors. Beyond oncology, acetylomics can pinpoint metabolic bottlenecks in heart failure, epigenetic deficits in neurodegenerative conditions, and inflammatory signaling nodes. With advances in high-throughput workflows, FFPE and liquid biopsy compatibility, and microfluidic platforms, acetylation stoichiometry is poised for clinical translation. We highlight both the promise and challenges of this emerging dimension of precision medicine, emphasizing the need for integrated multi-omics approaches and robust clinical validation to fully realize the potential of quantitative acetylomics in disease diagnosis and therapy.</div></div><div><h3>Significance</h3><div>Understanding the extent of acetylation occupancy in proteins, beyond simply determining presence or absence of acetylation, has profound implications for biology and medicine. This review emphasizes the importance of acetylation stoichiometry, connecting advanced proteomic technologies with translational science. We emphasize that quantifying site occupancy reveals which acetylation events truly modulate enzyme function. For instance, it can identify which acetylation events truly modulate enzyme activity or gene expression. Additionally, it can highlight molecular changes in diseases like cancer that are not apparent through qualitative analyses. These quantitative insights pave the way for clinical innovations, including novel biomarkers that stratify patients based on their acetylation profiles and targeted therapies that modulate acetylation levels. In summary, this work highlights the evolving landscape of protein acetylation research over the past two decades and its increasing influence on translational proteomics, celebrating milestones achieved by the global research community.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105522"},"PeriodicalIF":2.8,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144842547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-12DOI: 10.1016/j.jprot.2025.105521
Changheng Yang , Haiyang Li , Zijun Xu , Yaqiu Lin , Yong Wang , Lian Huang , Hua Xiang , Jiangjiang Zhu
Enhancing intramuscular fat (IMF) to improve the quality of livestock product has long been a goal in animal breeding. Recent studies have revealed a strong connection between malonylation and lipid metabolism, yet the function of malonylated proteins in ruminants largely unclear. In the present study, we identified the third day of goat intramuscular preadipocyte differentiation as a critical time point for lipid accumulation, with no significant alterations in malonylation levels. We identified 212 and 216 malonylated proteins on day 0 (d0) and day 3 (d3) of differentiation, respectively, enrichment in pathways such as glycolysis/gluconeogenesis, tight junctions, and actin cytoskeleton regulation. Our findings demonstrate the consistent presence of malonylation during preadipocyte differentiation, with minor quantitative variations, and highlight key malonylated proteins closely associated with lipid metabolism, including acetyl-CoA carboxylase (ACACA), translation control tumor protein 1 (TPT1), phosphoglycerate kinase 1 (PGK1), annexin A6 (ANXA6), and annexin A2 (ANXA2). Collectively, our study uncovers critical malonylated proteins during preadipocyte differentiation, establishing a foundation for exploring their roles in intramuscular fat deposition.
Significance
Currently, efforts are being made to improve meat quality by enhancing intramuscular fat (IMF) deposition, thereby promoting the development of the livestock industry. This study addresses a critical gap in our understanding of malonylation, a key post-translational modification, in livestock. By constructing the first malonylation protein modification map in goats and revealing dynamic changes during intramuscular preadipocyte differentiation, this research offers novel insights into the regulatory roles of malonylation in fat deposition. The findings not only advance the field of livestock proteomics but also provide a theoretical foundation for improving meat quality and exploring metabolic regulation in animals.
