Molecular & Cellular Proteomics最新文献

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Proteome Birthdating Reveals Age-Selectivity of Protein Ubiquitination. 蛋白质组出生日期揭示了蛋白质泛素化的年龄选择性。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-07-01 Epub Date: 2024-05-24 DOI: 10.1016/j.mcpro.2024.100791
Michael E Meadow, Sarah Broas, Margaret Hoare, Fatemeh Alimohammadi, Kevin A Welle, Kyle Swovick, Jennifer R Hryhorenko, John C Martinez, Seyed Ali Biashad, Andrei Seluanov, Vera Gorbunova, Abigail Buchwalter, Sina Ghaemmaghami
{"title":"Proteome Birthdating Reveals Age-Selectivity of Protein Ubiquitination.","authors":"Michael E Meadow, Sarah Broas, Margaret Hoare, Fatemeh Alimohammadi, Kevin A Welle, Kyle Swovick, Jennifer R Hryhorenko, John C Martinez, Seyed Ali Biashad, Andrei Seluanov, Vera Gorbunova, Abigail Buchwalter, Sina Ghaemmaghami","doi":"10.1016/j.mcpro.2024.100791","DOIUrl":"10.1016/j.mcpro.2024.100791","url":null,"abstract":"<p><p>Within a cell, proteins have distinct and highly variable half-lives. As a result, the molecular ages of proteins can range from seconds to years. How the age of a protein influences its environmental interactions is a largely unexplored area of biology. To investigate the age-selectivity of cellular pathways, we developed a methodology termed \"proteome birthdating\" that barcodes proteins based on their time of synthesis. We demonstrate that this approach provides accurate measurements of protein turnover kinetics from a single biological sample encoding multiple labeling time-points. As a first application of the birthdated proteome, we investigated the age distribution of the human ubiquitinome. Our results indicate that the vast majority of ubiquitinated proteins in a cell consist of newly synthesized proteins and that these young proteins constitute the bulk of the degradative flux through the proteasome. Rapidly ubiquitinated nascent proteins are enriched in cytosolic subunits of large protein complexes. Conversely, proteins destined for the secretory pathway and vesicular transport have older ubiquitinated populations. Our data also identify a smaller subset of older ubiquitinated cellular proteins that do not appear to be targeted to the proteasome for rapid degradation. Together, our data provide an age census of the human ubiquitinome and establish proteome birthdating as a robust methodology for investigating the protein age-selectivity of diverse cellular pathways.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100791"},"PeriodicalIF":6.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11260378/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141155613","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
Improved Mass Spectrometry-Based Methods Reveal Abundant Propionylation and Tissue-Specific Histone Propionylation Profiles. 基于质谱的改进方法揭示了丰富的丙酰化和组织特异性组蛋白丙酰化概况。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-07-01 Epub Date: 2024-06-11 DOI: 10.1016/j.mcpro.2024.100799
Alessandro Vai, Roberta Noberini, Chiara Ghirardi, Dieggo Rodrigues de Paula, Michele Carminati, Rani Pallavi, Nathália Araújo, Patrick Varga-Weisz, Tiziana Bonaldi
{"title":"Improved Mass Spectrometry-Based Methods Reveal Abundant Propionylation and Tissue-Specific Histone Propionylation Profiles.","authors":"Alessandro Vai, Roberta Noberini, Chiara Ghirardi, Dieggo Rodrigues de Paula, Michele Carminati, Rani Pallavi, Nathália Araújo, Patrick Varga-Weisz, Tiziana Bonaldi","doi":"10.1016/j.mcpro.2024.100799","DOIUrl":"10.1016/j.mcpro.2024.100799","url":null,"abstract":"<p><p>Histone posttranslational modifications (PTMs) have crucial roles in a multitude of cellular processes, and their aberrant levels have been linked with numerous diseases, including cancer. Although histone PTM investigations have focused so far on methylations and acetylations, alternative long-chain acylations emerged as new dimension, as they are linked to cellular metabolic states and affect gene expression through mechanisms distinct from those regulated by acetylation. Mass spectrometry is the most powerful, comprehensive, and unbiased method to study histone PTMs. However, typical mass spectrometry-based protocols for histone PTM analysis do not allow the identification of naturally occurring propionylation and butyrylation. Here, we present improved state-of-the-art sample