Journal of Proteome Research最新文献_第9页

Protein–Protein Interaction Networks Derived from Classical and Machine Learning-Based Natural Language Processing Tools

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-11 DOI: 10.1021/acs.jproteome.4c0053510.1021/acs.jproteome.4c00535

David J. Degnan, Clayton W. Strauch, Moses Y. Obiri, Erik D. VonKaenel, Grace S. Kim, James D. Kershaw, David L. Novelli, Karl TL Pazdernik and Lisa M. Bramer*,

{"title":"Protein–Protein Interaction Networks Derived from Classical and Machine Learning-Based Natural Language Processing Tools","authors":"David J. Degnan, Clayton W. Strauch, Moses Y. Obiri, Erik D. VonKaenel, Grace S. Kim, James D. Kershaw, David L. Novelli, Karl TL Pazdernik and Lisa M. Bramer*, ","doi":"10.1021/acs.jproteome.4c0053510.1021/acs.jproteome.4c00535","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00535https://doi.org/10.1021/acs.jproteome.4c00535","url":null,"abstract":"The study of protein–protein interactions (PPIs) provides insight into various biological mechanisms, including the binding of antibodies to antigens, enzymes to inhibitors or promoters, and receptors to ligands. Recent studies of PPIs have led to significant biological breakthroughs. For example, the study of PPIs involved in the human:SARS-CoV-2 viral infection mechanism aided in the development of SARS-CoV-2 vaccines. Though several databases exist for the manual curation of PPI networks, text mining methods have been routinely demonstrated as useful alternatives for newly studied or understudied species, where databases are incomplete. Here, the relationship extraction performance of several open-source classical text processing, machine learning (ML)-based natural language processing (NLP), and large language model (LLM)-based NLP tools was compared. Overall, our results indicated that networks derived from classical methods tend to have high true positive rates at the expense of having overconnected networks, ML-based NLP methods have lower true positive rates but networks with the closest structures to the target network, and LLM-based NLP methods tend to exist between the two other approaches, with variable performances. The selection of a specific NLP approach should be tied to the needs of a study and text availability, as models varied in performance due to the amount of text provided.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"23 12","pages":"5395–5404 5395–5404"},"PeriodicalIF":3.8,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142850286","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 2024 Report on the Human Proteome from the HUPO Human Proteome Project

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-08 DOI: 10.1021/acs.jproteome.4c0077610.1021/acs.jproteome.4c00776

Gilbert S. Omenn*, Sandra Orchard, Lydie Lane, Cecilia Lindskog, Charles Pineau, Christopher M. Overall, Bogdan Budnik, Jonathan M. Mudge, Nicolle H. Packer, Susan T. Weintraub, Michael H. A. Roehrl, Edouard Nice, Tiannan Guo, Jennifer E. Van Eyk, Uwe Völker, Gong Zhang, Nuno Bandeira, Ruedi Aebersold, Robert L. Moritz and Eric W. Deutsch*,

{"title":"The 2024 Report on the Human Proteome from the HUPO Human Proteome Project","authors":"Gilbert S. Omenn*, Sandra Orchard, Lydie Lane, Cecilia Lindskog, Charles Pineau, Christopher M. Overall, Bogdan Budnik, Jonathan M. Mudge, Nicolle H. Packer, Susan T. Weintraub, Michael H. A. Roehrl, Edouard Nice, Tiannan Guo, Jennifer E. Van Eyk, Uwe Völker, Gong Zhang, Nuno Bandeira, Ruedi Aebersold, Robert L. Moritz and Eric W. Deutsch*, ","doi":"10.1021/acs.jproteome.4c0077610.1021/acs.jproteome.4c00776","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00776https://doi.org/10.1021/acs.jproteome.4c00776","url":null,"abstract":"The Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify at least one isoform of every protein-coding gene and (2) to make proteomics an integral part of multiomics studies of human health and disease. The past year has seen major transitions for the HPP. neXtProt was retired as the official HPP knowledge base, UniProtKB became the reference proteome knowledge base, and Ensembl-GENCODE provides the reference protein target list. A function evidence FE1–5 scoring system has been developed for functional annotation of proteins, parallel to the PE1–5 UniProtKB/neXtProt scheme for evidence of protein expression. This report includes updates from neXtProt (version 2023–09) and UniProtKB release 2024_04, with protein expression detected (PE1) for 18138 of the 19411 GENCODE protein-coding genes (93%). The number of non-PE1 proteins (“missing proteins”) is now 1273. The transition to GENCODE is a net reduction of 367 proteins (19,411 PE1–5 instead of 19,778 PE1–4 last year in neXtProt). We include reports from the Biology and Disease-driven HPP, the Human Protein Atlas, and the HPP Grand Challenge Project. We expect the new Functional Evidence FE1–5 scheme to energize the Grand Challenge Project for functional annotation of human proteins throughout the global proteomics community, including π-HuB in China.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"23 12","pages":"5296–5311 5296–5311"},"PeriodicalIF":3.8,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142844059","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

