Journal of Proteome Research最新文献

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SpecPeptidOMS Directly and Rapidly Aligns Mass Spectra on Whole Proteomes and Identifies Peptides That Are Not Necessarily Tryptic: Implications for Peptidomics.
IF 3.8 2区 生物学
Journal of Proteome Research Pub Date : 2025-03-27 DOI: 10.1021/acs.jproteome.4c00870
Émile Benoist, Géraldine Jean, Hélène Rogniaux, Guillaume Fertin, Dominique Tessier
{"title":"<i>SpecPeptidOMS</i> Directly and Rapidly Aligns Mass Spectra on Whole Proteomes and Identifies Peptides That Are Not Necessarily Tryptic: Implications for Peptidomics.","authors":"Émile Benoist, Géraldine Jean, Hélène Rogniaux, Guillaume Fertin, Dominique Tessier","doi":"10.1021/acs.jproteome.4c00870","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00870","url":null,"abstract":"<p><p><i>SpecPeptidOMS</i> directly aligns peptide fragmentation spectra to whole and undigested protein sequences. The algorithm was specifically and initially designed for peptidomics, where the aim is to identify peptides that do not result from the hydrolysis of a known protein and therefore, whose termini cannot be predicted. Thus, <i>SpecPeptidOMS</i> can perform alignments starting and ending anywhere in the protein sequence. The underlying computational method of <i>SpecPeptidOMS</i>, which is based on a dynamic programming approach, was drastically optimized. As a result, <i>SpecPeptidOMS</i> can process around 12,000 spectra per hour on an ordinary laptop, with alignment performed against the entire human proteome. The performance of <i>SpecPeptidOMS</i> was first evaluated on a publicly available data set of (nontryptic) synthetic mass spectra. Accuracy was estimated by considering the results obtained by <i>MaxQuant</i> on the same data set as the \"ground truth\". A second series of tests on a larger, well-known proteomics data set (HEK293) highlighted <i>SpecPeptidOMS</i>' additional ability to search for open modifications, a feature of interest in peptidomics but also more broadly in conventional proteomics. <i>SpecPeptidOMS</i> is open-source, cross-platform (written in Java), and freely available.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143717667","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
HYTANE-Identified Latrophilin-3 Cleavage by Meprin β Leads to Loss of the Interaction Domains.
IF 3.8 2区 生物学
Journal of Proteome Research Pub Date : 2025-03-26 DOI: 10.1021/acs.jproteome.4c00912
Fred Armbrust, Kira Bickenbach, Tomas Koudelka, Corentin Joos, Maximilian Keller, Andreas Tholey, Claus U Pietrzik, Christoph Becker-Pauly
{"title":"HYTANE-Identified Latrophilin-3 Cleavage by Meprin β Leads to Loss of the Interaction Domains.","authors":"Fred Armbrust, Kira Bickenbach, Tomas Koudelka, Corentin Joos, Maximilian Keller, Andreas Tholey, Claus U Pietrzik, Christoph Becker-Pauly","doi":"10.1021/acs.jproteome.4c00912","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00912","url":null,"abstract":"<p><p>The metalloprotease meprin β is upregulated in neurons and astrocytes of Alzheimer's disease patients' brains. While the role of meprin β as the β-secretase of amyloid precursor protein (APP) has been characterized, its broader substrate profile within the brain remains largely unexplored. Hence, to identify additional substrates, we conducted N-terminomics of brain lysates from mice overexpressing meprin β in astrocytes employing the Hydrophobic Tagging-Assisted N-terminal Enrichment (HYTANE) strategy. We observed 3906 (82.2%) N-terminal peptides and identified seven new substrates that match meprin β in terms of localization and cleavage specificity. Of note, the meprin β overexpressing mice show mild cognitive impairments caused by amyloidogenic APP processing alongside hyperactivity and altered exploratory behavior seemingly independent of APP cleavage. Hence, latrophilin-3 was of particular interest, as latrophilin-3 defects are associated with hyperactivity in mice and human. In brain lysates from mice overexpressing meprin β in astrocytes as well as in cellulo, we validated the cleavage of latrophilin-3, resulting in the release of two N-terminal domains. These domains promote interactions with neuronal proteins such as fibronectin leucine-rich repeat transmembrane proteins, promoting adequate synapse formation. Thus, meprin β might affect synaptic integrity by cleaving interaction domains of latrophilin-3, potentially exacerbating the observed hyperactivity phenotype.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143707765","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
Antioxidant Impact of Soft Knotwood Extracts on Human Keratinocytes Shown by NMR Metabolomic Analysis.