preparation and analysis protocols to quantitate these classes of modifications. After testing different derivatization methods coupled to protease digestion, we profiled common histone PTMs and histone acylations in seven mouse tissues and human normal and tumor breast clinical samples, obtaining a map of propionylations and butyrylations found in different tissue contexts. A quantitative histone PTM analysis also revealed a contribution of histone acylations in discriminating different tissues, also upon perturbation with antibiotics, and breast cancer samples from the normal counterpart. Our results show that profiling only classical modifications is limiting and highlight the importance of using sample preparation methods that allow the analysis of the widest possible spectrum of histone modifications, paving the way for deeper insights into their functional significance in cellular processes and disease states.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100799"},"PeriodicalIF":6.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11277384/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141311128","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
Global View of Domain-Specific O-Linked Mannose Glycosylation in Glycoengineered Cells. 糖工程细胞中域特异性 O 链接甘露糖基化的全貌。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-07-01 Epub Date: 2024-06-06 DOI: 10.1016/j.mcpro.2024.100796
Lorenzo Povolo, Weihua Tian, Sergey Y Vakhrushev, Adnan Halim
{"title":"Global View of Domain-Specific O-Linked Mannose Glycosylation in Glycoengineered Cells.","authors":"Lorenzo Povolo, Weihua Tian, Sergey Y Vakhrushev, Adnan Halim","doi":"10.1016/j.mcpro.2024.100796","DOIUrl":"10.1016/j.mcpro.2024.100796","url":null,"abstract":"<p><p>Protein O-linked mannose (O-Man) glycosylation is an evolutionary conserved posttranslational modification that fulfills important biological roles during embryonic development. Three nonredundant enzyme families, POMT1/POMT2, TMTC1-4, and TMEM260, selectively coordinate the initiation of protein O-Man glycosylation on distinct classes of transmembrane proteins, including α-dystroglycan, cadherins, and plexin receptors. However, a systematic investigation of their substrate specificities is lacking, in part due to the ubiquitous expression of O-Man glycosyltransferases in cells, which precludes analysis of pathway-specific O-Man glycosylation on a proteome-wide scale. Here, we apply a targeted workflow for membrane glycoproteomics across five human cell lines to extensively map O-Man substrates and genetically deconstruct O-Man initiation by individual and combinatorial knockout of O-Man glycosyltransferase genes. We established a human cell library for the analysis of substrate specificities of individual O-Man initiation pathways by quantitative glycoproteomics. Our results identify 180 O-Man glycoproteins, demonstrate new protein targets for the POMT1/POMT2 pathway, and show that TMTC1-4 and TMEM260 pathways widely target distinct Ig-like protein domains of plasma membrane proteins involved in cell-cell and cell-extracellular matrix interactions. The identification of O-Man on Ig-like folds adds further knowledge on the emerging concept of domain-specific O-Man glycosylation which opens for functional studies of O-Man-glycosylated adhesion molecules and receptors.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100796"},"PeriodicalIF":6.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11292533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141293565","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
Cerebrospinal Fluid Proteome Map Reveals Molecular Signatures of Reversible Cerebral Vasoconstriction Syndrome. 脑脊液蛋白质组图谱揭示可逆性脑血管收缩综合征的分子特征
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-07-01 Epub Date: 2024-06-03 DOI: 10.1016/j.mcpro.2024.100794
Jhih-Ci Yang, Shih-Pin Chen, Yen-Feng Wang, Chan-Hua Chang, Kun-Hao Chang, Jong-Ling Fuh, Lok-Hi Chow, Chia-Li Han, Yu-Ju Chen, Shuu-Jiun Wang
