Journal of Proteome Research最新文献_第8页

Proteomic Characterization of Urinary Exosomes with Pancreatic Cancer by Phosphatidylserine Imprinted Polymer Enrichment and Mass Spectrometry Analysis. 通过磷脂酰丝氨酸印迹聚合物富集和质谱分析确定胰腺癌患者尿液外泌体的蛋白质组特征

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-10-11 DOI: 10.1021/acs.jproteome.4c00508

Xianhui Cheng, Wenjing Yu, Yuanyuan Liu, Shengnan Jia, Dongxue Wang, Lianghai Hu

{"title":"Proteomic Characterization of Urinary Exosomes with Pancreatic Cancer by Phosphatidylserine Imprinted Polymer Enrichment and Mass Spectrometry Analysis.","authors":"Xianhui Cheng, Wenjing Yu, Yuanyuan Liu, Shengnan Jia, Dongxue Wang, Lianghai Hu","doi":"10.1021/acs.jproteome.4c00508","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00508","url":null,"abstract":"Exosomes, as carriers of cell-to-cell communication, can serve as promising biomarkers for probing the early diagnosis of cancer. Pancreatic cancer is a common malignant tumor of the pancreas with an insidious onset and difficult early diagnosis. The aim of this study was to capture exosomes in urine samples by phosphatidylserine-molecularly imprinted polymers (PS-MIPs). Transmission electron microscopy and nanoparticle tracking analysis as well as Western blot showed that our molecularly imprinted material can effectively capture urinary exosomes. Three parallel tests verified the reproducibility of the mass spectrometry assay and the stability of the material capture efficiency. Mass Spectrometry with nontargeted proteomics was combined to show differentially expressed proteins in exosomes between 5 pancreatic cancer patients and 5 healthy controls. The most significant changes in the proteomic profile in pancreatic cancer patients compared to healthy controls were the overexpression of SLC9A3R1, SPAG9, and ferritin light chain (FTL) These proteins may have an important role in diagnosis and prognostic assessment, supporting further scientific and clinical studies on pancreatic cancer.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142398632","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

Clean and Complete Protein Digestion with an Autolysis Resistant Trypsin for Peptide Mapping 使用抗自溶胰蛋白酶进行干净彻底的蛋白质消化，以绘制肽图谱

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-10-11 DOI: 10.1021/acs.jproteome.4c0059810.1021/acs.jproteome.4c00598

Beatrice Muriithi*, Samantha Ippoliti, Abraham Finny, Balasubrahmanyam Addepalli and Matthew Lauber,

{"title":"Clean and Complete Protein Digestion with an Autolysis Resistant Trypsin for Peptide Mapping","authors":"Beatrice Muriithi*, Samantha Ippoliti, Abraham Finny, Balasubrahmanyam Addepalli and Matthew Lauber, ","doi":"10.1021/acs.jproteome.4c0059810.1021/acs.jproteome.4c00598","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00598https://doi.org/10.1021/acs.jproteome.4c00598","url":null,"abstract":"Peptide mapping requires cleavage of proteins in a predictable fashion so that target protein-specific peptides can be reliably identified and quantified. Trypsin, a commonly used protease in this process, can also undergo self-cleavage or autolysis, thereby reducing the effectivity and even cleavage specificity at lysine and arginine residues. Here, we report highly efficient and reproducible peptide mapping of biotherapeutic monoclonal antibodies. We highlight the properties of a homogeneous chemically modified trypsin on thermal stability, a 54% increase in melting temperature with an 84% increase in energy required for unfolding, an indication of more thermally stable trypsin, >90% retained intact mass peak area after exposure to digestion conditions confirming autolysis resistance, 10× more intensity for intact enzyme compared to trypsin of similar source and narrower molecular weight distribution with LC-MS indicative of low degradation compared to 3 other types of trypsin. Finally, we show the utility of this autolysis-resistant trypsin in characterizing biotherapeutic monoclonal antibodies consistently and reliably showing a >30% reduction in missed cleavage for a short-duration protein digestion time of 30 min compared to heterogeneously modified trypsin of a similar source.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jproteome.4c00598","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142571003","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

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

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-10-09 DOI: 10.1021/acs.jproteome.4c0068110.1021/acs.jproteome.4c00681