IF 3.8 2区 生物学
Journal of Proteome Research Pub Date : 2025-03-26 DOI: 10.1021/acs.jproteome.4c00836
Océane Quin, Marylène Bertrand, Pauline Gerardin, Philippe Gerardin, Christine Gerardin-Charbonnier, Céline Landon, Chantal Pichon
{"title":"Antioxidant Impact of Soft Knotwood Extracts on Human Keratinocytes Shown by NMR Metabolomic Analysis.","authors":"Océane Quin, Marylène Bertrand, Pauline Gerardin, Philippe Gerardin, Christine Gerardin-Charbonnier, Céline Landon, Chantal Pichon","doi":"10.1021/acs.jproteome.4c00836","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00836","url":null,"abstract":"<p><p>The <i>Pin</i>o<i>phyta</i> family has long been used to protect the skin from oxidation, thanks to the action of molecules such as stilbenes, flavonoids, and lignans, which are particularly concentrated in knotwood. These molecules are of interest from a cosmetic perspective. The present study focuses on four species from larch (<i>Larix decidua</i> Mill.), silver fir (<i>Abies alba</i> Mill.), Norway spruce (<i>Picea abies</i> (L.) H.Karst), and Douglas fir (<i>Pseudotsuga menziesii</i> (Mirb.) Franco) knotwood, recovered from byproducts of the wood industry. The molecules are extracted from knotwood and used <i>in vitro</i> on human keratinocytes (HaCaT). Studies quantifying reactive oxygen species (ROS) have demonstrated its ability to eliminate hydroxyl radicals and superoxides. Metabolomic analyses using proton nuclear magnetic resonance (<sup>1</sup>H NMR) and multivariate statistics (PLS-DA) demonstrated that keratinocytes modulate metabolite expression after treatment with knot extracts. Indeed, our findings indicate an increase in metabolites such as glutathione, glycine, glutamate, sarcosine, taurine, and proline, which are known to reduce intracellular oxidative stress and validate the effect on ROS levels. They also indicate that knotwood extracts may affect membrane balance, collagen formation, and oxidative stress levels. This study highlights the value of metabolomic analysis in the cosmetic industry for a detailed understanding of the mechanisms implemented in a whole cell.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143707756","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
Elucidating the Molecular Mechanisms of Hederagenin-Regulated Mitophagy in Cervical Cancer SiHa Cells through an Integrative Approach Combining Proteomics and Advanced Network Association Algorithm.
IF 3.8 2区 生物学
Journal of Proteome Research Pub Date : 2025-03-26 DOI: 10.1021/acs.jproteome.5c00022
Hao Sun, Dan Wang, Yongquan Zheng, Yiqing Ye
{"title":"Elucidating the Molecular Mechanisms of Hederagenin-Regulated Mitophagy in Cervical Cancer SiHa Cells through an Integrative Approach Combining Proteomics and Advanced Network Association Algorithm.","authors":"Hao Sun, Dan Wang, Yongquan Zheng, Yiqing Ye","doi":"10.1021/acs.jproteome.5c00022","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00022","url":null,"abstract":"<p><p>Hederagenin (Hed), a natural triterpenoid, exhibits antitumor potential in cervical cancer. The present study was designed to explore Hed's regulatory mechanisms on mitophagy in SiHa cervical cancer cells, employing tandem mass tag (TMT) proteomics and an advanced network association algorithm (NAA). Our findings revealed that Hed decreased SiHa cell viability, induced apoptosis, and altered mitochondrial membrane potential. Notably, Hed inhibited mitophagic flux under both normoxic and hypoxic conditions. Through TMT proteomics analysis and innovative NAA, we identified a close association between the HIF-1 signaling pathway and mitophagy. Network analysis further suggested that Hed acts on a target network centered on SRC, STAT3, AKT1, and HIF1A. Western blot analysis confirmed the expression and phosphorylation status of these targets in response to Hed. This study elucidates the molecular mechanisms underlying Hed's regulation of mitophagy in SiHa cells, offering novel insights and potential therapeutic targets for cervical cancer treatment.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143707762","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
High-Coverage Metabolomics Reveals Gut Microbiota-Related Metabolic Traits of Type-2 Diabetes in Serum.
