Proteomics最新文献_第7页

Characterization of Exosomes Released from Mycobacterium abscessus-Infected Macrophages 受脓肿分枝杆菌感染的巨噬细胞释放的外泌体的特征。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-09-16 DOI: 10.1002/pmic.202400181

Charlie A. Vermeire, Xuejuan Tan, Aidaly Ramos-Leyva, Ava Wood, Stephen K. Kotey, Steven D. Hartson, Yurong Liang, Lin Liu, Yong Cheng

{"title":"Characterization of Exosomes Released from Mycobacterium abscessus-Infected Macrophages","authors":"Charlie A. Vermeire, Xuejuan Tan, Aidaly Ramos-Leyva, Ava Wood, Stephen K. Kotey, Steven D. Hartson, Yurong Liang, Lin Liu, Yong Cheng","doi":"10.1002/pmic.202400181","DOIUrl":"10.1002/pmic.202400181","url":null,"abstract":"<div>\u0000 \u0000 Extracellular vesicles (EVs), such as exosomes, play a critical role in cell-to-cell communication and regulating cellular processes in recipient cells. Non-tuberculous mycobacteria (NTM), such as Mycobacterium abscessus, are a group of environmental bacteria that can cause severe lung infections in populations with pre-existing lung conditions, such as cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD). There is limited knowledge of the engagement of EVs in the host–pathogen interactions in the context of NTM infections. In this study, we found that M. abscessus infection increased the release of a subpopulation of exosomes (CD9, CD63, and/or CD81 positive) by mouse macrophages in cell culture. Proteomic analysis of these vesicles demonstrated that M. abscessus infection affects the enrichment of host proteins in exosomes released by macrophages. When compared to exosomes from uninfected macrophages, exosomes released by M. abscessus-infected macrophages significantly improved M. abscessus growth and downregulated the intracellular level of glutamine in recipient macrophages in cell culture. Increasing glutamine concentration in the medium rescued intracellular glutamine levels and M. abscessus killing in recipient macrophages that were treated with exosomes from M. abscessus-infected macrophages. Taken together, our results indicate that exosomes may serve as extracellular glutamine eliminators that interfere with glutamine-dependent M. abscessus killing in recipient macrophages.\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142277692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Standard abbreviations 标准缩略语

IF 3.4 4区生物学

Proteomics Pub Date : 2024-09-13 DOI: 10.1002/pmic.202470144

引用次数: 0

Editorial Board: Proteomics 18'24 编辑委员会：蛋白质组学 18'24

IF 3.4 4区生物学

Proteomics Pub Date : 2024-09-13 DOI: 10.1002/pmic.202470142

引用次数: 0

Contents: Proteomics 18'24 内容：蛋白质组学 18'24

IF 3.4 4区生物学

Proteomics Pub Date : 2024-09-13 DOI: 10.1002/pmic.202470143

引用次数: 0

A semi-automated workflow for DIA-based global discovery to pathway-driven PRM analysis 从基于 DIA 的全球发现到通路驱动的 PRM 分析的半自动化工作流程。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-09-05 DOI: 10.1002/pmic.202400129

Jennifer Guergues, Jessica Wohlfahrt, John M. Koomen, Jonathan R. Krieger, Sameer Varma, Stanley M. Stevens Jr.

{"title":"A semi-automated workflow for DIA-based global discovery to pathway-driven PRM analysis","authors":"Jennifer Guergues, Jessica Wohlfahrt, John M. Koomen, Jonathan R. Krieger, Sameer Varma, Stanley M. Stevens Jr.","doi":"10.1002/pmic.202400129","DOIUrl":"10.1002/pmic.202400129","url":null,"abstract":"Targeted proteomics, which includes parallel reaction monitoring (PRM), is typically utilized for more precise detection and quantitation of key proteins and/or pathways derived from complex discovery proteomics datasets. Initial discovery-based analysis using data independent acquisition (DIA) can obtain deep proteome coverage with low data missingness while targeted PRM assays can provide additional benefits in further eliminating missing data and optimizing measurement precision. However, PRM method development from bioinformatic predictions can be tedious and time-consuming because of the DIA output complexity. We address this limitation with a Python script that rapidly generates a PRM method for the TIMS-TOF platform using DIA data and a user-defined target list. To evaluate the script, DIA data obtained from HeLa cell lysate (200 ng, 45-min gradient method) as well as canonical pathway information from Ingenuity Pathway Analysis was utilized to generate a pathway-driven PRM method. Subsequent PRM analysis of targets within the example pathway, regulation of apoptosis, resulted in improved chromatographic data and enhanced quantitation precision (100% peptides below 10% CV with a median CV of 2.9%, n = 3 technical replicates). The script is freely available at https://github.com/StevensOmicsLab/PRM-script and provides a framework that can be adapted to multiple DDA/DIA data outputs and instrument-specific PRM method types.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142131400","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Top-down mass spectrometry analysis of capsid proteins of recombinant adeno-associated virus using multiple ion activations and proton transfer charge reduction. 利用多重离子活化和质子转移电荷还原对重组腺相关病毒的囊膜蛋白进行自上而下的质谱分析。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-09-05 DOI: 10.1002/pmic.202400223

