Journal of proteomics最新文献

{"title":"SequenceAssembler: A tool for protein sequence assembly from mass spectrometry data","authors":"Celso Vitor A.Q. Calomeno ,&nbsp;Hulyana Brum ,&nbsp;Rodrigo S.C. Brant ,&nbsp;Marlon D.M. Santos ,&nbsp;Luis Miguel Muñoz-Gómez ,&nbsp;Ana Gisele da Costa Neves-Ferreira ,&nbsp;Richard Hemmi Valente ,&nbsp;Michel Batista ,&nbsp;Paulo C. Carvalho","doi":"10.1016/j.jprot.2025.105542","DOIUrl":"10.1016/j.jprot.2025.105542","url":null,"abstract":"<div><div>Accurate sequencing of complete proteoforms—that is, all molecular variants generated by post-translational modification or sequence change—is essential for advancing our understanding of biological systems, guiding biopharmaceutical development, and enabling new biotechnological applications. We present SequenceAssembler (SA), a user-friendly software post-identification tool designed to assemble full-length protein sequences by integrating both peptide-spectrum matching (PSM) and <em>de novo</em> sequencing data. SA is compatible with widely used proteomics tools, including Novor Cloud, PEAKS Studio, and PatternLab for Proteomics, from which it efficiently aggregates input data. Our software offers an accessible and intuitive interface, enhancing its usability. We demonstrated SA's effectiveness by analyzing bovine serum albumin and the monoclonal antibody trastuzumab, each subjected to multiple enzymatic digestions followed by high-resolution mass spectrometry. The results were consistent with those of established tools like Stitch, with performance varying depending on threshold parameters. Notably, SA distinguishes itself through its user-friendly graphical interface, one-click installation, and streamlined workflow, making it an attractive solution for a wide range of proteomics researchers. The software is freely available for academic use at <span><span>http://patternlabforproteomics.org/sa</span><svg><path></path></svg></span>.</div></div><div><h3>Significance</h3><div>SequenceAssembler fills a critical gap in proteomics by unifying peptide-spectrum matching and <em>de novo</em> sequencing into a single assembly platform, enabling reconstruction of full-length proteins. The intuitive graphical interface lowers barriers to adoption in core laboratories, minimizing manual steps and enhancing reproducibility. By streamlining sequence assembly workflows, SequenceAssembler empowers rapid protein sequencing to broad protein research applications.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"322 ","pages":"Article 105542"},"PeriodicalIF":2.8,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145274908","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":"Two decades of the Mexican Proteomics Society: the history and evolution of proteomics and metabolomics in Mexico","authors":"José Ángel Huerta-Ocampo ,&nbsp;Robert Winkler ,&nbsp;Aldo Moreno-Ulloa ,&nbsp;Sergio Encarnación-Guevara","doi":"10.1016/j.jprot.2025.105545","DOIUrl":"10.1016/j.jprot.2025.105545","url":null,"abstract":"<div><div>The establishment of the Mexican Proteomics Society (Sociedad Mexicana de Proteómica, SMP) has provided a platform for researchers in proteomics and metabolomics to share ideas and collaborate on research. This initiative promotes scientific knowledge in México and facilitates the integration of national researchers into international projects. Founded twenty years ago, the SMP is the oldest proteomics society in Latin America. It is a non-profit organization that advocates for research in proteomics, metabolomics, and MS within the country.</div><div>This review seeks to trace the development of the field by highlighting the contributions of researchers, laboratories, institutions, and organizations such as the SMP that have played a role in establishing and advancing this science in México. However, we are an enthusiastic and diverse community that, through imagination, collaboration, and determination, will continue to advance proteomics, metabolomics, and related fields in México.</div></div><div><h3>Significance</h3><div>The Mexican Proteomics Society (Sociedad Mexicana de Proteómica, SMP) was established 20 years ago to foster proteomics in México. The organization of a biannual symposium has since evolved into a reliable academic event in proteomics, metabolomics, and mass spectrometry (MS), where international experts present their discoveries to our community, and vendors present their latest products. We encourage students and professionals to learn through hands-on workshops on protein electrophoresis, proteomics, metabolomics, and open-access computer tools for analyzing omics data. Additionally, SMP has hosted the Ibero-American Symposium on Mass Spectrometry, the Pan-American Human Proteome Organization (Pan-HUPO) meeting, and most recently, the Human Proteome Organization World Congress (HUPO-2022). This commentary does not offer a comprehensive overview of proteomics in México; instead, it follows its evolution by emphasizing the contributions of researchers, laboratories, and institutions that have played a significant role in establishing and expanding this field in México. It also endeavors to offer a comprehensive understanding of the current state of proteomics in México. The challenges, opportunities, and perspectives related to the SMP's role in advancing proteomics in the country will be discussed in a parallel commentary included in this special issue entitled “Advancing post-genomics research in México: Opportunities and strategies for the next decade”.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"322 ","pages":"Article 105545"},"PeriodicalIF":2.8,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145258237","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":"2026-01-06","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":"Expression of concern for ‘Evaluation of electron spin resonance for studies of superoxide anion production by human neutrophils interacting with Staphylococcus aureus and Staphylococcus epidermidis’, [J. Proteom. (Formerly J. Biochem. Biophys. Meth.) 70(6) (2008) 1059–1065]","authors":"Helen Lundqvist,&nbsp;Staffan Dånmark,&nbsp;Uno Johansson,&nbsp;Håkan Gustafsson,&nbsp;Karin Öllinger","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"331 ","pages":"Article 105701"},"PeriodicalIF":3.1,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148958612","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Expanding the landscape of lysine acetylation stoichiometry and clinical impact","authors":"Sergio Encarnación-Guevara ,&nbsp;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":"2025-10-30","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}

