Molecular & Cellular Proteomics最新文献

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Single-Cell Proteomic Characterization of Drug-Resistant Prostate Cancer Cells Reveals Molecular Signatures Associated with Morphological Changes.
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2025-03-14 DOI: 10.1016/j.mcpro.2025.100949
Jongmin Woo, Michael Loycano, Md Amanullah, Jiang Qian, Sarah R Amend, Kenneth J Pienta, Hui Zhang
{"title":"Single-Cell Proteomic Characterization of Drug-Resistant Prostate Cancer Cells Reveals Molecular Signatures Associated with Morphological Changes.","authors":"Jongmin Woo, Michael Loycano, Md Amanullah, Jiang Qian, Sarah R Amend, Kenneth J Pienta, Hui Zhang","doi":"10.1016/j.mcpro.2025.100949","DOIUrl":"10.1016/j.mcpro.2025.100949","url":null,"abstract":"<p><p>This study delves into the proteomic intricacies of drug-resistant cells (DRCs) within prostate cancer, which are known for their pivotal roles in therapeutic resistance, relapse, and metastasis. Utilizing single-cell proteomics (SCP) with an optimized high-throughput Data Independent Acquisition (DIA) approach with the throughput of 60 sample per day, we characterized the proteomic landscape of DRCs in comparison to parental PC3 cells. This DIA method allowed for robust and reproducible protein quantification at the single-cell level, enabling the identification and quantification of over 1,300 proteins per cell on average. Distinct proteomic sub-clusters within the DRC population were identified, closely linked to variations in cell size. The study uncovered novel protein signatures, including the regulation of proteins critical for cell adhesion and metabolic processes, as well as the upregulation of surface proteins and transcription factors pivotal for cancer progression. Furthermore, by conducting single-cell RNA-seq (scRNA-seq) analysis, we identified six upregulated and ten downregulated genes consistently altered in drug-treated cells across both SCP and scRNA-seq platforms. These findings underscore the heterogeneity of DRCs and their unique molecular signatures, providing valuable insights into their biological behavior and potential therapeutic targets.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100949"},"PeriodicalIF":6.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143639750","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}
引用次数: 0
Metabolic Reprogramming into a Glycolysis Phenotype Induced by Extracellular Vesicles Derived from Prostate Cancer Cells.
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2025-03-13 DOI: 10.1016/j.mcpro.2025.100944
Yoon-Jin Lee, Chul Won Seo, Shinwon Chae, Chang Yeol Lee, Sang Soo Kim, Yoon-Hee Shin, Hyun-Mee Park, Yong Song Gho, Seongho Ryu, Sang-Han Lee, Dongsic Choi
{"title":"Metabolic Reprogramming into a Glycolysis Phenotype Induced by Extracellular Vesicles Derived from Prostate Cancer Cells.","authors":"Yoon-Jin Lee, Chul Won Seo, Shinwon Chae, Chang Yeol Lee, Sang Soo Kim, Yoon-Hee Shin, Hyun-Mee Park, Yong Song Gho, Seongho Ryu, Sang-Han Lee, Dongsic Choi","doi":"10.1016/j.mcpro.2025.100944","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.100944","url":null,"abstract":"<p><p>Most cancer cells adopt a less efficient metabolic process of aerobic glycolysis with high level of glucose uptake followed by lactic acid production, known as the Warburg effect. This phenotypic transition enables cancer cells to achieve increased cellular survival and proliferation in a harsh low-oxygen tumor microenvironment. Also, the resulting acidic microenvironment causes inactivation of the immune system such as T-cell impairment that favors escape by immune surveillance. While lots of studies have revealed that tumor-derived EVs can deliver parental materials to adjacent cells and contribute to oncogenic reprogramming, their functionality in energy metabolism is not well addressed. In this study, we established prostate cancer cells PC3-AcT resistant to cellular death in an acidic culture medium driven by lactic acid. Quantitative proteomics between EVs derived from PC-3 and PC-3AcT cells identified 935 confident EV proteins. According to cellular adaptation to lactic acidosis, we revealed 159 regulated EV proteins related to energy metabolism, cellular shape, and extracellular matrix. These EVs contained a high abundance of glycolytic enzymes. In particular, PC-3AcT EVs were enriched with apolipoproteins including apolipoprotein B100 (APOB). APOB on PC-3AcT EVs could facilitate their endocytic uptake depending on low density lipoprotein receptor of recipient PC-3 cells, encouraging increases of cellular proliferation and survival in acidic culture media via increased activity and expression of hexokinases and phosphofructokinase. The activation of recipient PC-3 cells can increase glucose consumption and ATP generation, representing an acquired metabolic reprogramming into the Warburg phenotype. Our study first revealed that EVs derived from prostate cancer cells could contribute to energy metabolic reprogramming and that the acquired metabolic phenotypic transition of recipient cells could favor cellular survival in tumor microenvironment.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100944"},"PeriodicalIF":6.1,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143634291","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}
引用次数: 0
Ca2+-triggered (de)ubiquitination events in synapses.
