Journal of proteomics最新文献

{"title":"Label-free proteomics revealed drought stress tolerance mechanisms in the sugar beet monosomic addition line M14","authors":"Xinyi Guo,&nbsp;Wenjing Qiu,&nbsp;Jiaming Zhu,&nbsp;Yingxiao He,&nbsp;Bing Yu","doi":"10.1016/j.jprot.2026.105608","DOIUrl":"10.1016/j.jprot.2026.105608","url":null,"abstract":"<div><div>Sugar beet M14 line is a diploid cultivated sugar beet (<em>Beta vulgaris</em> L.) that carries a monosomic addition of chromosome 9 from the wild white-flowered beet (<em>B. corolliflora</em> Zoss.), developed through distant hybridization. It exhibits enhanced salt and drought tolerance compared to the diploid cultivated beets. In this study, the M14 line exhibited superior water retention capacity under dehydration conditions compared with five major diploid cultivated varieties grown in northern China. Through integrated analysis of phenotype, photosynthetic parameters, physiological and biochemical indicators, and the expression of key drought-responsive genes, 3 days and 5 days of 20% PEG-6000 treatment were identified as two critical time points for the drought stress response of the M14 line. Through label-free quantitative proteomics, 903 and 526 DAPs were identified at 3 and 5 days, respectively. PPI network analysis further revealed key protein interaction modules in the M14 line under drought stress. Furthermore, qRT-PCR analysis of 12 key DAP-encoding genes revealed that their transcript levels generally corresponded to the protein expression trends. This study helped to produce molecular network maps of drought tolerance in the M14 line, uncovering the mechanisms underlying its drought tolerance.</div></div><div><h3>Significance</h3><div>The drought tolerance of the sugar beet M14 line and ive major diploid sugar beet varieties cultivated in northern China was evaluated, revealing that the M14 line showed the strongest drought resistance. This study uncovered the dynamic regulatory network responsible for drought tolerance in the M14 line at the proteomic level, highlighting the main response pathways and key functional proteins at 3 and 5 days after stress exposure. These results not only deepen our understanding of the molecular mechanisms behind the sugar beet drought tolerance but also identify important candidate proteins and key regulatory modules for molecular breeding drought-tolerant varieties.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"327 ","pages":"Article 105608"},"PeriodicalIF":2.8,"publicationDate":"2026-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146046663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The untapped potential of metaproteomics in microbial systems ecology","authors":"Jingxuan Hu ,&nbsp;Yuan Zheng ,&nbsp;Leyuan Li","doi":"10.1016/j.jprot.2026.105604","DOIUrl":"10.1016/j.jprot.2026.105604","url":null,"abstract":"<div><div>As a direct readout of protein presence and abundance in complex microbiomes, metaproteomics has become central to uncovering functionality across diverse microbial ecosystems. Recent collaborative efforts within the research community have driven methodological advances, computational innovations, and diverse applications. With the advancing maturity of metaproteomics techniques, we highlight the Proteome-level Microbial Systems Ecology (ProMiSE) framework as a complementary framework for the next phase, providing a conceptual lens to interpret metaproteomics data with a bottom-up perspective that extends beyond functional profile and taxonomic composition to the quantitative assessment of system properties, processes, and dynamics. Building on existing metrics such as β-diversity and functional redundancy, future work can further develop quantitative approaches for resilience, exergy, and functional energy landscapes, thereby enabling a deeper systems-level understanding of microbiome dynamics and opening new avenues for the precise functional regulation of microbiomes.</div></div><div><h3>Significance</h3><div>This Perspective reviews the development of metaproteomics—particularly in the Journal of Proteomics—and envisions it as a transformative tool in microbial systems ecology, introducing the ProMiSE framework to integrate protein-resolved data with ecological theory and properties such as redundancy, resilience, and functional energy landscapes for the future of precise microbiome modulation.