Quantification and Site-Specific Analysis of Co-occupied N- and O-Glycopeptides

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-05 DOI: 10.1021/acs.jproteome.4c0057410.1021/acs.jproteome.4c00574

Joann Chongsaritsinsuk, Valentina Rangel-Angarita, Taryn M. Lucas, Keira E. Mahoney, Olivia M. Enny, Mitchelle Katemauswa and Stacy A. Malaker*,

{"title":"Quantification and Site-Specific Analysis of Co-occupied N- and O-Glycopeptides","authors":"Joann Chongsaritsinsuk, Valentina Rangel-Angarita, Taryn M. Lucas, Keira E. Mahoney, Olivia M. Enny, Mitchelle Katemauswa and Stacy A. Malaker*, ","doi":"10.1021/acs.jproteome.4c0057410.1021/acs.jproteome.4c00574","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00574https://doi.org/10.1021/acs.jproteome.4c00574","url":null,"abstract":"Protein glycosylation is a complex post-translational modification that is generally classified as N- or O-linked. Site-specific analysis of glycopeptides is accomplished with a variety of fragmentation methods, depending on the type of glycosylation being investigated and the instrumentation available. For instance, collisional dissociation methods are frequently used for N-glycoproteomic analysis with the assumption that one N-sequon exists per tryptic peptide. Alternatively, electron-based methods are preferable for O-glycosite localization. However, the presence of simultaneously N- and O-glycosylated peptides could suggest the necessity of electron-based fragmentation methods for N-glycoproteomics, which is not commonly performed. Thus, we quantified the prevalence of N- and O-glycopeptides in mucins and other glycoproteins. A much higher frequency of co-occupancy within mucins was detected whereas only a negligible occurrence occurred within nonmucin glycoproteins. This was demonstrated from analyses of recombinant and/or purified proteins, as well as more complex samples. Where co-occupancy occurred, O-glycosites were frequently localized to the Ser/Thr within the N-sequon. Additionally, we found that O-glycans in close proximity to the occupied Asn were predominantly unelaborated core 1 structures, while those further away were more extended. Overall, we demonstrate electron-based methods are required for robust site-specific analysis of mucins, wherein co-occupancy is more prevalent. Conversely, collisional methods are generally sufficient for analyses of other types of glycoproteins.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"23 12","pages":"5449–5461 5449–5461"},"PeriodicalIF":3.8,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142843992","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

Exploring the Molecular Mechanisms underlying SADI-S Improves Glucose Metabolism in Type 2 Diabetic Rats through Liver Transcriptomics and Proteomics Analysis

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-05 DOI: 10.1021/acs.jproteome.4c0053210.1021/acs.jproteome.4c00532

