Molecular & Cellular Proteomics最新文献

筛选
英文 中文
Molecular Signatures of Neurodegenerative Diseases Identified by Proteomic and Phosphoproteomic Analyses in Aging Mouse Brain. 通过对衰老小鼠大脑进行蛋白质组学和磷酸化蛋白质组学分析,确定神经退行性疾病的分子特征。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-09-01 Epub Date: 2024-07-26 DOI: 10.1016/j.mcpro.2024.100819
Rodrigo Mohallem, Allison J Schaser, Uma K Aryal
{"title":"Molecular Signatures of Neurodegenerative Diseases Identified by Proteomic and Phosphoproteomic Analyses in Aging Mouse Brain.","authors":"Rodrigo Mohallem, Allison J Schaser, Uma K Aryal","doi":"10.1016/j.mcpro.2024.100819","DOIUrl":"10.1016/j.mcpro.2024.100819","url":null,"abstract":"<p><p>A central hallmark of neurodegenerative diseases is the irreversible accumulation of misfolded proteins in the brain by aberrant phosphorylation. Understanding the mechanisms underlying protein phosphorylation and its role in pathological protein aggregation within the context of aging is crucial for developing therapeutic strategies aimed at preventing or reversing such diseases. Here, we applied multi-protease digestion and quantitative mass spectrometry to compare and characterize dysregulated proteins and phosphosites in the mouse brain proteome using three different age groups: young-adult (3-4 months), middle-age (10 months), and old mice (19-21 months). Proteins associated with senescence, neurodegeneration, inflammation, cell cycle regulation, the p53 hallmark pathway, and cytokine signaling showed significant age-dependent changes in abundances and level of phosphorylation. Several proteins implicated in Alzheimer's disease (AD) and Parkinson's disease (PD) including tau (Mapt), Nefh, and Dpysl2 (also known as Crmp2) were hyperphosphorylated in old mice brain suggesting their susceptibility to the diseases. Cdk5 and Gsk3b, which are known to phosphorylate Dpysl2 at multiple specific sites, had also increased phosphorylation levels in old mice suggesting a potential crosstalk between them to contribute to AD. Hapln2, which promotes α-synuclein aggregation in patients with PD, was one of the proteins with highest abundance in old mice. CD9, which regulates senescence through the PI3K-AKT-mTOR-p53 signaling was upregulated in old mice and its regulation was correlated with the activation of phosphorylated AKT1. Overall, the findings identify a significant association between aging and the dysregulation of proteins involved in various pathways linked to neurodegenerative diseases with potential therapeutic implications.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100819"},"PeriodicalIF":6.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11381985/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141788628","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
Development of a Fit-For-Purpose Multi-Marker Panel for Early Diagnosis of Pancreatic Ductal Adenocarcinoma. 开发用于早期诊断胰腺导管腺癌的适用多标记物面板。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-09-01 Epub Date: 2024-08-05 DOI: 10.1016/j.mcpro.2024.100824
Hyeonji Kim, Sunghyun Huh, Jungkap Park, Youngmin Han, Kyung-Geun Ahn, Yiyoung Noh, Seong-Jae Lee, Hyosub Chu, Sung-Soo Kim, Hye-Sol Jung, Won-Gun Yun, Young Jae Cho, Wooil Kwon, Jin-Young Jang, Un-Beom Kang
{"title":"Development of a Fit-For-Purpose Multi-Marker Panel for Early Diagnosis of Pancreatic Ductal Adenocarcinoma.","authors":"Hyeonji Kim, Sunghyun Huh, Jungkap Park, Youngmin Han, Kyung-Geun Ahn, Yiyoung Noh, Seong-Jae Lee, Hyosub Chu, Sung-Soo Kim, Hye-Sol Jung, Won-Gun Yun, Young Jae Cho, Wooil Kwon, Jin-Young Jang, Un-Beom Kang","doi":"10.1016/j.mcpro.2024.100824","DOIUrl":"10.1016/j.mcpro.2024.100824","url":null,"abstract":"<p><p>Pancreatic ductal adenocarcinoma (PDAC) suffers from a lack of an effective diagnostic method, which hampers improvement in patient survival. Carbohydrate antigen 19-9 (CA19-9) is the only FDA-approved blood biomarker for PDAC, yet its clinical utility is limited due to suboptimal performance. Liquid chromatography-mass spectrometry (LC-MS) has emerged as a burgeoning technology in clinical proteomics for the discovery, verification, and validation of novel biomarkers. A plethora of protein biomarker candidates for PDAC have been identified using LC-MS, yet few has