{"title":"Global profiling of protein lysine Malonylation during goat intramuscular Preadipocyte differentiation","authors":"Changheng Yang , Haiyang Li , Zijun Xu , Yaqiu Lin , Yong Wang , Lian Huang , Hua Xiang , Jiangjiang Zhu","doi":"10.1016/j.jprot.2025.105521","DOIUrl":"10.1016/j.jprot.2025.105521","url":null,"abstract":"<div><div>Enhancing intramuscular fat (IMF) to improve the quality of livestock product has long been a goal in animal breeding. Recent studies have revealed a strong connection between malonylation and lipid metabolism, yet the function of malonylated proteins in ruminants largely unclear. In the present study, we identified the third day of goat intramuscular preadipocyte differentiation as a critical time point for lipid accumulation, with no significant alterations in malonylation levels. We identified 212 and 216 malonylated proteins on day 0 (d0) and day 3 (d3) of differentiation, respectively, enrichment in pathways such as glycolysis/gluconeogenesis, tight junctions, and actin cytoskeleton regulation. Our findings demonstrate the consistent presence of malonylation during preadipocyte differentiation, with minor quantitative variations, and highlight key malonylated proteins closely associated with lipid metabolism, including acetyl-CoA carboxylase (ACACA), translation control tumor protein 1 (TPT1), phosphoglycerate kinase 1 (PGK1), annexin A6 (ANXA6), and annexin A2 (ANXA2). Collectively, our study uncovers critical malonylated proteins during preadipocyte differentiation, establishing a foundation for exploring their roles in intramuscular fat deposition.</div></div><div><h3>Significance</h3><div>Currently, efforts are being made to improve meat quality by enhancing intramuscular fat (IMF) deposition, thereby promoting the development of the livestock industry. This study addresses a critical gap in our understanding of malonylation, a key post-translational modification, in livestock. By constructing the first malonylation protein modification map in goats and revealing dynamic changes during intramuscular preadipocyte differentiation, this research offers novel insights into the regulatory roles of malonylation in fat deposition. The findings not only advance the field of livestock proteomics but also provide a theoretical foundation for improving meat quality and exploring metabolic regulation in animals.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105521"},"PeriodicalIF":2.8,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144855619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-11DOI: 10.1016/j.jprot.2025.105520
Juan Carlos Vizuet-de-Rueda , Josaphat M. Montero-Vargas , Alberto C. López-Calleja , María Z.T. Manríquez-Ventura , Luis M. Teran
<div><div>Pollen aeroallergens cause up to 40 % of respiratory allergies and are challenging to control due to their widespread distribution in the environment. The pollen of <em>Ligustrum lucidum</em> (privet) is a significant source of inhalant allergens. However, despite its clinical relevance, the protein composition of <em>L. lucidum</em> pollen remains poorly characterized. Therefore, we employed an integrated proteomic and transcriptomic approach to explore its potential allergen composition, focusing on possible cross-reactivity with <em>Olea europea</em> (olive), a well-studied allergenic relative. Using LC-MS/MS-based proteomics and RNA-seq transcriptomics, we detected 13 of the 15 known olive-like allergens, demonstrating high cross-species conservation. Proteomic analysis identified nine homologous allergens, including Ole e 1, Ole e 2, Ole e 3, Ole e 5, Ole e 6, Ole e 9, Ole e 12, Ole e 13, and Ole e 14. Transcriptomic analysis revealed four additional putative allergens: Ole e 8, Ole e 10, Ole e 11, and Ole e 15. These proteins shared 74–95 % sequence identity with their olive counterparts and exhibited multiple isoforms. Our findings provide a set of <em>L. lucidum</em> pollen potential allergens and highlight the utility of multi-omics in allergen discovery. However, further clinical validation of these putative novel allergens is needed to assess their role in sensitization and cross-reactivity.