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2025-03-13 DOI: 10.1016/j.mcpro.2025.100946
Sofia Ainatzi, Svenja V Kaufmann, Ivan Silbern, Svilen V Georgiev, Sonja Lorenz, Silvio O Rizzoli, Henning Urlaub
{"title":"Ca<sup>2+</sup>-triggered (de)ubiquitination events in synapses.","authors":"Sofia Ainatzi, Svenja V Kaufmann, Ivan Silbern, Svilen V Georgiev, Sonja Lorenz, Silvio O Rizzoli, Henning Urlaub","doi":"10.1016/j.mcpro.2025.100946","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.100946","url":null,"abstract":"<p><p>Neuronal communication relies on neurotransmitter release from synaptic vesicles (SVs), whose dynamics are controlled by Ca<sup>2+</sup>-dependent pathways, as many thoroughly studied phosphorylation cascades. However, little is known about other post-translational modifications, as ubiquitination. To address this, we analysed resting and stimulated synaptosomes (isolated synapses) by quantitative mass spectrometry. We identified more than 5,000 ubiquitination sites on ∼2,000 proteins, the majority of which participate in SV recycling processes. Several proteins showed significant changes in ubiquitination in response to Ca<sup>2+</sup> influx, with the most pronounced changes in CaMKIIα and the clathrin adaptor protein AP180. To validate this finding, we generated a CaMKIIα mutant lacking the ubiquitination target site (K291) and analysed it both in neurons and non-neuronal cells. K291 ubiquitination, close to an important site for CaMKIIα autophosphorylation (T286), influences the synaptic function of this kinase. We suggest that ubiquitination in response to synaptic activity is an important regulator of synaptic function.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100946"},"PeriodicalIF":6.1,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143634288","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}
引用次数: 0
Comprehensive proteomics metadata and integrative web portals facilitate sharing and integration of LINCS multiomics data.