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"326 ","pages":"Article 105604"},"PeriodicalIF":2.8,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146041021","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":"Rapid high-throughput antibody analysis using microwave-assisted digestion","authors":"Thais Mingatos de Toledo ,&nbsp;Hellen Paula Valerio ,&nbsp;Antônio Moreira Marques Neto ,&nbsp;Simon Ngao Mule ,&nbsp;Priscila Robertina dos Santos Donado ,&nbsp;Claudia Blanes Angeli Pascale ,&nbsp;Giuseppe Palmisano","doi":"10.1016/j.jprot.2026.105601","DOIUrl":"10.1016/j.jprot.2026.105601","url":null,"abstract":"<div><div>Monoclonal antibodies are a class of biotherapeutic proteins that have been developed over the past decade, leading to improved standards of care for the treatment of multiple diseases. Multi-attribute methods have emerged as powerful tools for critical quality attributes (CQAs). They leverage high-resolution accurate mass spectrometry and automated computational pipelines to identify pre-established modifications using DDA. In this study, we describe the development of a mass spectrometry–based workflow capable of processing up to 96 samples simultaneously while monitoring a broad panel of PTMs. We evaluated microwave-assisted digestion under different buffers and pHs, assessing sequence coverage, missed cleavages, and the occurrence of chemical artifacts. Analyses were performed using both DDA and DIA. Raw data were processed in dependent-peptide search(DDA) and PTM-probing search(DIA), enabling PTM discovery without prior knowledge. Our results demonstrate that microwave-assisted digestion, combined with control of temperature and pH, provides a fast and reliable alternative for efficiently digesting biotherapeutic proteins. It achieves high sequence coverage while minimizing artificial PTM formation. We also show that DIA combined with MW digestion improved peptide identification, highlighting its potential for comprehensive characterization of antibodies. Among the tested buffers, sodium acetate under MW conditions was the most effective in reducing deamidation and oxidation levels.</div></div><div><h3>Significance</h3><div>This study presents a detailed and optimized protocol for microwave-assisted (MW) protein digestion, enabling simultaneous reduction and alkylation for antibody samples. The method is rapid and minimizes chemical artifacts typically introduced during sample preparation. By combining MW-assisted digestion with both data-dependent (DDA) and data-independent acquisition (DIA), we performed a comprehensive and unbiased multi-attribute analysis (MAM). Notably, the use of DIA alongside MW digestion allowed for higher reproducibility and more complete peptide and post-translational modification (PTM) detection compared to DDA alone. Compared to conventional overnight digestion, MW-assisted digestion significantly reduced deamidation levels, with evident influences of buffer composition and pH on PTM identification. Although the levels of protein oxidation persisted, indicating that further optimization is necessary, this approach substantially decreased other artifacts, particularly deamidation, highlighting its potential as a fast, reliable, and highly informative strategy for antibody characterization.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"326 ","pages":"Article 105601"},"PeriodicalIF":2.8,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146030053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The in vitro effect of omentin-1 on the global proteome of granulosa cells from normal weight Large White and fat Meishan pigs","authors":"Karolina Pich ,&nbsp;Natalia Respekta-Długosz ,&nbsp;Edyta Rytelewska ,&nbsp;Bianka Świderska ,&nbsp;Agata Malinowska ,&nbsp;Nina Smolińska ,&nbsp;Joëlle Dupont ,&nbsp;Agnieszka Rak","doi":"10.1016/j.jprot.2026.105606","DOIUrl":"10.1016/j.jprot.2026.105606","url":null,"abstract":"<div><div>Ovarian granulosa cells (Gc) play a vital role in follicle maturation and successful ovulation. Omentin-1 (ITLN1) is an adipokine involved in energy metabolism and insulin resistance; its expression has been demonstrated in the ovary and varies depending on the degree of pig fatness. However, its effect on the global proteome of Gc has not been previously investigated. It was hypothesized that ITLN1 affects the abundance of proteins involved in key processes occurring in Gc in pigs. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of Gc identified 208 significantly differentially abundant proteins (DAPs) in the Large White pigs, with 99 proteins upregulated and 109 downregulated. In fatter Meishan pigs, 42 statistically significant DAPs were identified, including 25 upregulated and 17 downregulated proteins. The identified DAPs were associated with the estrogen signaling pathway, cell cycle and DNA replication, protein synthesis, transport and maturation, cytoskeleton dynamics, cell signaling, and hormonal regulation. Notably, the number and identity of DAPs differed markedly between the two breeds, suggesting that ITLN1-mediated effects are modulated by fatness and breed-specific metabolic status. To further illustrate the observed differences, selected proteins were also analyzed using Western blotting and ELISA, which were consistent with the LC-MS/MS findings. The results indicate that ITLN1 has a modulatory influence on the porcine Gc proteome, which is dependent on fat content. This highlights the important role of ITLN1 in regulating ovarian functions.