Lun Wang, Zhengfu Chen, Subo Ma and Tao Jiang*,

{"title":"Exploring the Molecular Mechanisms underlying SADI-S Improves Glucose Metabolism in Type 2 Diabetic Rats through Liver Transcriptomics and Proteomics Analysis","authors":"Lun Wang, Zhengfu Chen, Subo Ma and Tao Jiang*, ","doi":"10.1021/acs.jproteome.4c0053210.1021/acs.jproteome.4c00532","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00532https://doi.org/10.1021/acs.jproteome.4c00532","url":null,"abstract":"Metabolic surgery could improve or even reverse type 2 diabetes mellitus (T2DM). Single-anastomosis duodenal-ileal bypass with sleeve gastrectomy (SADI-S) is one of the most effective metabolic surgeries for T2DM. However, the molecular mechanisms behind the SADI-S-induced T2DM improvement are not fully understood.Here,T2DM rats received SADI-S and were sacrificed after 8 weeks; the controls received sham surgery; Liver tissues were collected for transcriptomics and proteomics analysis to identify differentially expressed genes (DEGs) and proteins (DEPs). Parallel reaction monitoring (PRM) was performed to validate the accuracy of the proteomics results.SADI-S significantly improved glucose metabolism in T2DM rats.A total of 120 genes/proteins(e.g., phosphoenolpyruvate carboxykinase (Pck1) and pyruvate kinase (Pklr)) exhibited consistent expression trends at both mRNA and protein levels. Among the upregulated genes/proteins involved in glucose metabolic pathways, enrichment was observed in pathways such as the pyruvate metabolic pathway, insulin signaling pathway, glycolysis/gluconeogenesis biological processes, glucagon signaling pathway, and AMPK signaling pathway. Downregulated genes/proteins were enriched in the pyruvate metabolic pathway. The above-mentioned signaling pathways are implicated in glucose metabolism, suggesting a potential mechanism for SADI-S-mediated alleviation of T2DM. The PRM validation results indicated that all selected proteins showed consistent trends between PRM and proteomics data. This consistency suggests the reliability of the proteomics results.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"23 12","pages":"5380–5394 5380–5394"},"PeriodicalIF":3.8,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142850846","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

Pilot Study for Deciphering Post-Translational Modifications and Proteoforms of Tau Protein by Capillary Electrophoresis-Mass Spectrometry. 利用毛细管电泳-质谱法破译 Tau 蛋白翻译后修饰和蛋白形式的试点研究

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-01 Epub Date: 2024-09-27 DOI: 10.1021/acs.jproteome.4c00587

Fei Fang, Tian Xu, Hsiao-Tien Chien Hagar, Stacy Hovde, Min-Hao Kuo, Liangliang Sun

{"title":"Pilot Study for Deciphering Post-Translational Modifications and Proteoforms of Tau Protein by Capillary Electrophoresis-Mass Spectrometry.","authors":"Fei Fang, Tian Xu, Hsiao-Tien Chien Hagar, Stacy Hovde, Min-Hao Kuo, Liangliang Sun","doi":"10.1021/acs.jproteome.4c00587","DOIUrl":"10.1021/acs.jproteome.4c00587","url":null,"abstract":"Abnormal accumulation of tau protein in the brain is one pathological hallmark of Alzheimer's disease (AD). Many tau protein post-translational modifications (PTMs) are associated with the development of AD, such as phosphorylation, acetylation, and methylation. Therefore, a complete picture of the PTM landscape of tau is critical for understanding the molecular mechanisms of AD progression. Here, we offered a pilot study of combining two complementary analytical techniques, capillary zone electrophoresis (CZE)-tandem mass spectrometry (MS/MS) and reversed-phase liquid chromatography (RPLC)-MS/MS, for bottom-up proteomics of recombinant human tau-0N3R. We identified 50 phosphorylation sites of tau-0N3R in total, which is about 25% higher than that from RPLC-MS/MS alone. CZE-MS/MS provided more PTM sites (i.e., phosphorylation) and modified peptides of tau-0N3R than RPLC-MS/MS, and its predicted electrophoretic mobility helped improve the confidence of the identified modified peptides. We developed a highly efficient capillary isoelectric focusing (cIEF)-MS technique to offer a bird's-eye view of tau-0N3R proteoforms, with 11 putative tau-0N3R proteoforms carrying up to nine phosphorylation sites and lower pI values from more phosphorylated proteoforms detected. Interestingly, under native-like cIEF-MS conditions, we observed three putative tau-0N3R dimers carrying phosphate groups. The findings demonstrate that CE-MS is a valuable analytical technique for the characterization of tau PTMs, proteoforms, and even oligomerization.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"5085-5095"},"PeriodicalIF":3.8,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11536466/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142337365","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}