</div></div><div><h3>Significance</h3><div>Privet (<em>Ligustrum</em>), a genus within the Oleaceae family, is biologically significant due to its role in triggering allergic respiratory diseases worldwide. As a close relative of olive (<em>Olea europaea</em>) and ash (<em>Fraxinus</em>), privet shares allergenic proteins that contribute to cross-reactivity among sensitized individuals. Climate change has been shown to extend their flowering period, increasing pollen exposure and exacerbating allergic symptoms. <em>Ligustrum</em> is widely used in urban landscaping due to its rapid growth, resistance to pollution, and adaptability to diverse soil conditions, which facilitates its global spread across North America, Europe, Asia, and South America. Notably, <em>L. lucidum</em> is a major sensitizing agent in Mexico City, where 37 % of allergic patients react to its pollen. The first identified allergen, Lig v 1, shares homology with Ole e 1 and Fra e 1. At the same time, Lig v 2 (profilin) mirrors Ole e 2, highlighting the molecular basis for cross-reactivity within the Oleaceae family. Recent proteomic studies have uncovered additional allergens, including enolase, β-1,3-glucanase, and ATP synthase subunits, further elucidating privet's allergenic potential. The absence of genomic data for <em>L. lucidum</em> has hindered research; however, advances in transcriptomic and proteomic approaches have enabled the identification of 13 of 15 known olive-like allergens in privet pollen, paving the way for improved diagnostics and targeted therapie
花粉致敏原导致高达40%的呼吸道过敏，由于其在环境中的广泛分布，很难控制。女贞的花粉是吸入性过敏原的重要来源。然而，尽管其临床相关性，露珠l.l lucidum花粉的蛋白质组成特征仍然很差。因此，我们采用了综合的蛋白质组学和转录组学方法来探索其潜在的过敏原组成，重点是与橄榄树（Olea europea）可能的交叉反应性，橄榄树是一种已经得到充分研究的过敏原亲缘关系。利用LC-MS/MS-based蛋白质组学和RNA-seq转录组学，我们检测到15个已知橄榄样过敏原中的13个，显示出高度的跨物种保守性。蛋白质组学分析鉴定出9个同源过敏原，包括Ole e 1、Ole e 2、Ole e 3、Ole e 5、Ole e 6、Ole e 9、Ole e 12、Ole e 13和Ole e 14。转录组学分析显示了另外四种可能的过敏原：Ole e8、Ole e10、Ole e11和Ole e15。这些蛋白与橄榄蛋白具有74 - 95%的序列一致性，并表现出多种同工型。我们的发现提供了一组露珠菌花粉潜在的过敏原，并强调了多组学在过敏原发现中的应用。然而，这些假定的新型过敏原需要进一步的临床验证来评估它们在致敏和交叉反应中的作用。鸢尾属（Ligustrum）是油科植物中的一个属，因其在全球范围内引发过敏性呼吸道疾病而具有重要的生物学意义。作为橄榄（Olea europaea）和白蜡树（Fraxinus）的近亲，女贞具有致敏个体之间交叉反应的致敏蛋白。气候变化延长了它们的花期，增加了花粉暴露，加剧了过敏症状。女贞草因其生长迅速、抗污染、适应多种土壤条件而被广泛应用于城市园林绿化中，这使得其在北美、欧洲、亚洲和南美等地广泛传播。值得注意的是，L. lucidum是墨西哥城的主要致敏剂，其中37%的过敏患者对其花粉有反应。第一个发现的过敏原ligv1与Ole e1和frae1具有同源性。与此同时，lig2 （profilin）与ole2相对应，突出了油科植物交叉反应的分子基础。最近的蛋白质组学研究发现了其他过敏原，包括烯醇化酶、β-1,3-葡聚糖酶和ATP合成酶亚基，进一步阐明了女贞的致敏潜力。缺乏lucidum的基因组数据阻碍了研究；然而，转录组学和蛋白质组学方法的进步已经能够在女贞花粉中鉴定出15种已知橄榄样过敏原中的13种，为改进诊断和靶向治疗铺平了道路。这强调了进一步调查女贞子过敏成分的必要性，特别是在气候变化和城市化放大其公共卫生影响的情况下，以及改进诊断和靶向治疗的潜力。
{"title":"Proteomic and transcriptomic analyses reveal new insights into allergens in Ligustrum lucidum pollen","authors":"Juan Carlos Vizuet-de-Rueda , Josaphat M. Montero-Vargas , Alberto C. López-Calleja , María Z.T. Manríquez-Ventura , Luis M. Teran","doi":"10.1016/j.jprot.2025.105520","DOIUrl":"10.1016/j.jprot.2025.105520","url":null,"abstract":"<div><div>Pollen aeroallergens cause up to 40 % of respiratory allergies and are challenging to control due to their widespread distribution in the environment. The pollen of <em>Ligustrum lucidum</em> (privet) is a significant source of inhalant allergens. However, despite its clinical relevance, the protein composition of <em>L. lucidum</em> pollen remains poorly characterized. Therefore, we employed an integrated proteomic and transcriptomic approach to explore its potential allergen composition, focusing on possible cross-reactivity with <em>Olea europea</em> (olive), a well-studied allergenic relative. Using LC-MS/MS-based proteomics and RNA-seq transcriptomics, we detected 13 of the 15 known olive-like allergens, demonstrating high cross-species conservation. Proteomic