</div></div><div><h3>Significance</h3><div>This study provides a comprehensive proteomic analysis of porcine granulosa cells (Gc) after treatment with omentin-1 (ITLN1) in pigs with different fat content (Large White &lt; Meishan). The identified differentially abundant proteins (DAPs) are intricately linked to critical biological pathways, including estrogen signaling, cell cycle regulation, DNA replication, protein synthesis and transport, cytoskeleton organization, and hormonal regulation. These findings enhance our understanding of the molecular mechanisms underpinning ovarian follicle development and breed-related reproductive traits in pigs. The insights gained could inform future strategies to improve fertility and reproductive efficiency in swine production, as well as provide a valuable resource for comparative studies on ovarian biology across species.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"326 ","pages":"Article 105606"},"PeriodicalIF":2.8,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146030022","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":"Time-resolved proteomic and phosphoproteomic profiling of Angiotensin-(1–7) signaling in A549 cells","authors":"Marcella N. Melo-Braga ,&nbsp;Gabriela C. Magalhães ,&nbsp;Filipe A. Silva ,&nbsp;Frank Kjeldsen ,&nbsp;Martin R. Larsen ,&nbsp;Robson A.S. Santos ,&nbsp;Thiago Verano-Braga","doi":"10.1016/j.jprot.2026.105607","DOIUrl":"10.1016/j.jprot.2026.105607","url":null,"abstract":"<div><div>Angiotensin-(1–7) [Ang-(1–7)] is a heptapeptide of the renin-angiotensin system (RAS) with antitumoral effects reported in various tumoral cell lines, including the human lung adenocarcinoma A549 lineage. While previous studies have shown that Ang-(1–7) modulates MAPK and PI3K-AKT signaling, the precise molecular mechanisms involved remain incompletely understood. To investigate the signaling events of Ang-(1–7) in lung cancer-derived cells, we employed an integrated proteomic and phosphoproteomic approach in A549 cells. We analyzed early (minutes) and late (hours) molecular responses to Ang-(1–7) treatment. The treatment resulted in time-dependent modulation of multiple signaling pathways, including significant alterations in the MAPK, PI3K-AKT, and mTOR pathways at both the protein and phosphorylation levels. Notably, widespread early dephosphorylation events were observed, similar to the effects seen with other RAS peptides with antitumoral effects. Additionally, Ang-(1–7) promoted a long-lasting nuclear accumulation (up to 24 h) of the transcription factor FOXO1 indicating its activation. FOXO1 is known to regulate genes involved in apoptosis, cell cycle arrest, and oxidative stress, suggesting a role in mediating the peptide's antitumoral effects. The study provides new insights into the molecular basis of Ang-(1–7)’s antitumoral activity in A549 cells and reinforce its therapeutic potential in lung cancer. Raw data are available via ProteomeXchange with identifier <span><span>PXD066687</span><svg><path></path></svg></span>.</div></div><div><h3>Significance</h3><div>This study provides the first comprehensive, time-resolved proteomic and phosphoproteomic analysis of Angiotensin-(1–7) signaling in the lung cancer cell line A549. By capturing both early and late molecular events in A549 cells, we reveal that Ang-(1–7) modulates critical pathways involved in tumor progression, including MAPK, PI3K-AKT, and mTOR signaling. Importantly, we demonstrate the nuclear accumulation of FOXO1, a key transcription factor associated with tumor suppression, as part of the Ang-(1–7) response in A549 cells.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"326 ","pages":"Article 105607"},"PeriodicalIF":2.8,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146025908","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sputum proteomics and phosphoproteomics for improving chronic obstructive pulmonary disease knowledge","authors":"Fei Long ,&nbsp;Xiaoyin Zeng ,&nbsp;Fengyan Wang ,&nbsp;Xufei Wang ,&nbsp;Weijuan Shi ,&nbsp;Yanting Lan ,&nbsp;Jiahao Cheng ,&nbsp;Chen Zhu ,&nbsp;Yiqi Yang ,&nbsp;Jing Xiao ,&nbsp;Longbo Hu ,&nbsp;Long Tan ,&nbsp;Yuqiong Yang ,&nbsp;Rongchang Chen ,&nbsp;Zhenyu Liang ,&nbsp;Tao Peng ,&nbsp;Shaohua Lu","doi":"10.1016/j.jprot.2026.105605","DOIUrl":"10.1016/j.jprot.2026.105605","url":null,"abstract":"<div><div>Analysis of proteins and other molecular components in induced sputum provides critical insights for the diagnosis, pathological assessment, and therapeutic monitoring of respiratory diseases. In this study, we collected three distinct types of induced sputum samples from patients with chronic obstructive pulmonary disease (COPD) and subjected them to proteomic and phosphoproteomic analysis using three different enzymatic digestion methods. We found that raw sputum samples yielded a higher number of uniquely identified proteins and phosphoproteins (1313 proteins and 1603 phosphorylation sites, corresponding to 782 phosphoproteins) and provided a more comprehensive characterization of COPD pathology. Furthermore, compared to in-gel digestion and in-solution digestion, the filter-aided sample preparation method increased protein identification by approximately 30% and yielded the highest number of unique protein identifications. Our study is the first to demonstrate that raw induced sputum can serve as a viable alternative source for liquid biopsy in respiratory diseases. We have also established the first methodological framework and dataset for proteomic and phosphoproteomic analysis of raw induced sputum, generating a preliminary map of the COPD sputum proteome and phosphoproteome. This novel proteomic and phosphoproteomic approach has untangled biologically relevant pathways in respiratory physiology, highlighting potential avenues for future research.