引用次数: 0

DiDBiT-TMT: A Novel Method to Quantify Changes in the Proteomic Landscape Induced by Neural Plasticity. DiDBiT-TMT：量化神经可塑性引起的蛋白质组景观变化的新方法。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-01 Epub Date: 2024-10-07 DOI: 10.1021/acs.jproteome.4c00180

Mariam Gamaleldin, Nam-Kyung Yu, Jolene K Diedrich, Yuanhui Ma, Anne Wienand, Daniel B McClatchy, Anders Nykjaer, Sadegh Nabavi, John R Yates

{"title":"DiDBiT-TMT: A Novel Method to Quantify Changes in the Proteomic Landscape Induced by Neural Plasticity.","authors":"Mariam Gamaleldin, Nam-Kyung Yu, Jolene K Diedrich, Yuanhui Ma, Anne Wienand, Daniel B McClatchy, Anders Nykjaer, Sadegh Nabavi, John R Yates","doi":"10.1021/acs.jproteome.4c00180","DOIUrl":"10.1021/acs.jproteome.4c00180","url":null,"abstract":"Direct detection of biotinylated proteins (DiDBiT) is a proteomic method that can enrich and detect newly synthesized proteins (NSPs) labeled with bio-orthogonal amino acids with 20-fold improved detectability compared to conventional methods. However, DiDBiT has currently been used to compare only two conditions per experiment. Here, we present DiDBiT-TMT, a method that can be used to quantify NSPs across many conditions and replicates in the same experiment by combining isobaric tandem mass tagging (TMT) with DiDBiT. We applied DiDBiT-TMT to brain slices to determine changes in the de novo proteome that occur after inducing chemical long-term potentiation (cLTP) or treatment with the neuromodulator norepinephrine. We successfully demonstrated DiDBiT-TMT's capacity to quantitatively compare up to 9 samples in parallel. We showed that there is a minimal overlap among NSPs that are differentially expressed in cLTP-treated organotypic brain slices, norepinephrine-treated organotypic brain slices, and organotypic slices undergoing combinatorial treatment with norepinephrine and cLTP. Our results point to the possible divergence of the molecular mechanisms underlying these treatments and showcase the applicability of DiDBiT-TMT for studying neurobiology.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"4878-4895"},"PeriodicalIF":3.8,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142386406","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

In-Depth Proteomic Analysis Reveals Phenotypic Diversity of Macrophages in Liver Fibrosis. 深入的蛋白质组分析揭示了肝纤维化中巨噬细胞的表型多样性

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-01 Epub Date: 2024-10-09 DOI: 10.1021/acs.jproteome.4c00681

Wenting Yang, Liling Chen, Jian Zhang, Chenyi Qiu, Wenhao Hou, Xiangye Zhang, Bin Fu, Dianyuan Zhao, Huan Wang, Di Liu, Fang Yan, Wantao Ying, Li Tang

{"title":"In-Depth Proteomic Analysis Reveals Phenotypic Diversity of Macrophages in Liver Fibrosis.","authors":"Wenting Yang, Liling Chen, Jian Zhang, Chenyi Qiu, Wenhao Hou, Xiangye Zhang, Bin Fu, Dianyuan Zhao, Huan Wang, Di Liu, Fang Yan, Wantao Ying, Li Tang","doi":"10.1021/acs.jproteome.4c00681","DOIUrl":"10.1021/acs.jproteome.4c00681","url":null,"abstract":"Macrophages make up a heterogeneous population of immune cells that exhibit diverse phenotypes and functions in health and disease. Although macrophage epigenomic and transcriptomic profiles have been reported, the proteomes of distinct macrophage populations under various pathological conditions remain largely elusive. Here, we employed a label-free proteomic approach to characterize the diversity of the hepatic macrophage pool in an experimental model of CCl4-induced liver fibrosis. We found a decrease in the proportion of liver resident embryo-derived KCs (EmKCs), and a drastic increase in the proportion of monocyte-derived KCs (MoKCs) and CLEC2-Macs. Proteomic profiling revealed that MoKCs largely resembled EmKCs, whereas CLEC2-Macs exhibited greater proteomic alternations compared with EmKCs, suggesting two distinct destinations for monocyte differentiation during liver fibrosis. Furthermore, CLEC2-Macs were characterized by increased expression of proteins associated with inflammatory response, antigen processing and presentation processes, which may be involved in the pathogenesis of liver fibrosis. Collectively, our study provides insights into the considerable heterogeneity within the hepatic macrophage pool during liver fibrosis.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"5166-5176"},"PeriodicalIF":3.8,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142386408","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