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2025-03-13 DOI: 10.1016/j.mcpro.2025.100947
Dušica Vidović, Behrouz Shamsaei, Stephan C Schürer, Phillip Kogan, Szymon Chojnacki, Michal Kouril, Mario Medvedovic, Wen Niu, Evren U Azeloglu, Marc R Birtwistle, Yibang Chen, Tong Chen, Jens Hansen, Bin Hu, Ravi Iyengar, Gomathi Jayaraman, Hong Li, Tong Liu, Eric A Sobie, Yuguang Xiong, Matthew J Berberich, Gary Bradshaw, Mirra Chung, Robert A Everley, Ben Gaudio, Marc Hafner, Marian Kalocsay, Caitlin E Mills, Maulik K Nariya, Peter K Sorger, Kartik Subramanian, Chiara Victor, Maria Banuelos, Victoria Dardov, Ronald Holewinski, Danica-Mae Manalo, Berhan Mandefro, Andrea D Matlock, Loren Ornelas, Dhruv Sareen, Clive N Svendsen, Vineet Vaibhav, Jennifer E Van Eyk, Vidya Venkatraman, Steve Finkbiener, Ernest Fraenkel, Jeffrey Rothstein, Leslie Thompson, Jacob Asiedu, Steven A Carr, Karen E Christianson, Desiree Davison, Deborah O Dele-Oni, Katherine C DeRuff, Shawn B Egri, Alvaro Sebastian Vaca Jacome, Jacob D Jaffe, Daniel Lam, Lev Litichevskiy, Xiaodong Lu, James Mullahoo, Adam Officer, Malvina Papanastasiou, Ryan Peckner, Caidin Toder, Joel Blanchard, Michael Bula, Tak Ko, Li-Huei Tsai, Jennie Z Young, Vagisha Sharma, Ajay Pillai, Jarek Meller, Michael J MacCoss
{"title":"Comprehensive proteomics metadata and integrative web portals facilitate sharing and integration of LINCS multiomics data.","authors":"Dušica Vidović, Behrouz Shamsaei, Stephan C Schürer, Phillip Kogan, Szymon Chojnacki, Michal Kouril, Mario Medvedovic, Wen Niu, Evren U Azeloglu, Marc R Birtwistle, Yibang Chen, Tong Chen, Jens Hansen, Bin Hu, Ravi Iyengar, Gomathi Jayaraman, Hong Li, Tong Liu, Eric A Sobie, Yuguang Xiong, Matthew J Berberich, Gary Bradshaw, Mirra Chung, Robert A Everley, Ben Gaudio, Marc Hafner, Marian Kalocsay, Caitlin E Mills, Maulik K Nariya, Peter K Sorger, Kartik Subramanian, Chiara Victor, Maria Banuelos, Victoria Dardov, Ronald Holewinski, Danica-Mae Manalo, Berhan Mandefro, Andrea D Matlock, Loren Ornelas, Dhruv Sareen, Clive N Svendsen, Vineet Vaibhav, Jennifer E Van Eyk, Vidya Venkatraman, Steve Finkbiener, Ernest Fraenkel, Jeffrey Rothstein, Leslie Thompson, Jacob Asiedu, Steven A Carr, Karen E Christianson, Desiree Davison, Deborah O Dele-Oni, Katherine C DeRuff, Shawn B Egri, Alvaro Sebastian Vaca Jacome, Jacob D Jaffe, Daniel Lam, Lev Litichevskiy, Xiaodong Lu, James Mullahoo, Adam Officer, Malvina Papanastasiou, Ryan Peckner, Caidin Toder, Joel Blanchard, Michael Bula, Tak Ko, Li-Huei Tsai, Jennie Z Young, Vagisha Sharma, Ajay Pillai, Jarek Meller, Michael J MacCoss","doi":"10.1016/j.mcpro.2025.100947","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.100947","url":null,"abstract":"<p><p>The Library of Integrated Network-based Cellular Signatures (LINCS), an NIH Common Fund program, has cataloged and analyzed cellular function and molecular activity profiles in response to >80,000 perturbing agents that are potentially disruptive to cells. Because of the importance of proteins and their modifications to the response of specific cellular perturbations, four of the six LINCS centers have included significant proteomics efforts in the characterization of the resulting phenotype. This manuscript aims to describe this effort and the data harmonization and integration of the LINCS proteomics data discussed in recent LINCS papers.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100947"},"PeriodicalIF":6.1,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143634289","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}
引用次数: 0
Benchmarking of quantitative proteomics workflows for Limited proteolysis mass spectrometry.