IF 3.8 2区 生物学
Journal of Proteome Research Pub Date : 2025-03-25 DOI: 10.1021/acs.jproteome.4c00507
Wangshu Qin, Sijia Zheng, Lina Zhou, Xinyu Liu, Tiantian Chen, Xiaolin Wang, Qi Li, Ying Zhao, Difei Wang, Guowang Xu
{"title":"High-Coverage Metabolomics Reveals Gut Microbiota-Related Metabolic Traits of Type-2 Diabetes in Serum.","authors":"Wangshu Qin, Sijia Zheng, Lina Zhou, Xinyu Liu, Tiantian Chen, Xiaolin Wang, Qi Li, Ying Zhao, Difei Wang, Guowang Xu","doi":"10.1021/acs.jproteome.4c00507","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00507","url":null,"abstract":"<p><p>Metabolic perturbations of the gut microbiome have been implicated in the pathogenesis of multiple human diseases, including type-2 diabetes (T2D). However, our understanding of the global metabolic alterations of the gut microbiota in T2D and their functional roles remains limited. To address this, we conducted a high-coverage metabolomics profiling analysis of serum samples from 1282 Chinese individuals with and without T2D. Among the 220 detected microbiota-associated compounds detected, 111 were significantly altered, forming a highly interactive regulatory network associated with T2D development. Pathway enrichment and correlation analyses revealed aberrant metabolic pathways, primarily including the activation of pyrimidine metabolism, unsaturated fatty acid biosynthesis, and diverse amino acid metabolisms such as Tryptophan metabolism, Lysine metabolism, and Branched-chain amino acid biosynthesis. A microbiota-dependent biomarker panel, comprising pipecolinic acid, methoxysalicylic acid, <i>N</i>-acetylhistamine, and 3-hydroxybutyrylcarnitine, was defined and validated with satisfactory sensitivity (>78%) for large-scale, population-based T2D screening. The functional role of a gut microbial product, <i>N</i>-acetylhistamine, was further elucidated in T2D progression through its inhibition of adenosine monophosphate-activated protein kinase phosphorylation. Overall, this study expands our understanding of gut microbiota-driven metabolic dysregulation in T2D and suggests that monitoring these metabolic changes could facilitate the diagnosis and treatment of T2D.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699107","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
Enhanced Detection of Escherichia coli Lipids and Proteins Using Graphene-Polyglycerol Amine via Mass Spectrometry.
IF 3.8 2区 生物学
Journal of Proteome Research Pub Date : 2025-03-25 DOI: 10.1021/acs.jproteome.4c01116
Seyed Mohammad Jafar Seyed Golestan, Andrew Smith, Farnaz Fatahian, Atousa Aliahmadi, Greta Bindi, Hassan Baghernia, Vanna Denti, Ahmad Shahir Sadr, Davoud Kazemi, Alireza Ghassempour
{"title":"Enhanced Detection of <i>Escherichia coli</i> Lipids and Proteins Using Graphene-Polyglycerol Amine via Mass Spectrometry.","authors":"Seyed Mohammad Jafar Seyed Golestan, Andrew Smith, Farnaz Fatahian, Atousa Aliahmadi, Greta Bindi, Hassan Baghernia, Vanna Denti, Ahmad Shahir Sadr, Davoud Kazemi, Alireza Ghassempour","doi":"10.1021/acs.jproteome.4c01116","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01116","url":null,"abstract":"<p><p>The accurate and rapid identification of bacterial pathogens poses a significant challenge in clinical diagnostics, environmental monitoring, and microbial research. Lipidomics and proteomics serve as powerful methodologies for bacterial characterization; however, the complexity of biological matrices and the low abundance of bacterial lipids often limit effective detection. This study introduces graphene-polyglycerol amine (G-PGA) as a novel nanomaterial that enhances the selective trapping and detection of <i>Escherichia coli</i> <i>(E. coli)</i> using desorption electrospray ionization mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The antimicrobial properties of G-PGA reveal a minimum inhibitory concentration (MIC) of 250 μg/μL and a minimum bactericidal concentration (MBC) of 500 μg/μL. Optimal sonication conditions (10 min) maximize G-PGA's surface activity, facilitating effective bacterial trapping while maintaining cellular integrity, as confirmed by scanning electron microscopy and atomic force microscopy. Molecular docking simulations show a strong affinity between G-PGA and the β-barrel assembly machinery (BAM) proteins of <i>E. coli</i>, suggesting potential disruption of critical bacterial processes. Preconcentration with G-PGA significantly improves detection sensitivity and signal-to-noise ratio in mass spectrometry analyses, highlighting its potential as a transformative tool for rapid, sensitive, and highly specific bacterial identification in lipidomics and proteomics.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699106","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
Effect of Capacitation on Proteomic Profile and Mitochondrial Parameters of Spermatozoa in Bulls.