</div></div><div><h3>Significance</h3><div>In this study, we aimed to investigate the feasibility of establishing and evaluating proteomic research methods using sputum samples from patients with chronic obstructive pulmonary disease (COPD). The ultimate goal was to develop analytical approaches suitable for sputum proteomics and phosphoproteomics and to preliminarily map the sputum proteome and phosphoproteome in COPD. It was found that raw sputum samples more comprehensively reflect the disease characteristics of COPD and are therefore more suitable for proteomic and phosphoproteomic studies of COPD. Among three mainstream enzymatic digestion methods, the Filter-Aided Sample Preparation (FASP) method demonstrated superior identification rates and was deemed most suitable for processing raw sputum samples. Furthermore, this study reports for the first time a draft map of the proteome and phosphoproteome of COPD sputum. This research provides valuable insights into sputum proteomic analysis and offers a useful resource for the study of respiratory diseases.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"326 ","pages":"Article 105605"},"PeriodicalIF":2.8,"publicationDate":"2026-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146018988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Barley protein: From agricultural staple to sustainable protein solution","authors":"Fatma Boukid","doi":"10.1016/j.jprot.2026.105603","DOIUrl":"10.1016/j.jprot.2026.105603","url":null,"abstract":"<div><div>Barley protein is a multifunctional, sustainable plant-based ingredient with potential in food, nutraceutical, and industrial applications. This review synthesizes current knowledge on barley protein, emphasizing how proteomics and processing methods influence its composition, digestibility, and functional properties. Proteomic analyses reveal the distribution of major protein fractions, albumins, globulins, hordeins, and glutelins and their bioactive peptides, which exhibit antioxidant, antihypertensive, antidiabetic, and appetite-regulating activities. Protein concentrates and isolates offer improved digestibility and functional quality, though lysine remains limiting. Advanced techniques, including enzymatic hydrolysis, ultrasound-assisted extraction, and post-processing modifications, are evaluated for their impact on protein structure and functionality. Barley protein's potential applications in novel foods, micro- and nano-encapsulation, and targeted bioactive delivery are highlighted. By integrating proteomics insights with nutritional and technological perspectives, this work underscores the role of barley proteins in sustainable food systems.</div></div><div><h3>Significance</h3><div>This review synthesizes current knowledge on barley protein composition, emphasizing insights gained from proteomic analyses. By characterizing protein fractions, bioactive peptides, and allergenic determinants, proteomics enables a deeper understanding of barley's functional, nutritional, and health-related properties. The work highlights how extraction and processing influence protein quality and bioactivity, informing strategies for the development of novel plant-based foods. These insights provide a foundation for future research and industrial applications, advancing barley as a sustainable and functional protein source in human nutrition.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"326 ","pages":"Article 105603"},"PeriodicalIF":2.8,"publicationDate":"2026-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146003744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Two-dimensional electrophoresis-based proteomics reveals soybean seed hypocotyl proteoforms","authors":"Jian-Zhong Tan ,&nbsp;Hiroyuki Kagawa ,&nbsp;Keiko Kizawa ,&nbsp;Hisashi Hirano","doi":"10.1016/j.jprot.2026.105600","DOIUrl":"10.1016/j.jprot.2026.105600","url":null,"abstract":"<div><div>Shotgun proteomics is widely used for comprehensive profiling of protein expression. However, this approach has inherent limitations in resolving “proteoforms”. Two-dimensional gel electrophoresis (2DE) has the potential to separate and visualize proteoforms effectively. To evaluate its utility, proteins extracted from soybean seed hypocotyls were analyzed by 2DE/LC-MS/MS. As a result, a total of 693 proteins were separated by 2DE, of which 302 were identified by LC-MS/MS. The dynamic range of protein abundance was approximately 10² to 10⁴. This analysis revealed that the hypocotyls contain numerous proteoforms of proteins essential for seed physiology, including late embryogenesis abundant protein, glycinin, β-conglycinin, trypsin inhibitor, sucrose-binding protein, and glyceraldehyde-3-phosphate dehydrogenase. Furthermore, 2DE revealed that the expression of proteoforms of the major seed storage proteins, glycinin A2 and A3 subunits, and β-conglycinin β subunit in hypocotyls differed from that in cotyledons, suggesting distinct functional roles beyond nutrient storage during germination. Overall, the results demonstrate that 2DE is a valuable complementary technique to shotgun proteomics, providing proteoform-specific information that cannot be resolved by shotgun analysis alone.