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2025-03-13 DOI: 10.1016/j.mcpro.2025.100945
Tomas Koudelka, Claudio Bassot, Ilaria Piazza
{"title":"Benchmarking of quantitative proteomics workflows for Limited proteolysis mass spectrometry.","authors":"Tomas Koudelka, Claudio Bassot, Ilaria Piazza","doi":"10.1016/j.mcpro.2025.100945","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.100945","url":null,"abstract":"<p><p>Limited proteolysis coupled with mass spectrometry (LiP-MS) has emerged as a powerful technique for detecting protein structural changes and drug-protein interactions on a proteome-wide scale. However, there is no consensus on the best quantitative proteomics workflow for analyzing LiP-MS data. In this study, we comprehensively benchmarked two major quantification approaches-data-independent acquisition (DIA) and tandem mass tag (TMT) isobaric labeling-in combination with LiP-MS, using a drug-target deconvolution assay as a model system. Our results show that while TMT labeling enabled the quantification of more peptides and proteins with lower coefficients of variation (CVs), DIA-MS exhibited greater accuracy in identifying true drug targets and stronger dose-response correlation in protein targets peptides. Additionally, we evaluated the performance of freely available (FragPipe) versus commercial (Spectronaut) software tools for DIA-MS analysis, revealing that the choice between precision (FragPipe) and sensitivity (Spectronaut) largely depends on the specific experimental context. Our findings underscore the importance of selecting the appropriate LiP-MS quantification strategy based on the study objectives. This work provides valuable guidelines for researchers in structural proteomics and drug discovery, and highlights how advancements in mass spectrometry instrumentation, such as the Astral mass spectrometer, may further improve sensitivity and protein sequence coverage, potentially reducing the need for TMT labeling.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100945"},"PeriodicalIF":6.1,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143634287","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}
引用次数: 0
Addressing NHS chemistry: Efficient quenching of excess TMT reagent and reversing TMT-over labelling in proteomic samples by methylamine. 解决 NHS 化学问题:高效淬灭过量的 TMT 试剂,用甲胺逆转蛋白质组样品中的 TMT 过度标记。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2025-03-13 DOI: 10.1016/j.mcpro.2025.100948
Yana Demyanenko, Xintong Sui, Andrew M Giltrap, Benjamin G Davis, Bernhard Küster, Shabaz Mohammed
{"title":"Addressing NHS chemistry: Efficient quenching of excess TMT reagent and reversing TMT-over labelling in proteomic samples by methylamine.","authors":"Yana Demyanenko, Xintong Sui, Andrew M Giltrap, Benjamin G Davis, Bernhard Küster, Shabaz Mohammed","doi":"10.1016/j.mcpro.2025.100948","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.100948","url":null,"abstract":"<p><p>N-Hydroxysuccinimide (NHS) ester chemistry is used extensively across proteomics sample preparation. One of its increasingly prevalent applications is in isobaric reagent-based quantitation such as iTRAQ (isobaric tags for relative and absolute quantitation) and TMT (tandem mass tag) approaches. In these methods, labelling on the primary amines of lysine residues and N-termini of tryptic peptides via amide formation (N-derivatives) from corresponding NHS ester reagents is the intended reactive outcome. However, the role of NHS esters as activated carboxyls can also drive the formation of serine-, tyrosine-, and threonine- derived esters (O-derivatives). These O-derivative peptides are typically classed as over-labelled and are disregarded for quantitation, leading to loss of information and hence potential sensitivity. Their presence also unnecessarily increases sample complexity, which reduces the overall identification rates. One common approach for removing these unwanted labelling events has involved treatment with hydroxylamine. We show here that this approach is not efficient and can still leave substantial levels of unwanted over-labelled peptides. Through systematic study of nucleophilic aminolysis reagents and reaction conditions, we have now developed a robust method to efficiently remove over-labelled peptides. The new method reduces the proportion of over-labelled peptides in the sample to less than 1% without affecting the labelling rate or introducing other modifications, leading to superior identification rates and quantitation precision.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100948"},"PeriodicalIF":6.1,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143634285","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}