analysis identified nine homologous allergens, including Ole e 1, Ole e 2, Ole e 3, Ole e 5, Ole e 6, Ole e 9, Ole e 12, Ole e 13, and Ole e 14. Transcriptomic analysis revealed four additional putative allergens: Ole e 8, Ole e 10, Ole e 11, and Ole e 15. These proteins shared 74–95 % sequence identity with their olive counterparts and exhibited multiple isoforms. Our findings provide a set of <em>L. lucidum</em> pollen potential allergens and highlight the utility of multi-omics in allergen discovery. However, further clinical validation of these putative novel allergens is needed to assess their role in sensitization and cross-reactivity.</div></div><div><h3>Significance</h3><div>Privet (<em>Ligustrum</em>), a genus within the Oleaceae family, is biologically significant due to its role in triggering allergic respiratory diseases worldwide. As a close relative of olive (<em>Olea europaea</em>) and ash (<em>Fraxinus</em>), privet shares allergenic proteins that contribute to cross-reactivity among sensitized individuals. Climate change has been shown to extend their flowering period, increasing pollen exposure and exacerbating allergic symptoms. <em>Ligustrum</em> is widely used in urban landscaping due to its rapid growth, resistance to pollution, and adaptability to diverse soil conditions, which facilitates its global spread across North America, Europe, Asia, and South America. Notably, <em>L. lucidum</em> is a major sensitizing agent in Mexico City, where 37 % of allergic patients react to its pollen. The first identified allergen, Lig v 1, shares homology with Ole e 1 and Fra e 1. At the same time, Lig v 2 (profilin) mirrors Ole e 2, highlighting the molecular basis for cross-reactivity within the Oleaceae family. Recent proteomic studies have uncovered additional allergens, including enolase, β-1,3-glucanase, and ATP synthase subunits, further elucidating privet's allergenic potential. The absence of genomic data for <em>L. lucidum</em> has hindered research; however, advances in transcriptomic and proteomic approaches have enabled the identification of 13 of 15 known olive-like allergens in privet pollen, paving the way for improved diagnostics and targeted therapie","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105520"},"PeriodicalIF":2.8,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144842548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-05DOI: 10.1016/j.jprot.2025.105494
Jorge Noé García-Chávez , Robert Winkler
The rapid pace of shotgun proteomics data generation presents challenges for timely data analysis. In parallel, the scientific community is creating novel data interpretation tools, such as artificial intelligence, that have not yet been integrated into commercial software. Off-site data processing with free and open-source software (FOSS) enables the decentralization and scaling of informatics workflows. FOSS platforms also lower the costs of education and research. MASSyPupX is a FOSS mass spectrometry (MS) software collection that runs directly from a USB drive. Alternatively, setting up a MASSyPupX workstation or server provides a ready-to-use and reproducible MS analysis platform. Installed programming languages and libraries support the development of custom MS software and workflows. This paper demonstrates using MASSyPupX to convert and process raw shotgun proteomics data. Raw Thermo files were downloaded from ProteomeXchange and converted to the HUPO community format mzML. Data-dependent acquisition (DDA) data were evaluated with Comet, PeptideProphet, ProteinProphet, ProtyQuant, and the Trans-Proteomic Pipeline. Data-independent acquisition (DIA) shotgun proteomics data were analyzed with DIA-NN. Custom Bash, Python, and R scripts were used to post-process and visualize the results. The MASSyPupX project is hosted at https://codeberg.org/LabABI/MASSyPupX, and the current ISO can be downloaded from https://doi.org/10.5281/zenodo.14618430.