successfully transitioned into clinical practice. This translational standstill is owed partly to insufficient considerations of practical needs and perspectives of clinical implementation during biomarker development pipelines, such as demonstrating the analytical robustness of proposed biomarkers which is critical for transitioning from research-grade to clinical-grade assays. Moreover, the throughput and cost-effectiveness of proposed assays ought to be considered concomitantly from the early phases of the biomarker pipelines for enhancing widespread adoption in clinical settings. Here, we developed a fit-for-purpose multi-marker panel for PDAC diagnosis by consolidating analytically robust biomarkers as well as employing a relatively simple LC-MS protocol. In the discovery phase, we comprehensively surveyed putative PDAC biomarkers from both in-house data and prior studies. In the verification phase, we developed a multiple-reaction monitoring (MRM)-MS-based proteomic assay using surrogate peptides that passed stringent analytical validation tests. We adopted a high-throughput protocol including a short gradient (<10 min) and simple sample preparation (no depletion or enrichment steps). Additionally, we developed our assay using serum samples, which are usually the preferred biospecimen in clinical settings. We developed predictive models based on our final panel of 12 protein biomarkers combined with CA19-9, which showed improved diagnostic performance compared to using CA19-9 alone in discriminating PDAC from non-PDAC controls including healthy individuals and patients with benign pancreatic diseases. A large-scale clinical validation is underway to demonstrate the clinical validity of our novel panel.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100824"},"PeriodicalIF":6.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406441/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141889756","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
Immunopeptidomics Mapping of Listeria monocytogenes T Cell Epitopes in Mice. 小鼠李斯特菌 T 细胞表位的免疫肽组学图谱。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-09-01 Epub Date: 2024-08-13 DOI: 10.1016/j.mcpro.2024.100829
Adillah Gul, Lecia L Pewe, Patrick Willems, Rupert Mayer, Fabien Thery, Caroline Asselman, Ilke Aernout, Rein Verbeke, Denzel Eggermont, Laura Van Moortel, Ellen Upton, Yifeng Zhang, Katie Boucher, Laia Miret-Casals, Hans Demol, Stefaan C De Smedt, Ine Lentacker, Lilliana Radoshevich, John T Harty, Francis Impens
{"title":"Immunopeptidomics Mapping of Listeria monocytogenes T Cell Epitopes in Mice.","authors":"Adillah Gul, Lecia L Pewe, Patrick Willems, Rupert Mayer, Fabien Thery, Caroline Asselman, Ilke Aernout, Rein Verbeke, Denzel Eggermont, Laura Van Moortel, Ellen Upton, Yifeng Zhang, Katie Boucher, Laia Miret-Casals, Hans Demol, Stefaan C De Smedt, Ine Lentacker, Lilliana Radoshevich, John T Harty, Francis Impens","doi":"10.1016/j.mcpro.2024.100829","DOIUrl":"10.1016/j.mcpro.2024.100829","url":null,"abstract":"<p><p>Listeria monocytogenes is a foodborne intracellular bacterial model pathogen. Protective immunity against Listeria depends on an effective CD8<sup>+</sup> T cell response, but very few T cell epitopes are known in mice as a common animal infection model for listeriosis. To identify epitopes, we screened for Listeria immunopeptides presented in the spleen of infected mice by mass spectrometry-based immunopeptidomics. We mapped more than 6000 mouse self-peptides presented on MHC class I molecules, including 12 high confident Listeria peptides from 12 different bacterial proteins. Bacterial immunopeptides with confirmed fragmentation spectra were further tested for their potential to activate CD8<sup>+</sup> T cells, revealing VTYNYINI from the putative cell wall surface anchor family protein LMON_0576 as a novel bona fide peptide epitope. The epitope showed high biological potency in a prime boost model and can be used as a research tool to probe CD8<sup>+</sup> T cell responses in the mouse models of Listeria infection. Together, our results demonstrate the power of immunopeptidomics for bacterial antigen identification.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100829"},"PeriodicalIF":6.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11414675/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141988343","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