引用次数: 0
The Hunt lab weighs in on mass spectrometry-based analysis of protein post-translational modifications. 亨特实验室重磅推出基于质谱的蛋白质翻译后修饰分析。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2025-03-11 DOI: 10.1016/j.mcpro.2025.100943
Joshua J Coon, Jarrod A Marto, John E P Syka, Forest M White
{"title":"The Hunt lab weighs in on mass spectrometry-based analysis of protein post-translational modifications.","authors":"Joshua J Coon, Jarrod A Marto, John E P Syka, Forest M White","doi":"10.1016/j.mcpro.2025.100943","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.100943","url":null,"abstract":"<p><p>Protein post-translational modifications have traditionally been challenging to identify due to their dynamic regulation and typically low stoichiometry. Methods for phosphopeptide enrichment from complex proteomes developed in the Hunt lab in the late 1990's and early 2000's launched the field of phosphoproteomics, the large-scale analysis of protein phosphorylation sites. To improve phosphopeptide tandem mass spectra and address the further challenge of identifying other labile PTMs such as glycosylation or tyrosine sulfation, the Hunt lab invented and disseminated electron transfer dissociation (ETD), a novel method for peptide and protein fragmentation. Here we provide a brief historical accounting of these discoveries and their ensuing applications.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100943"},"PeriodicalIF":6.1,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625469","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}
引用次数: 0
Proteomics analysis of porcine endometrial cell-derived extracellular vesicles involved in embryo attachment. 参与胚胎附着的猪子宫内膜细胞衍生细胞外囊泡的蛋白质组学分析。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2025-03-11 DOI: 10.1016/j.mcpro.2025.100942
Seonggyu Bang, Ahmad Yar Qamar, Sang-Yeop Lee, Ayeong Han, Heejae Kang, Bereket Molla Tanga, Sung Ho Yun, Hye Sun Park, Seung Il Kim, Won Gi Yoo, Islam M Saadeldin, Sanghoon Lee, Jongki Cho
{"title":"Proteomics analysis of porcine endometrial cell-derived extracellular vesicles involved in embryo attachment.","authors":"Seonggyu Bang, Ahmad Yar Qamar, Sang-Yeop Lee, Ayeong Han, Heejae Kang, Bereket Molla Tanga, Sung Ho Yun, Hye Sun Park, Seung Il Kim, Won Gi Yoo, Islam M Saadeldin, Sanghoon Lee, Jongki Cho","doi":"10.1016/j.mcpro.2025.100942","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.100942","url":null,"abstract":"<p><p>Maternal-embryo interactions play a critical role in early mammalian development, with extracellular vesicles (EVs) playing a key role in intercellular communication. Recent studies have focused on the mechanisms by which maternal-derived factors, such as RNA, proteins, and metabolites influence gap junctions, EVs, and direct cell-to-cell interactions, contributing to embryonic development. In this study, using a proteomics approach, we investigated the impact of EVs secreted from porcine endometrial cells (pEECs) and their protein cargoes on embryonic development. We characterized EVs isolated from pEECs (pEEC-EVs) during the diestrus stage using a nanoparticle tracking analysis and cryo-transmission electron microscopy. Furthermore, the effects of pEEC-EVs with or without hormone treatment on the in vitro attachment of hatched blastocysts were evaluated. The attachment rate of porcine embryos was significantly higher for pEEC-EVs in the hormone treatment group than the control group (23.0 ± 1.7% vs. 36.9 ± 1.9% for control and pEEC-EVs, respectively). Furthermore, hormone treatment altered the expression of proteins involved in cellular organization, protein transport, and immunity. Proteomic analysis revealed distinct biological processes between groups: control EVs supported cytoskeletal organization and adhesion, while hormone-treated EVs were enriched in protein transport, immune regulation, and stress response pathways. Key signaling pathways, including VEGFA-VEGFR2, focal adhesion, and TGF-β, were modulated, influencing implantation and embryogenesis. EVs play a crucial role in maternal-embryo interactions, optimizing implantation conditions and supporting embryo-derived stem cell establishment. These findings enhance our understanding of EV-mediated communication and suggest potential applications for improving reproductive health and assisted reproductive technologies.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100942"},"PeriodicalIF":6.1,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625465","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}
引用次数: 0
Analysis of limited proteolysis-coupled mass spectrometry data.