IF 3.8 2区 生物学
Journal of Proteome Research Pub Date : 2025-03-25 DOI: 10.1021/acs.jproteome.4c00910
María Castelló-Ruiz, Sabrina Gacem, Manuel M Sánchez Del Pino, Carlos O Hidalgo, Carolina Tamargo, Manuel Álvarez-Rodríguez, Jesús L Yániz, Miguel A Silvestre
{"title":"Effect of Capacitation on Proteomic Profile and Mitochondrial Parameters of Spermatozoa in Bulls.","authors":"María Castelló-Ruiz, Sabrina Gacem, Manuel M Sánchez Del Pino, Carlos O Hidalgo, Carolina Tamargo, Manuel Álvarez-Rodríguez, Jesús L Yániz, Miguel A Silvestre","doi":"10.1021/acs.jproteome.4c00910","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00910","url":null,"abstract":"<p><p>Sperm capacitation is a critical process for fertilization. This work aims to analyze the effect <i>in vitro</i> capacitation had on the proteome and mitochondrial parameters of bull spermatozoa. Viability, mitochondrial membrane potential (MMP), and reactive oxygen species (mROS) were assessed by flow cytometry in noncapacitated (NC) and <i>in vitro</i> capacitated (IVC) sperm. Proteome was evaluated using SWATH-MS. <i>In vitro</i> capacitation significantly induced a decrease in sperm viability, a high MMP, and an increase in mROS production. Within the group of living spermatozoa, the capacitation significantly induced a decrease in healthy mitochondrial spermatozoa, as well as an increase in mROS production, without affecting the MMP intensity. A total number of 72 differentially abundant proteins were found of which 63 were over-represented in the NC sperm group and 9 in the IVC sperm group. It was observed that many proteins associated with the sperm membrane and acrosome were lost during the capacitation process. For the IVC sperm, the functional enrichment was found in proteins related to the oxidative phosphorylation process. Our results indicate that the capacitation process induces a significant loss of seminal plasma-derived membrane proteins and a significant increase in proteins related with the oxidative phosphorylation (OXPHOS) pathway. Data are available via ProteomeXchange with identifiers PXD056424 and PXD042286.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143707759","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
1H NMR Urinary Metabolomics Profiling of Newborns with Congenital Human Cytomegalovirus Infection: Insights into Metabolic Alterations.
IF 3.8 2区 生物学
Journal of Proteome Research Pub Date : 2025-03-25 DOI: 10.1021/acs.jproteome.5c00017
Alessia Spadavecchia, Marta Zoccarato, Gaia Tedone, Matteo Biolatti, Valentina Dell'Oste, Agata Leone, Alessandro Cossard, Mattia Sozzi, Ilia Bresesti, Enrico Bertino, Roberto Gobetto, Alessandra Coscia, Angelo Gallo
{"title":"<sup>1</sup>H NMR Urinary Metabolomics Profiling of Newborns with Congenital Human Cytomegalovirus Infection: Insights into Metabolic Alterations.","authors":"Alessia Spadavecchia, Marta Zoccarato, Gaia Tedone, Matteo Biolatti, Valentina Dell'Oste, Agata Leone, Alessandro Cossard, Mattia Sozzi, Ilia Bresesti, Enrico Bertino, Roberto Gobetto, Alessandra Coscia, Angelo Gallo","doi":"10.1021/acs.jproteome.5c00017","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00017","url":null,"abstract":"<p><p>Human cytomegalovirus (HCMV) is the leading cause of congenital infections resulting in severe morbidity and mortality among newborns worldwide. Currently, the most significant prognostic factor of congenital cytomegalovirus (cCMV) infection is the time of maternal infection, with a more severe clinical phenotype if the mother's first outbreak occurs during the first trimester of pregnancy. Nonetheless, the pathogenesis of cCMV infection has still to be completely characterized. In particular, little is known about the metabolic response triggered by HCMV in congenitally infected newborns. As such, urinary metabolic profiling by <sup>1</sup>H nuclear magnetic resonance (NMR) might represent a promising tool to be exploited in the context of cCMV. This study aims to investigate the impact of HCMV infection on the urine metabolome in a population of congenitally infected newborns and uninfected controls by <sup>1</sup>H NMR spectroscopy combined with multivariate statistical analysis. The <sup>1</sup>H NMR spectra of patients (<i>n</i> = 35) and controls (<i>n</i> = 15) allowed the identification of an overall amount of 55 metabolites. Principal Component Analysis (PCA) and clustering correctly assigned 49 out of 50 newborns into the infected and control groups. Partial Least-Squares-Discriminant Analysis (PLS-DA) revealed that newborns with cCMV resulted in having increased betaine, citrate, 3-hydroxybutyrate, 4-hydroxybutyrate, acetoacetate, formate, glycolate, lactate, succinate, and threonine levels in the urine. On the other hand, healthy controls showed increased 4-aminohippurate, creatine, creatinine, fumarate, mannitol, taurine, and dimethylamine levels. These results showed a clear difference in metabolomic fingerprint between newborns with cCMV infection and healthy controls. Thus, metabolomics can be considered a new, promising diagnostic and prognostic tool in the clinical management of cCMV patients.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699105","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
Identification of Serum Metabolites to Improve Diagnostic Efficacy in Pulmonary Embolism.