Secretome Analysis Using Affinity Proteomics and Immunoassays: A Focus on Tumor Biology. 利用亲和蛋白质组学和免疫测定进行分泌组分析:聚焦肿瘤生物学。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-09-01 Epub Date: 2024-08-13 DOI: 10.1016/j.mcpro.2024.100830
Vanessa M Beutgen, Veronika Shinkevich, Johanna Pörschke, Celina Meena, Anna M Steitz, Elke Pogge von Strandmann, Johannes Graumann, María Gómez-Serrano
{"title":"Secretome Analysis Using Affinity Proteomics and Immunoassays: A Focus on Tumor Biology.","authors":"Vanessa M Beutgen, Veronika Shinkevich, Johanna Pörschke, Celina Meena, Anna M Steitz, Elke Pogge von Strandmann, Johannes Graumann, María Gómez-Serrano","doi":"10.1016/j.mcpro.2024.100830","DOIUrl":"10.1016/j.mcpro.2024.100830","url":null,"abstract":"<p><p>The study of the cellular secretome using proteomic techniques continues to capture the attention of the research community across a broad range of topics in biomedical research. Due to their untargeted nature, independence from the model system used, historically superior depth of analysis, as well as comparative affordability, mass spectrometry-based approaches traditionally dominate such analyses. More recently, however, affinity-based proteomic assays have massively gained in analytical depth, which together with their high sensitivity, dynamic range coverage as well as high throughput capabilities render them exquisitely suited to secretome analysis. In this review, we revisit the analytical challenges implied by secretomics and provide an overview of affinity-based proteomic platforms currently available for such analyses, using the study of the tumor secretome as an example for basic and translational research.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100830"},"PeriodicalIF":6.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11417252/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141988345","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
Variation of Site-Specific Glycosylation Profiles of Recombinant Influenza Glycoproteins. 重组流感糖蛋白特定位点糖基化图谱的变化。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-09-01 Epub Date: 2024-08-10 DOI: 10.1016/j.mcpro.2024.100827
Zachary C Goecker, Meghan C Burke, Concepcion A Remoroza, Yi Liu, Yuri A Mirokhin, Sergey L Sheetlin, Dmitrii V Tchekhovskoi, Xiaoyu Yang, Stephen E Stein
{"title":"Variation of Site-Specific Glycosylation Profiles of Recombinant Influenza Glycoproteins.","authors":"Zachary C Goecker, Meghan C Burke, Concepcion A Remoroza, Yi Liu, Yuri A Mirokhin, Sergey L Sheetlin, Dmitrii V Tchekhovskoi, Xiaoyu Yang, Stephen E Stein","doi":"10.1016/j.mcpro.2024.100827","DOIUrl":"10.1016/j.mcpro.2024.100827","url":null,"abstract":"<p><p>This work presents a detailed determination of site-specific N-glycan distributions of the recombinant influenza glycoproteins hemagglutinin (HA) and neuraminidase. Variation in glycosylation among recombinant glycoproteins is not predictable and can depend on details of the biomanufacturing process as well as details of protein structure. In this study, recombinant influenza proteins were analyzed from eight strains of four different suppliers. These include five HA and three neuraminidase proteins, each produced from a HEK293 cell line. Digestion was conducted using a series of complex multienzymatic methods designed to isolate glycopeptides containing single N-glycosylated sites. Site-specific glycosylation profiles of intact glycopeptides were produced using a recently developed method and comparisons were made using spectral similarity scores. Variation in glycan abundances and distribution was most pronounced between different strains of virus (similarity score = 383 out of 999), whereas digestion replicates and injection replicates showed relatively little variation (similarity score = 957). Notably, glycan distributions for homologous regions of influenza glycoprotein variants showed low variability. Due to the multiple possible sources of variation and inherent analytical difficulties in site-specific glycan determinations, variations were individually examined for multiple factors, including differences in supplier, production batch, protease digestion, and replicate measurement. After comparing all glycosylation distributions, four distinguishable classes could be identified for the majority of sites. Finally, attempts to identify glycosylation distributions on adjacent potential N-glycosylated sites of one HA variant were made. Only the second site (NnST) was found to be occupied using two rarely used proteases in proteomics, subtilisin and esperase, both of which did selectively cleave these adjacent sites.