{"title":"Cerebrospinal Fluid Proteome Map Reveals Molecular Signatures of Reversible Cerebral Vasoconstriction Syndrome.","authors":"Jhih-Ci Yang, Shih-Pin Chen, Yen-Feng Wang, Chan-Hua Chang, Kun-Hao Chang, Jong-Ling Fuh, Lok-Hi Chow, Chia-Li Han, Yu-Ju Chen, Shuu-Jiun Wang","doi":"10.1016/j.mcpro.2024.100794","DOIUrl":"10.1016/j.mcpro.2024.100794","url":null,"abstract":"<p><p>Reversible cerebral vasoconstriction syndrome (RCVS) is a complex neurovascular disorder characterized by repetitive thunderclap headaches and reversible cerebral vasoconstriction. The pathophysiological mechanism of this mysterious syndrome remains underexplored and there is no clinically available molecular biomarker. To provide insight into the pathogenesis of RCVS, this study reported the first landscape of dysregulated proteome of cerebrospinal fluid (CSF) in patients with RCVS (n  =  21) compared to the age- and sex-matched controls (n  =  20) using data-independent acquisition mass spectrometry. Protein-protein interaction and functional enrichment analysis were employed to construct functional protein networks using the RCVS proteome. An RCVS-CSF proteome library resource of 1054 proteins was established, which illuminated large groups of upregulated proteins enriched in the brain and blood-brain barrier (BBB). Personalized RCVS-CSF proteomic profiles from 17 RCVS patients and 20 controls reveal proteomic changes involving the complement system, adhesion molecules, and extracellular matrix, which may contribute to the disruption of BBB and dysregulation of neurovascular units. Moreover, an additional validation cohort validated a panel of biomarker candidates and a two-protein signature predicted by machine learning model to discriminate RCVS patients from controls with an area under the curve of 0.997. This study reveals the first RCVS proteome and a potential pathogenetic mechanism of BBB and neurovascular unit dysfunction. It also nominates potential biomarker candidates that are mechanistically plausible for RCVS, which may offer potential diagnostic and therapeutic opportunities beyond the clinical manifestations.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100794"},"PeriodicalIF":6.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11263949/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141261989","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
De Novo Multi-Omics Pathway Analysis Designed for Prior Data Independent Inference of Cell Signaling Pathways. 新的多组学通路分析(DMPA),设计用于独立于先验数据的细胞信号通路推断。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-07-01 Epub Date: 2024-05-03 DOI: 10.1016/j.mcpro.2024.100780
Katri Vaparanta, Johannes A M Merilahti, Veera K Ojala, Klaus Elenius
{"title":"De Novo Multi-Omics Pathway Analysis Designed for Prior Data Independent Inference of Cell Signaling Pathways.","authors":"Katri Vaparanta, Johannes A M Merilahti, Veera K Ojala, Klaus Elenius","doi":"10.1016/j.mcpro.2024.100780","DOIUrl":"10.1016/j.mcpro.2024.100780","url":null,"abstract":"<p><p>New tools for cell signaling pathway inference from multi-omics data that are independent of previous knowledge are needed. Here, we propose a new de novo method, the de novo multi-omics pathway analysis (DMPA), to model and combine omics data into network modules and pathways. DMPA was validated with published omics data and was found accurate in discovering reported molecular associations in transcriptome, interactome, phosphoproteome, methylome, and metabolomics data, and signaling pathways in multi-omics data. DMPA was benchmarked against module discovery and multi-omics integration methods and outperformed previous methods in module and pathway discovery especially when applied to datasets of relatively low sample sizes. Transcription factor, kinase, subcellular location, and function prediction algorithms were devised for transcriptome, phosphoproteome, and interactome modules and pathways, respectively. To apply DMPA in a biologically relevant context, interactome, phosphoproteome, transcriptome, and proteome data were collected from analyses carried out using melanoma cells to address gamma-secretase cleavage-dependent signaling characteristics of the receptor tyrosine kinase TYRO3. The pathways modeled with DMPA reflected the predicted function and its direction in validation experiments.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100780"},"PeriodicalIF":6.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11259815/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140860965","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