</div></div><div><h3>Significance</h3><div>Shotgun proteomics is widely used for comprehensive profiling of protein expression. However, this approach has inherent limitations when analyzing “proteoforms”. In the present study, we analyzed soybean seed hypocotyls using two-dimensional gel electrophoresis (2DE)-LC-MS/MS, demonstrating that 2DE is useful for effective proteoform analysis. 2DE provides proteoform-specific information that cannot be obtained from shotgun proteomics alone, making it a useful complementary method.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"326 ","pages":"Article 105600"},"PeriodicalIF":2.8,"publicationDate":"2026-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146003749","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":"Early regulatory networks driving somatic embryogenesis in Saccharum spp. L. revealed by time-resolved proteomics","authors":"Roberta Pena da Paschoa ,&nbsp;Lucas Rodrigues Xavier ,&nbsp;Caio Cezar Guedes Corrêa ,&nbsp;Karina da Silva Vieira ,&nbsp;Daniel Dastan Rezabala Pacheco ,&nbsp;Lucas do Espirito Santo Gomes ,&nbsp;Carlos Eduardo Assis da Silva ,&nbsp;Laura Eliza de Oliveira Alves ,&nbsp;Vitor Batista Pinto ,&nbsp;Claudete Santa-Catarina ,&nbsp;Vanildo Silveira","doi":"10.1016/j.jprot.2026.105602","DOIUrl":"10.1016/j.jprot.2026.105602","url":null,"abstract":"<div><div>The induction of somatic embryogenesis is controlled by various genes and proteins involved in hormonal pathways and stress responses, which act as key regulators of in vitro cellular reprogramming. In this study, we employed a temporal proteomic approach to investigate the underlying molecular mechanisms governing sugarcane (<em>Saccharum</em> spp.) embryogenic callus formation in response to 2,4-dichlorophenoxyacetic acid (2,4-D) during induction. Proteomic profiling revealed 996 differentially accumulated proteins (DAPs) across at least one pairwise comparison among time points (0, 7, 14 and 21 days) during callus induction. These DAPs were classified into different clusters on the basis of their accumulation profile. Proteins involved in embryogenesis, histone epigenetic regulation, hormone responses and protein post-translational modification accumulate during callus induction. The predicted interactions between the TOPLESS protein and auxin response proteins (SKP1, CUL1 and CAND1) are associated with increased accumulation of the histone deacetylase HDT2 protein, a regulator of chromatin condensation, during embryogenic callus initiation. Moreover, proteomic analysis revealed a temporal reduction in methylation cycle enzymes during callus induction, whereas global DNA methylation showed only a slight, non-significant increase, suggesting that additional regulatory layers are present. The identified protein dynamics provide valuable targets for refining somatic embryogenesis protocols and advancing their biotechnological applications in sugarcane.</div></div><div><h3>Significance</h3><div>Genetic engineering and plant cloning usually involve the induction of embryogenic competence using 2,4-dichlorophenoxyacetic acid (2,4-D). This study presents protein-protein interaction (PPI) networks regulated during the induction of sugarcane callus using 2,4-D, in addition to the morphological aspects of the explant during the process. Proteomic analysis of time series shows the regulation of protein kinases and transcriptional regulators TOPLESS, CUL1, SKP1, CAND1, and ARGONAUTE kinases, revealing mechanisms of activation of induction and multiplication of embryogenic callus. Furthermore, the possible interaction between GH3.8 and SnRK/SAPK kinases suggests a link between hormonal responses.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"326 ","pages":"Article 105602"},"PeriodicalIF":2.8,"publicationDate":"2026-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145986725","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":"Emphasizing the importance of interactions and networks in proteomics","authors":"Jean Armengaud","doi":"10.1016/j.jprot.2026.105599","DOIUrl":"10.1016/j.jprot.2026.105599","url":null,"abstract":"","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"325 ","pages":"Article 105599"},"PeriodicalIF":2.8,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145985097","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}