{"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":"2025-10-30","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}

{"title":"Off-site processing of data-dependent and data-independent acquisition shotgun proteomics data with MASSyPupX","authors":"Jorge Noé García-Chávez ,&nbsp;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":"2025-10-30","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}

{"title":"Mining the plasma proteome: Evaluation of enrichment methods for depth and reproducibility","authors":"K. Roger ,&nbsp;I. Metatla ,&nbsp;S. Ceccacci ,&nbsp;K. Wahbi ,&nbsp;L. Motté ,&nbsp;C. Chhuon ,&nbsp;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":"2025-10-30","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}

{"title":"Proteomic and transcriptomic analyses reveal new insights into allergens in Ligustrum lucidum pollen","authors":"Juan Carlos Vizuet-de-Rueda ,&nbsp;Josaphat M. Montero-Vargas ,&nbsp;Alberto C. López-Calleja ,&nbsp;María Z.T. Manríquez-Ventura ,&nbsp;Luis M. Teran","doi":"10.1016/j.jprot.2025.105520","DOIUrl":"10.1016/j.jprot.2025.105520","url":null,"abstract":"&lt;div&gt;&lt;div&gt;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 &lt;em&gt;Ligustrum lucidum&lt;/em&gt; (privet) is a significant source of inhalant allergens. However, despite its clinical relevance, the protein composition of &lt;em&gt;L. lucidum&lt;/em&gt; 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 &lt;em&gt;Olea europea&lt;/em&gt; (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 &lt;em&gt;L. lucidum&lt;/em&gt; 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.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Significance&lt;/h3&gt;&lt;div&gt;Privet (&lt;em&gt;Ligustrum&lt;/em&gt;), 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 (&lt;em&gt;Olea europaea&lt;/em&gt;) and ash (&lt;em&gt;Fraxinus&lt;/em&gt;), 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. &lt;em&gt;Ligustrum&lt;/em&gt; 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, &lt;em&gt;L. lucidum&lt;/em&gt; 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 &lt;em&gt;L. lucidum&lt;/em&gt; 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":"2025-10-30","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}

{"title":"Proteoformics: Current status and future perspectives","authors":"Zheng Fang ,&nbsp;Yanjun Zhang ,&nbsp;Xiaoxia Feng ,&nbsp;Na Li ,&nbsp;Liang Chen ,&nbsp;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":"2025-10-30","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}