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100827"},"PeriodicalIF":6.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11417209/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141917120","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
One-step N-Terminomics Based on Isolation of Protein N-Terminal Peptides From LysargiNase Digests by Tip-Based Strong Cation Exchange Chromatography. 基于尖端强阳离子交换色谱法从 LysargiNase 消化液中分离蛋白质 N 端肽的一步式 N 端组学。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-09-01 Epub Date: 2024-07-26 DOI: 10.1016/j.mcpro.2024.100820
Kazuya Morikawa, Hiroshi Nishida, Koshi Imami, Yasushi Ishihama
{"title":"One-step N-Terminomics Based on Isolation of Protein N-Terminal Peptides From LysargiNase Digests by Tip-Based Strong Cation Exchange Chromatography.","authors":"Kazuya Morikawa, Hiroshi Nishida, Koshi Imami, Yasushi Ishihama","doi":"10.1016/j.mcpro.2024.100820","DOIUrl":"10.1016/j.mcpro.2024.100820","url":null,"abstract":"<p><p>We have developed a one-step isolation method for protein N-terminal peptides from LysargiNase digests by pipette tip-based strong cation exchange (SCX) chromatography. This CHAMP-N (CHromatographic AMplification of Protein N-terminal peptides) method using disposable and parallel-processable SCX tips instead of conventional HPLC SCX columns facilitates simple, sensitive, reproducible, and high-throughput N-terminomic profiling without sacrificing the high identification numbers and selectivity achieved by the HPLC-based method. By applying the CHAMP-N method to HEK293T cells, we identified novel cleavage sites for signal and transit peptides and non-canonical translation initiation sites. Finally, for proteome-wide terminomics, we present a simple and comprehensive N- and C-terminomics platform employing three different tip-based approaches, including CHAMP-N, in which protease digestion and one-step isolation by tip LC are commonly used to achieve complementary terminome coverages.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100820"},"PeriodicalIF":6.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11382313/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141788629","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
GRable Version 1.0: A Software Tool for Site-Specific Glycoform Analysis With Improved MS1-Based Glycopeptide Detection With Parallel Clustering and Confidence Evaluation With MS2 Information. GRable 1.0 版:用于特定位点糖形分析的软件工具,改进了基于 MS1 的糖肽检测,并利用 MS2 信息进行平行聚类和置信度评估。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-09-01 Epub Date: 2024-08-23 DOI: 10.1016/j.mcpro.2024.100833
Chiaki Nagai-Okatani, Daisuke Tominaga, Azusa Tomioka, Hiroaki Sakaue, Norio Goda, Shigeru Ko, Atsushi Kuno, Hiroyuki Kaji
{"title":"GRable Version 1.0: A Software Tool for Site-Specific Glycoform Analysis With Improved MS1-Based Glycopeptide Detection With Parallel Clustering and Confidence Evaluation With MS2 Information.","authors":"Chiaki Nagai-Okatani, Daisuke Tominaga, Azusa Tomioka, Hiroaki Sakaue, Norio Goda, Shigeru Ko, Atsushi Kuno, Hiroyuki Kaji","doi":"10.1016/j.mcpro.2024.100833","DOIUrl":"10.1016/j.mcpro.2024.100833","url":null,"abstract":"<p><p>High-throughput intact glycopeptide analysis is crucial for elucidating the physiological and pathological status of the glycans attached to each glycoprotein. Mass spectrometry-based glycoproteomic methods are challenging because of the diversity and heterogeneity of glycan structures. Therefore, we developed an MS1-based site-specific glycoform analysis method named \"Glycan heterogeneity-based Relational IDentification of Glycopeptide signals on Elution profile (Glyco-RIDGE)\" for a more comprehensive analysis. This method detects glycopeptide signals as a cluster based on the mass and chromatographic properties of glycopeptides and then searches for each combination of core peptides and glycan compositions by matching their mass and retention time differences. Here, we developed a novel browser-based software named GRable for semi-automated Glyco-RIDGE analysis with significant improvements in glycopeptide detection algorithms, including \"parallel clustering.