Jake T Kline, Jingjing Huang, Linda B Lieu, Kristina Srzentić, David Bergen, Christopher Mullen, Graeme C McAlister, Kenneth R Durbin, Rafael D Melani, Luca Fornelli

{"title":"Top-down mass spectrometry analysis of capsid proteins of recombinant adeno-associated virus using multiple ion activations and proton transfer charge reduction.","authors":"Jake T Kline, Jingjing Huang, Linda B Lieu, Kristina Srzentić, David Bergen, Christopher Mullen, Graeme C McAlister, Kenneth R Durbin, Rafael D Melani, Luca Fornelli","doi":"10.1002/pmic.202400223","DOIUrl":"10.1002/pmic.202400223","url":null,"abstract":"Adeno-associated viruses (AAVs) are common vectors for emerging gene therapies due to their lack of pathogenicity in humans. Here, we present our investigation of the viral proteins (i.e., VP1, VP2, and VP3) of the capsid of AAVs via top-down mass spectrometry (MS). These proteins, ranging from 59 to 81 kDa, were chromatographically separated using hydrophilic interaction liquid chromatography and characterized in the gas-phase by high-resolution Orbitrap Fourier transform MS. Complementary ion dissociation methods were utilized to improve the overall sequence coverage. By reducing the overlap of product ion signals via proton transfer charge reduction on the Orbitrap Ascend BioPharma Tribrid mass spectrometer, the sequence coverage of each VP was significantly increased, reaching up to ∼40% in the case of VP3. These results showcase the improvements in the sequencing of proteins >30 kDa that can be achieved by manipulating product ions via gas-phase reactions to obtain easy-to-interpret fragmentation mass spectra.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e2400223"},"PeriodicalIF":3.4,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142131401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Editorial Board: Proteomics 17'24 编辑委员会：蛋白质组学 17'24

IF 3.4 4区生物学

Proteomics Pub Date : 2024-09-04 DOI: 10.1002/pmic.202470132

引用次数: 0

Standard abbreviations 标准缩略语

IF 3.4 4区生物学

Proteomics Pub Date : 2024-09-04 DOI: 10.1002/pmic.202470134

引用次数: 0

Contents: Proteomics 17'24 内容：蛋白质组学 17'24

IF 3.4 4区生物学

Proteomics Pub Date : 2024-09-04 DOI: 10.1002/pmic.202470133

引用次数: 0

The role of protein corona in advancing plasma proteomics 蛋白质电晕在推进血浆蛋白质组学方面的作用。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-09-02 DOI: 10.1002/pmic.202400028

Amir Ata Saei, Liangliang Sun, Morteza Mahmoudi

{"title":"The role of protein corona in advancing plasma proteomics","authors":"Amir Ata Saei, Liangliang Sun, Morteza Mahmoudi","doi":"10.1002/pmic.202400028","DOIUrl":"10.1002/pmic.202400028","url":null,"abstract":"The protein corona, a layer of biomolecules forming around nanoparticles in biological environments, critically influences nanoparticle interactions with biosystems, affecting pharmacokinetics and biological outcomes. Initially, the protein corona presented challenges for nanomedicine and nanotoxicology, such as nutrient depletion in cell cultures and masking of nanoparticle-targeting species. However, recent advancements have highlighted its potential in environmental toxicity, proteomics, and immunology. This viewpoint focuses on leveraging the protein corona to enhance the depth of plasma proteome analysis, addressing challenges posed by the high dynamic range of protein concentrations in plasma. The protein corona simplifies sample preparation, enriches low-abundance proteins, and improves proteome coverage. Innovations include using diverse nanoparticles and spiking small molecules to increase the number of quantified proteins. Reproducibility issues across core facilities necessitate standardized protocols. Moreover, top-down proteomics enables proteoform-specific measurements, providing deeper insights into protein corona composition. Future research should aim at improving top-down proteomics techniques and integrating protein corona studies and proteomics for personalized medicine and advanced diagnostics.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 1-2","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11735278/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142102726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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