Promises and Challenges of populational Proteomics in Health and Disease. 群体蛋白质组学在健康和疾病方面的前景与挑战。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-07-01 Epub Date: 2024-05-17 DOI: 10.1016/j.mcpro.2024.100786
Benjamin B Sun, Karsten Suhre, Bradford W Gibson
{"title":"Promises and Challenges of populational Proteomics in Health and Disease.","authors":"Benjamin B Sun, Karsten Suhre, Bradford W Gibson","doi":"10.1016/j.mcpro.2024.100786","DOIUrl":"10.1016/j.mcpro.2024.100786","url":null,"abstract":"<p><p>Advances in proteomic assay technologies have significantly increased coverage and throughput, enabling recent increases in the number of large-scale population-based proteomic studies of human plasma and serum. Improvements in multiplexed protein assays have facilitated the quantification of thousands of proteins over a large dynamic range, a key requirement for detecting the lowest-ranging, and potentially the most disease-relevant, blood-circulating proteins. In this perspective, we examine how populational proteomic datasets in conjunction with other concurrent omic measures can be leveraged to better understand the genomic and non-genomic correlates of the soluble proteome, constructing biomarker panels for disease prediction, among others. Mass spectrometry workflows are discussed as they are becoming increasingly competitive with affinity-based array platforms in terms of speed, cost, and proteome coverage due to advances in both instrumentation and workflows. Despite much success, there remain considerable challenges such as orthogonal validation and absolute quantification. We also highlight emergent challenges associated with study design, analytical considerations, and data integration as population-scale studies are run in batches and may involve longitudinal samples collated over many years. Lastly, we take a look at the future of what the nascent next-generation proteomic technologies might provide to the analysis of large sets of blood samples, as well as the difficulties in designing large-scale studies that will likely require participation from multiple and complex funding sources and where data sharing, study designs, and financing must be solved.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100786"},"PeriodicalIF":6.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11193116/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140961457","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
Differential Analysis of Cereblon Neosubstrates in Rabbit Embryos Using Targeted Proteomics. 利用靶向蛋白质组学对兔胚胎中的 Cereblon 新基质进行差异分析。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-07-01 Epub Date: 2024-06-10 DOI: 10.1016/j.mcpro.2024.100797
Joel D Federspiel, Natasha R Catlin, William S Nowland, Christine M Stethem, Nagappan Mathialagan, Mireia Fernandez Ocaña, Christopher J Bowman
{"title":"Differential Analysis of Cereblon Neosubstrates in Rabbit Embryos Using Targeted Proteomics.","authors":"Joel D Federspiel, Natasha R Catlin, William S Nowland, Christine M Stethem, Nagappan Mathialagan, Mireia Fernandez Ocaña, Christopher J Bowman","doi":"10.1016/j.mcpro.2024.100797","DOIUrl":"10.1016/j.mcpro.2024.100797","url":null,"abstract":"<p><p>Targeted protein degradation is the selective removal of a protein of interest through hijacking intracellular protein cleanup machinery. This rapidly growing field currently relies heavily on the use of the E3 ligase cereblon (CRBN) to target proteins for degradation, including the immunomodulatory drugs (IMiDs) thalidomide, lenalidomide, and pomalidomide which work through a molecular glue mechanism of action with CRBN. While CRBN recruitment can result in degradation of a specific protein of interest (e.g., efficacy), degradation of other proteins (called CRBN neosubstrates) also occurs. Degradation of one or more of these CRBN neosubstrates is believed to play an important role in thalidomide-related developmental toxicity observed in rabbits and primates. We identified a set of 25 proteins of interest associated with CRBN-related protein homeostasis and/or embryo/fetal development. We developed a targeted assay for these proteins combining peptide immunoaffinity enrichment and high-resolution mass spectrometry and successfully applied this assay to rabbit embryo samples from pregnant rabbits dosed with three IMiDs. We confirmed previously reported in vivo decreases in neosubstrates like SALL4, as well as provided evidence of