\" This unique function improved the comprehensiveness of glycopeptide detection and allowed the analysis to focus on specific glycan structures, such as pauci-mannose. The other notable improvement is evaluating the \"confidence level\" of the GRable results, especially using MS2 information. This function facilitated reduced misassignment of the core peptide and glycan composition and improved the interpretation of the results. Additional improved points of the algorithms are \"correction function\" for accurate monoisotopic peak picking; one-to-one correspondence of clusters and core peptides even for multiply sialylated glycopeptides; and \"inter-cluster analysis\" function for understanding the reason for detected but unmatched clusters. The significance of these improvements was demonstrated using purified and crude glycoprotein samples, showing that GRable allowed site-specific glycoform analysis of intact sialylated glycoproteins on a large-scale and in-depth. Therefore, this software will help us analyze the status and changes in glycans to obtain biological and clinical insights into protein glycosylation by complementing the comprehensiveness of MS2-based glycoproteomics. GRable can be freely run online using a web browser via the GlyCosmos Portal (https://glycosmos.org/grable).</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100833"},"PeriodicalIF":6.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11421343/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142056092","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
LC-SRM Combined With Machine Learning Enables Fast Identification and Quantification of Bacterial Pathogens in Urinary Tract Infections. LC-SRM 与机器学习相结合,能够快速鉴定和定量尿路感染中的细菌病原体。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-08-22 DOI: 10.1016/j.mcpro.2024.100832
Clarisse Gotti, Florence Roux-Dalvai, Ève Bérubé, Antoine Lacombe-Rastoll, Mickaël Leclercq, Cristina C Jacob, Maurice Boissinot, Claudia Martins, Neloni R Wijeratne, Michel G Bergeron, Arnaud Droit
{"title":"LC-SRM Combined With Machine Learning Enables Fast Identification and Quantification of Bacterial Pathogens in Urinary Tract Infections.","authors":"Clarisse Gotti, Florence Roux-Dalvai, Ève Bérubé, Antoine Lacombe-Rastoll, Mickaël Leclercq, Cristina C Jacob, Maurice Boissinot, Claudia Martins, Neloni R Wijeratne, Michel G Bergeron, Arnaud Droit","doi":"10.1016/j.mcpro.2024.100832","DOIUrl":"10.1016/j.mcpro.2024.100832","url":null,"abstract":"<p><p>Urinary tract infections (UTIs) are a worldwide health problem. Fast and accurate detection of bacterial infection is essential to provide appropriate antibiotherapy to patients and to avoid the emergence of drug-resistant pathogens. While the gold standard requires 24 h to 48 h of bacteria culture prior to MALDI-TOF species identification, we propose a culture-free workflow, enabling bacterial identification and quantification in less than 4 h using 1 ml of urine. After rapid and automatable sample preparation, a signature of 82 bacterial peptides, defined by machine learning, was monitored in LC-MS, to distinguish the 15 species causing 84% of the UTIs. The combination of the sensitivity of the SRM mode on a triple quadrupole TSQ Altis instrument and the robustness of capillary flow enabled us to analyze up to 75 samples per day, with 99.2% accuracy on bacterial inoculations of healthy urines. We have also shown our method can be used to quantify the spread of the infection, from 8 × 10<sup>4</sup> to 3 × 10<sup>7</sup> CFU/ml. Finally, the workflow was validated on 45 inoculated urines and on 84 UTI-positive urine from patients, with respectively 93.3% and 87.1% of agreement with the culture-MALDI procedure at a level above 1 × 10<sup>5</sup> CFU/ml corresponding to an infection requiring antibiotherapy.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100832"},"PeriodicalIF":6.1,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11532907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142046892","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