LC-Orbitrap HRMS-Based Proteomics Reveals Novel Mitochondrial Dynamics Regulatory Proteins Associated with RasV12-Induced Glioblastoma (GBM) of Drosophila. 基于 LC-Orbitrap HRMS 的蛋白质组学揭示了与果蝇 RasV12 诱导的胶质母细胞瘤 (GBM) 相关的新型线粒体动力学调控蛋白。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-01 Epub Date: 2024-10-16 DOI: 10.1021/acs.jproteome.4c00502

Pradeep Kumar, Rohit Kumar, Prabhat Kumar, Sunaina Kushwaha, Sandhya Kumari, Neha Yadav, Saripella Srikrishna

{"title":"LC-Orbitrap HRMS-Based Proteomics Reveals Novel Mitochondrial Dynamics Regulatory Proteins Associated with RasV12-Induced Glioblastoma (GBM) of Drosophila.","authors":"Pradeep Kumar, Rohit Kumar, Prabhat Kumar, Sunaina Kushwaha, Sandhya Kumari, Neha Yadav, Saripella Srikrishna","doi":"10.1021/acs.jproteome.4c00502","DOIUrl":"10.1021/acs.jproteome.4c00502","url":null,"abstract":"Glioblastoma multiforme (GBM) is the most prevalent and aggressive brain tumor found in adult humans with a poor prognosis and average survival of 14-15 months. In order to have a comprehensive understanding of proteome and identify novel therapeutic targets, this study focused mainly on the differentially abundant proteins (DAPs) of RasV12-induced GBM. RasV12 is a constitutively active Ras mutant form essential for tumor progression by continuously activating signaling pathways leading to uncontrolled tumor growth. This study used a transgenic Drosophila model with RasV12 overexpression using the repo-GAL4 driver line, specifically in glial cells, to study GBM. The high-resolution mass spectrometry (HRMS)-based proteomic analysis of the GBM larval central nervous system identified three novel DAPs specific to mitochondria. These DAPs, probable maleylacetoacetate isomerase 2 (Q9VHD2), bifunctional methylene tetrahydrofolate dehydrogenase (Q04448), and glutamine synthetase1 (P20477), identified through HRMS were further validated by qRT-PCR. The protein-protein interaction analysis revealed interactions between RasV12 and DAPs, with functional links to mitochondrial dynamics regulators such as Drp1, Marf, Parkin, and HtrA2. Notably, altered expressions of Q9VHD2, P20477, and Q04448 were observed during GBM progression, which offers new insights into the involvement of mitochondrial dynamic regulators in RasV12-induced GBM pathophysiology.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"5030-5047"},"PeriodicalIF":3.8,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453389","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

Characterization of the Angiogenic and Proteomic Features of Circulating Exosomes in a Canine Mandibular Model of Distraction Osteogenesis. 犬下颌骨牵引成骨模型中循环外泌体的血管生成和蛋白质组学特征

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-01 Epub Date: 2024-10-17 DOI: 10.1021/acs.jproteome.4c00365

Fengchun Liao, Tao Zhang, Weidong Jiang, Peiqi Zhu, Xiaoping Su, Nuo Zhou, Xuanping Huang