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2025-03-07 DOI: 10.1016/j.mcpro.2025.100934
L Nagel, J Grossbach, V Cappelletti, C Dörig, P Picotti, A Beyer
{"title":"Analysis of limited proteolysis-coupled mass spectrometry data.","authors":"L Nagel, J Grossbach, V Cappelletti, C Dörig, P Picotti, A Beyer","doi":"10.1016/j.mcpro.2025.100934","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.100934","url":null,"abstract":"<p><p>Limited proteolysis combined with mass spectrometry (LiP-MS) facilitates probing structural changes on a proteome-wide scale. This method leverages differences in the proteinase K accessibility of native protein structures to concurrently assess structural alterations for thousands of proteins in situ. Distinguishing different contributions to the LiP-MS signal, such as changes in protein abundance or chemical modifications, from structural protein alterations remains challenging. Here, we present the first comprehensive computational pipeline to infer structural alterations for LiP-MS data using a two-step approach. (1) We remove unwanted variations from the LiP signal that are not caused by protein structural effects and (2) infer the effects of variables of interest on the remaining signal. Using LiP-MS data from three species we demonstrate that this approach outperforms previously employed approaches. Our framework provides a uniquely powerful approach for deconvolving LiP-MS signals and separating protein structural changes from changes in protein abundance, post-translational modifications and alternative splicing. Our approach may also be applied to analyze other types of peptide-centric structural proteomics data, such as FPOP or molecular painting data.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100934"},"PeriodicalIF":6.1,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586240","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}
引用次数: 0
Upregulation of protein O-GlcNAcylation levels promotes zebrafish fin regeneration.
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2025-03-03 DOI: 10.1016/j.mcpro.2025.100936
Liyuan Jia, Hanxue Zheng, Juantao Feng, Yi Ding, Xiaotian Sun, Yuan Yu, Xue Hao, Junxiang Wang, Xinyu Zhang, Yuanfeng Tian, Fulin Chen, Jihong Cui
{"title":"Upregulation of protein O-GlcNAcylation levels promotes zebrafish fin regeneration.","authors":"Liyuan Jia, Hanxue Zheng, Juantao Feng, Yi Ding, Xiaotian Sun, Yuan Yu, Xue Hao, Junxiang Wang, Xinyu Zhang, Yuanfeng Tian, Fulin Chen, Jihong Cui","doi":"10.1016/j.mcpro.2025.100936","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.100936","url":null,"abstract":"<p><p>As one of the most important post-translational modifications, glycosylation participates in various cellular activities in organisms and is closely associated with many pathogeneses. It has been reported that glycosylation affects liver, spinal cord, and heart tissue regeneration. The zebrafish fin has become a valuable model due to its high regenerative capacity. The molecular mechanism of regeneration has been a hot research topic in the field for a long time. However, studies on the influence of glycosylation during limb regeneration in zebrafish are relatively scarce. We discovered that O-GlcNAc expression, identified by WGA, was elevated during the regeneration of the injured fin in zebrafish using lectin microarray. This phenomenon is due to the upregulation of the expression of OGT enzymes and elevated O-GlcNAcylation levels. To investigate the effects on the fin regeneration when O-GlcNAcylation changes, we used OSMI-1 or Alloxan unilateral microinjection to decrease O-GlcNAcylation and observed that it prevented the fin regeneration. Conversely, the O-GlcNAcylation was impressed by a unilateral microinjection of Thiamet-G or Glucose into the fin, leading to a stimulation of the fin regeneration. To further understand the role of O-GlcNAcylation in fin regeneration, LC-MS/MS was performed to identify O-GlcNAc-glycoproteins. The results demonstrated that the O-GlcNAc glycoproteins, such as THBS4 and HSPG, were involved in the regulation of zebrafish fin regeneration process and were closely associated with certain biological processes, such as stem cell differentiation, ECM-receptor interaction pathway, tissue remodeling, etc. We demonstrated that O-GlcNAc glycoproteins are crucial for zebrafish fin regeneration, during which OGT promotes the process by upregulating the O-GlcNAcylation levels in the zebrafish fin.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100936"},"PeriodicalIF":6.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143567612","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}
引用次数: 0
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