neosubstrate changes for proteins only examined in vitro previously. While there were many proteins that were similarly decreased by all three IMiDs, no compound had the exact same neosubstrate degradation profile as another. We compared our data to previous literature reports of IMiD-induced degradation and known developmental biology associations. Based on our observations, we recommend monitoring at least a major subset of these neosubstrates in a developmental test system to improve CRBN-binding compound-specific risk assessment. A strength of our assay is that it is configurable, and the target list can be readily adapted to focus on only a subset of proteins of interest or expanded to incorporate new findings as additional information about CRBN biology is discovered.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100797"},"PeriodicalIF":6.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11263748/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141311127","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
Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors Into Peptide Identification. 肽谱匹配重评分:将多肽特性预测因子整合到多肽鉴定中,提升蛋白质组学性能。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-07-01 Epub Date: 2024-06-11 DOI: 10.1016/j.mcpro.2024.100798
Mostafa Kalhor, Joel Lapin, Mario Picciani, Mathias Wilhelm
{"title":"Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors Into Peptide Identification.","authors":"Mostafa Kalhor, Joel Lapin, Mario Picciani, Mathias Wilhelm","doi":"10.1016/j.mcpro.2024.100798","DOIUrl":"10.1016/j.mcpro.2024.100798","url":null,"abstract":"<p><p>Rescoring of peptide spectrum matches originating from database search engines enabled by peptide property predictors is exceeding the performance of peptide identification from traditional database search engines. In contrast to the peptide spectrum match scores calculated by traditional database search engines, rescoring peptide spectrum matches generates scores based on comparing observed and predicted peptide properties, such as fragment ion intensities and retention times. These newly generated scores enable a more efficient discrimination between correct and incorrect peptide spectrum matches. This approach was shown to lead to substantial improvements in the number of confidently identified peptides, facilitating the analysis of challenging datasets in various fields such as immunopeptidomics, metaproteomics, proteogenomics, and single-cell proteomics. In this review, we summarize the key elements leading up to the recent introduction of multiple data-driven rescoring pipelines. We provide an overview of relevant post-processing rescoring tools, introduce prominent data-driven rescoring pipelines for various applications, and highlight limitations, opportunities, and future perspectives of this approach and its impact on mass spectrometry-based proteomics.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100798"},"PeriodicalIF":6.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11269915/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141317747","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
A Targeted LC-MRM3 Proteomic Approach for the Diagnosis of SARS-CoV-2 Infection in Nasopharyngeal Swabs. 用于诊断鼻咽拭子中 SARS-CoV-2 感染的定向 LC-MRM3 蛋白质组学方法。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-07-01 Epub Date: 2024-06-17 DOI: 10.1016/j.mcpro.2024.100805
Nicolas Drouin, Hyung L Elfrink, Stefan A Boers, Sam van Hugten, Els Wessels, Jutte J C de Vries, Geert H Groeneveld, Paul Miggiels, Bart Van Puyvelde, Maarten Dhaenens, Andries E Budding, Leonie Ran, Roy Masius, Zoltan Takats, Arjen Boogaerds, Markus Bulters, Wouter Muurlink, Paul Oostvogel, Amy C Harms, Mariken van der Lubben, Thomas Hankemeier