{"title":"Characterization of the Angiogenic and Proteomic Features of Circulating Exosomes in a Canine Mandibular Model of Distraction Osteogenesis.","authors":"Fengchun Liao, Tao Zhang, Weidong Jiang, Peiqi Zhu, Xiaoping Su, Nuo Zhou, Xuanping Huang","doi":"10.1021/acs.jproteome.4c00365","DOIUrl":"10.1021/acs.jproteome.4c00365","url":null,"abstract":"Distraction osteogenesis (DO) represents a highly effective method for addressing significant bone defects; however, it necessitates a long treatment period. Exosomes are key mediators of intercellular communication. To investigate their role in the angiogenesis and osteogenesis of DO, we established a canine mandibular DO model with a bone defect (BD) group as the control. Higher levels of angiogenesis were observed in the regenerating tissue from the DO group compared to those from the BD group, accompanied by earlier osteogenesis. Proteomic analysis was performed on circulating exosomes at different phases of the DO using a data-independent acquisition method. Data are available via ProteomeXchange with the identifier PXD050531. The results indicated specific alterations in circulating exosome proteins at different phases of DO, reflecting the regenerative activities in the corresponding tissues. Notably, fibronectin 1 (FN1), thrombospondin 1 (THBS1), and transferrin receptor (TFRC) emerged as potential candidate proteins related to the angiogenic response in DO. Further cellular experiments validated the potential of DO-associated circulating exosomes to promote angiogenesis in endothelial cells. Collectively, these data reveal previously unknown mechanisms that may underlie the efficacy of DO and suggest that exosome-derived proteins may be useful as therapeutic targets for strategies designed to improve DO-related angiogenesis and bone regeneration.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"4924-4939"},"PeriodicalIF":3.8,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453373","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

Automated High-Throughput Biological Sex Identification from Archeological Human Dental Enamel Using Targeted Proteomics. 利用靶向蛋白质组学从考古人类牙釉质中自动进行高通量生物性别鉴定

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-01 Epub Date: 2024-09-26 DOI: 10.1021/acs.jproteome.4c00557

Claire Koenig, Patricia Bortel, Ryan S Paterson, Barbara Rendl, Palesa P Madupe, Gaudry B Troché, Nuno Vibe Hermann, Marina Martínez de Pinillos, María Martinón-Torres, Sandra Mularczyk, Marie Louise Schjellerup Jørkov, Christopher Gerner, Fabian Kanz, Ana Martinez-Val, Enrico Cappellini, Jesper V Olsen

{"title":"Automated High-Throughput Biological Sex Identification from Archeological Human Dental Enamel Using Targeted Proteomics.","authors":"Claire Koenig, Patricia Bortel, Ryan S Paterson, Barbara Rendl, Palesa P Madupe, Gaudry B Troché, Nuno Vibe Hermann, Marina Martínez de Pinillos, María Martinón-Torres, Sandra Mularczyk, Marie Louise Schjellerup Jørkov, Christopher Gerner, Fabian Kanz, Ana Martinez-Val, Enrico Cappellini, Jesper V Olsen","doi":"10.1021/acs.jproteome.4c00557","DOIUrl":"10.1021/acs.jproteome.4c00557","url":null,"abstract":"Biological sex is key information for archeological and forensic studies, which can be determined by proteomics. However, the lack of a standardized approach for fast and accurate sex identification currently limits the reach of proteomics applications. Here, we introduce a streamlined mass spectrometry (MS)-based workflow for the determination of biological sex using human dental enamel. Our approach builds on a minimally invasive sampling strategy by acid etching, a rapid online liquid chromatography (LC) gradient coupled to a high-resolution parallel reaction monitoring (PRM) assay allowing for a throughput of 200 samples per day (SPD) with high quantitative performance enabling confident identification of both males and females. Additionally, we developed a streamlined data analysis pipeline and integrated it into a Shiny interface for ease of use. The method was first developed and optimized using modern teeth and then validated in an independent set of deciduous teeth of known sex. Finally, the assay was successfully applied to archeological material, enabling the analysis of over 300 individuals. We demonstrate unprecedented performance and scalability, speeding up MS analysis by 10-fold compared to conventional proteomics-based sex identification methods. This work paves the way for large-scale archeological or forensic studies enabling the investigation of entire populations rather than focusing on individual high-profile specimens. Data are available via ProteomeXchange with the identifier PXD049326.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"5107-5121"},"PeriodicalIF":3.8,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11536428/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142337362","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}

引用次数: 0