The MASSyPupX platform significantly advances shotgun proteomics data processing by offering a free and open-source software (FOSS) solution that is portable, scalable, and accessible. Operating directly from a USB drive or server, this Debian-based Linux distribution enables researchers to analyze data-dependent (DDA) and data- independent (DIA) acquisition proteomics data without installation, decentralizing workflows, reducing costs, and fostering collaboration and mass spectrometry data processing training. With pre-installed programming languages, libraries, and support for tools like Comet, PeptideProphet, DIA-NN, and ProtyQuant, MASSyPupX facilitates reproducible analyses, integrates cutting-edge computational techniques, and provides a user-friendly environment for education, research, and custom workflow development.
MASSyPupX democratizes access to advanced proteomics analysis, serving as a versatile tool for advancing biological and medical research through decentralized and cost-effective workflows.
{"title":"Off-site processing of data-dependent and data-independent acquisition shotgun proteomics data with MASSyPupX","authors":"Jorge Noé García-Chávez , Robert Winkler","doi":"10.1016/j.jprot.2025.105494","DOIUrl":"10.1016/j.jprot.2025.105494","url":null,"abstract":"<div><div>The rapid pace of shotgun proteomics data generation presents challenges for timely data analysis. In parallel, the scientific community is creating novel data interpretation tools, such as artificial intelligence, that have not yet been integrated into commercial software. Off-site data processing with free and open-source software (FOSS) enables the decentralization and scaling of informatics workflows. FOSS platforms also lower the costs of education and research. MASSyPupX is a FOSS mass spectrometry (MS) software collection that runs directly from a USB drive. Alternatively, setting up a MASSyPupX workstation or server provides a ready-to-use and reproducible MS analysis platform. Installed programming languages and libraries support the development of custom MS software and workflows. This paper demonstrates using MASSyPupX to convert and process raw shotgun proteomics data. Raw Thermo files were downloaded from ProteomeXchange and converted to the HUPO community format <span>mzML</span>. Data-dependent acquisition (DDA) data were evaluated with Comet, PeptideProphet, ProteinProphet, ProtyQuant, and the Trans-Proteomic Pipeline. Data-independent acquisition (DIA) shotgun proteomics data were analyzed with DIA-NN. Custom Bash, Python, and R scripts were used to post-process and visualize the results. The MASSyPupX project is hosted at <span><span>https://codeberg.org/LabABI/MASSyPupX</span><svg><path></path></svg></span>, and the current ISO can be downloaded from <span><span>https://doi.org/10.5281/zenodo.14618430</span><svg><path></path></svg></span>.</div><div>The MASSyPupX platform significantly advances shotgun proteomics data processing by offering a free and open-source software (FOSS) solution that is portable, scalable, and accessible. Operating directly from a USB drive or server, this Debian-based Linux distribution enables researchers to analyze data-dependent (DDA) and data- independent (DIA) acquisition proteomics data without installation, decentralizing workflows, reducing costs, and fostering collaboration and mass spectrometry data processing training. With pre-installed programming languages, libraries, and support for tools like Comet, PeptideProphet, DIA-NN, and ProtyQuant, MASSyPupX facilitates reproducible analyses, integrates cutting-edge computational techniques, and provides a user-friendly environment for education, research, and custom workflow development.</div><div>MASSyPupX democratizes access to advanced proteomics analysis, serving as a versatile tool for advancing biological and medical research through decentralized and cost-effective workflows.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105494"},"PeriodicalIF":2.8,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144775710","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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