Pupylation-Based Proximity-Tagging of FERONIA-Interacting Proteins in Arabidopsis. 拟南芥中与 FERONIA 相互作用的蛋白质的基于稚嫩化的近似标记。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-08-13 DOI: 10.1016/j.mcpro.2024.100828
Zhuoran Lin, Di Liu, Yifan Xu, Mengyang Wang, YongQi Yu, Andrew C Diener, Kun-Hsiang Liu
{"title":"Pupylation-Based Proximity-Tagging of FERONIA-Interacting Proteins in Arabidopsis.","authors":"Zhuoran Lin, Di Liu, Yifan Xu, Mengyang Wang, YongQi Yu, Andrew C Diener, Kun-Hsiang Liu","doi":"10.1016/j.mcpro.2024.100828","DOIUrl":"10.1016/j.mcpro.2024.100828","url":null,"abstract":"<p><p>The plasma membrane-localized receptor kinase FERONIA (FER) plays critical roles in a remarkable variety of biological processes throughout the life cycle of Arabidopsis thaliana. Revealing the molecular connections of FER that underlie these processes starts with identifying the proteins that interact with FER. We applied pupylation-based interaction tagging (PUP-IT) to survey cellular proteins in proximity to FER, encompassing weak and transient interactions that can be difficult to capture for membrane proteins. We reproducibly identified 581, 115, and 736 specific FER-interacting protein candidates in protoplasts, seedlings, and flowers, respectively. We also confirmed 14 previously characterized FER-interacting proteins. Protoplast transient gene expression expedited the testing of new gene constructs for PUP-IT analyses and the validation of candidate proteins. We verified the proximity labeling of five selected candidates that were not previously characterized as FER-interacting proteins. The PUP-IT method could be a valuable tool to survey and validate protein-protein interactions for targets of interest in diverse subcellular compartments in plants.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100828"},"PeriodicalIF":6.1,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11532908/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141988344","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
MIB2 Functions in Oocyte Meiosis by Modulating Chromatin Configuration. MIB2 通过调节染色质构型在卵母细胞减数分裂中发挥作用。
IF 6.1 2区 生物学
Molecular & Cellular Proteomics Pub Date : 2024-08-01 Epub Date: 2024-07-15 DOI: 10.1016/j.mcpro.2024.100813
Yifei Jin, Guangyi Sun, Jiashuo Li, Qing Cheng, Hongzheng Sun, Longsen Han, Xuejiang Guo, Shuai Zhu, Qiang Wang
{"title":"MIB2 Functions in Oocyte Meiosis by Modulating Chromatin Configuration.","authors":"Yifei Jin, Guangyi Sun, Jiashuo Li, Qing Cheng, Hongzheng Sun, Longsen Han, Xuejiang Guo, Shuai Zhu, Qiang Wang","doi":"10.1016/j.mcpro.2024.100813","DOIUrl":"10.1016/j.mcpro.2024.100813","url":null,"abstract":"<p><p>Chromatin configuration serves as a principal indicator of GV (germinal vesicle)-stage oocyte quality. However, the underlying mechanisms governing the chromatin configuration transition from NSN (non-surrounded nucleolus) to SN (surrounded nucleolus) remain unclear. In this study, by conducting a quantitative proteomic analysis, we identified an increased expression of the MIB2 (MIB E3 ubiquitin protein ligase 2) protein in SN oocytes. Specific depletion of MIB2 in SN oocytes not only leads to severe disruption of the meiotic apparatus and a higher incidence of aneuploidy but also adversely affects meiotic maturation and early embryo development. Notably, overexpression of MIB2 in NSN oocytes facilitates the chromatin configuration transition. Meantime, we observed that forced expression of MIB2 in NSN oocytes significantly mitigates spindle/chromosome disorganization and aneuploidy. In summary, our results suggest that chromatin configuration transition regulated by MIB2 is crucial for oocytes to acquire developmental competence.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100813"},"PeriodicalIF":6.1,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364126/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141633940","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
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信