{"title":"A Targeted LC-MRM<sup>3</sup> Proteomic Approach for the Diagnosis of SARS-CoV-2 Infection in Nasopharyngeal Swabs.","authors":"Nicolas Drouin, Hyung L Elfrink, Stefan A Boers, Sam van Hugten, Els Wessels, Jutte J C de Vries, Geert H Groeneveld, Paul Miggiels, Bart Van Puyvelde, Maarten Dhaenens, Andries E Budding, Leonie Ran, Roy Masius, Zoltan Takats, Arjen Boogaerds, Markus Bulters, Wouter Muurlink, Paul Oostvogel, Amy C Harms, Mariken van der Lubben, Thomas Hankemeier","doi":"10.1016/j.mcpro.2024.100805","DOIUrl":"10.1016/j.mcpro.2024.100805","url":null,"abstract":"<p><p>Since its first appearance, severe acute respiratory syndrome coronavirus 2 quickly spread around the world and the lack of adequate PCR testing capacities, especially during the early pandemic, led the scientific community to explore new approaches such as mass spectrometry (MS). We developed a proteomics workflow to target several tryptic peptides of the nucleocapsid protein. A highly selective multiple reaction monitoring-cubed (MRM<sup>3</sup>) strategy provided a sensitivity increase in comparison to conventional MRM acquisition. Our MRM<sup>3</sup> approach was first tested on an Amsterdam public health cohort (alpha-variant, 760 participants) detecting viral nucleocapsid protein peptides from nasopharyngeal swabs samples presenting a cycle threshold value down to 35 with sensitivity and specificity of 94.2% and 100.0%, without immunopurification. A second iteration of the MS-diagnostic test, able to analyze more than 400 samples per day, was clinically validated on a Leiden-Rijswijk public health cohort (delta-variant, 2536 participants) achieving 99.9% specificity and 93.1% sensitivity for patients with cycle threshold values up to 35. In this manuscript, we also developed and brought the first proof of the concept of viral variant monitoring in a complex matrix using targeted MS.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100805"},"PeriodicalIF":6.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11284538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141427220","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
Histone Chaperone Deficiency in Arabidopsis Plants Triggers Adaptive Epigenetic Changes in Histone Variants and Modifications. 拟南芥植物中组蛋白伴侣蛋白的缺乏会引发组蛋白变体和修饰的适应性表观遗传变化。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-07-01 Epub Date: 2024-06-05 DOI: 10.1016/j.mcpro.2024.100795
Michal Franek, Martina Nešpor Dadejová, Pavlína Pírek, Karolína Kryštofová, Tereza Dobisová, Zbyněk Zdráhal, Martina Dvořáčková, Gabriela Lochmanová
{"title":"Histone Chaperone Deficiency in Arabidopsis Plants Triggers Adaptive Epigenetic Changes in Histone Variants and Modifications.","authors":"Michal Franek, Martina Nešpor Dadejová, Pavlína Pírek, Karolína Kryštofová, Tereza Dobisová, Zbyněk Zdráhal, Martina Dvořáčková, Gabriela Lochmanová","doi":"10.1016/j.mcpro.2024.100795","DOIUrl":"10.1016/j.mcpro.2024.100795","url":null,"abstract":"<p><p>At the molecular scale, adaptive advantages during plant growth and development rely on modulation of gene expression, primarily provided by epigenetic machinery. One crucial part of this machinery is histone posttranslational modifications, which form a flexible system, driving transient changes in chromatin, and defining particular epigenetic states. Posttranslational modifications work in concert with replication-independent histone variants further adapted for transcriptional regulation and chromatin repair. However, little is known about how such complex regulatory pathways are orchestrated and interconnected in cells. In this work, we demonstrate the utility of mass spectrometry-based approaches to explore how different epigenetic layers interact in Arabidopsis mutants lacking certain histone chaperones. We show that defects in histone chaperone function (e.g., chromatin assembly factor-1 or nucleosome assembly protein 1 mutations) translate into an altered epigenetic landscape, which aids the plant in mitigating internal instability. We observe changes in both the levels and distribution of H2A.W.7, altogether with partial repurposing of H3.3 and changes in the key repressive (H3K27me1/2) or euchromatic marks (H3K36me1/2). These shifts in the epigenetic profile serve as a compensatory mechanism in response to impaired integration of the H3.1 histone in the fas1 mutants. Altogether, our findings suggest that maintaining genome stability involves a two-tiered approach. The first relies on flexible adjustments in histone marks, while the second level requires the assistance of chaperones for histone variant replacement.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100795"},"PeriodicalIF":6.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11263794/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141288322","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}
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