IF 3.8 2区 生物学
Journal of Proteome Research Pub Date : 2025-03-24 DOI: 10.1021/acs.jproteome.4c00863
Shili Chen, Xue Xu, Xiaoming Li, Qiangqiang Qin, Guiyin Zhu, Haiyang Yu, Kun Du, Xueting Wang, Wenjing Ye, Wen Gu
{"title":"Identification of Serum Metabolites to Improve Diagnostic Efficacy in Pulmonary Embolism.","authors":"Shili Chen, Xue Xu, Xiaoming Li, Qiangqiang Qin, Guiyin Zhu, Haiyang Yu, Kun Du, Xueting Wang, Wenjing Ye, Wen Gu","doi":"10.1021/acs.jproteome.4c00863","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00863","url":null,"abstract":"<p><p>Pulmonary embolism (PE) is a life-threatening disease. Our aim was to search for potential biomarkers by using modern high-throughput metabolomics methods to improve diagnostic efficacy. The discovery cohort included 60 participants, including 30 PE patients and 30 healthy individuals. The validation cohort included 40 participants, including 20 PE patients and 20 healthy individuals. Gas chromatography-mass spectrometry (GC-MS) was combined with multivariate data analysis to determine serum metabolic profiles in patients with PE and healthy controls. The distribution of metabolic profiles in the two cohorts was assessed by unsupervised principal component analysis (PCA) and supervised partial least-squares discriminant analysis (PLS-DA). Sixteen metabolites were initially selected from the ranked variable of predictive importance (VIP) scores and applied to the correlation analysis of PE-related clinical indicators. Four metabolites that were correlated with D-dimer levels were selected, including l-tryptophan, <i>N</i>-alpha-acetyl-l-lysine, dopamine, and <i>N</i><sup>2</sup>-acetylornithine. Finally, the AUC values were calculated to be 0.958 (95% CI: 0.9072-1) for the combined biomarker panel, including the 4 specific metabolites in the discovery cohort, and 0.963 (95% CI: 0.9122-1) in the validation cohort. The results suggest that these four specific metabolites can be used as diagnostic biomarkers to improve diagnostic efficacy in pulmonary embolism.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699108","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
Large-Scale Quantitative Cross-Linking and Mass Spectrometry Provide New Insight into Protein Conformational Plasticity within Organelles, Cells, and Tissues.
IF 3.8 2区 生物学
Journal of Proteome Research Pub Date : 2025-03-24 DOI: 10.1021/acs.jproteome.4c01030
Andrew Keller, Anna Bakhtina, James E Bruce
{"title":"Large-Scale Quantitative Cross-Linking and Mass Spectrometry Provide New Insight into Protein Conformational Plasticity within Organelles, Cells, and Tissues.","authors":"Andrew Keller, Anna Bakhtina, James E Bruce","doi":"10.1021/acs.jproteome.4c01030","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01030","url":null,"abstract":"<p><p>Many proteins can exist in multiple conformational states <i>in vivo</i> to achieve distinct functional roles. These states include alternative conformations, variable post-translational modifications (PTMs), and associations with interacting protein, nucleotide, and ligand partners. Quantitative chemical cross-linking of live cells, organelles, or tissues together with mass spectrometry provides the relative abundance of cross-link levels formed in two or more compared samples, which depends both on the relative levels of existent protein conformational states in the compared samples and on the relative likelihood of the cross-link originating from each. Because cross-link conformational state preferences can vary widely, one expects intraprotein cross-link levels from proteins with high conformational plasticity to display divergent quantitation among samples with differing conformational ensembles. Here we use the large volume of quantitative cross-linking data available on the public XLinkDB database to cluster intraprotein cross-links according to their quantitation in many diverse compared samples to provide the first widescale glimpse of cross-links grouped according to the protein conformational state(s) from which they predominantly originate. We further demonstrate how cluster cross-links can be aligned with any protein structure to assess the likelihood that they were derived from it.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690444","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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