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

{"title":"In-Depth Proteomic Analysis Reveals Phenotypic Diversity of Macrophages in Liver Fibrosis","authors":"Wenting Yang, Liling Chen, Jian Zhang, Chenyi Qiu, Wenhao Hou, Xiangye Zhang, Bin Fu, Dianyuan Zhao, Huan Wang, Di Liu, Fang Yan, Wantao Ying* and Li Tang*, ","doi":"10.1021/acs.jproteome.4c0068110.1021/acs.jproteome.4c00681","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00681https://doi.org/10.1021/acs.jproteome.4c00681","url":null,"abstract":"Macrophages make up a heterogeneous population of immune cells that exhibit diverse phenotypes and functions in health and disease. Although macrophage epigenomic and transcriptomic profiles have been reported, the proteomes of distinct macrophage populations under various pathological conditions remain largely elusive. Here, we employed a label-free proteomic approach to characterize the diversity of the hepatic macrophage pool in an experimental model of CCl4-induced liver fibrosis. We found a decrease in the proportion of liver resident embryo-derived KCs (EmKCs), and a drastic increase in the proportion of monocyte-derived KCs (MoKCs) and CLEC2–Macs. Proteomic profiling revealed that MoKCs largely resembled EmKCs, whereas CLEC2–Macs exhibited greater proteomic alternations compared with EmKCs, suggesting two distinct destinations for monocyte differentiation during liver fibrosis. Furthermore, CLEC2–Macs were characterized by increased expression of proteins associated with inflammatory response, antigen processing and presentation processes, which may be involved in the pathogenesis of liver fibrosis. Collectively, our study provides insights into the considerable heterogeneity within the hepatic macrophage pool during liver fibrosis.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142560420","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

Deep Proteome Analysis of Cerebrospinal Fluid from Pediatric Patients with Central Nervous System Cancer 儿科中枢神经系统癌症患者脑脊液的深度蛋白质组分析

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-10-09 DOI: 10.1021/acs.jproteome.4c0047110.1021/acs.jproteome.4c00471

Christian Mirian, Ole Østergaard, Maria Thastrup, Signe Modvig, Jon Foss-Skiftesvik, Jane Skjøth-Rasmussen, Marianne Berntsen, Josefine Britze, Alex Christian Yde Nielsen, René Mathiasen, Kjeld Schmiegelow and Jesper Velgaard Olsen*,

{"title":"Deep Proteome Analysis of Cerebrospinal Fluid from Pediatric Patients with Central Nervous System Cancer","authors":"Christian Mirian, Ole Østergaard, Maria Thastrup, Signe Modvig, Jon Foss-Skiftesvik, Jane Skjøth-Rasmussen, Marianne Berntsen, Josefine Britze, Alex Christian Yde Nielsen, René Mathiasen, Kjeld Schmiegelow and Jesper Velgaard Olsen*, ","doi":"10.1021/acs.jproteome.4c0047110.1021/acs.jproteome.4c00471","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00471https://doi.org/10.1021/acs.jproteome.4c00471","url":null,"abstract":"The cerebrospinal fluid (CSF) is a key matrix for discovery of biomarkers relevant for prognosis and the development of therapeutic targets in pediatric central nervous system malignancies. However, the wide range of protein concentrations and age-related differences in children makes such discoveries challenging. In addition, pediatric CSF samples are often sparse and first prioritized for clinical purposes. The present work focused on optimizing each step of the proteome analysis workflow to extract the most detailed proteome information possible from the limited CSF resources available for research purposes. The strategy included applying sequential ultracentrifugation to enrich for extracellular vesicles (EV) in addition to analysis of a small volume of raw CSF, which allowed quantification of 1351 proteins (+55% relative to raw CSF) from 400 μL CSF. When including a spectral library, a total of 2103 proteins (+240%) could be quantified. The workflow was optimized for CSF input volume, tryptic digestion method, gradient length, mass spectrometry data acquisition method and database search strategy to quantify as many proteins a possible. The fully optimized workflow included protein aggregation capture (PAC) digestion, paired with data-independent acquisition (DIA, 21 min gradient) and allowed 2989 unique proteins to be quantified from only 400 μL CSF, which is a 340% increase in proteins compared to analysis of a tryptic digest of raw CSF.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jproteome.4c00471","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142560419","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

Carrier-Guided Proteome Analysis in a High Protein Background: An Improved Approach to Host Cell Protein Identification 高蛋白背景下的载体引导蛋白质组分析：宿主细胞蛋白质鉴定的改进方法

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-10-09 DOI: 10.1021/acs.jproteome.4c0015810.1021/acs.jproteome.4c00158

Divyanshi Karmani, Niloofar Seifihesar, Mukhayyo Sultonova, Beau Blackmore, Joao A. Paulo, Matthew Harty and J. Patrick Murphy*,

{"title":"Carrier-Guided Proteome Analysis in a High Protein Background: An Improved Approach to Host Cell Protein Identification","authors":"Divyanshi Karmani, Niloofar Seifihesar, Mukhayyo Sultonova, Beau Blackmore, Joao A. Paulo, Matthew Harty and J. Patrick Murphy*, ","doi":"10.1021/acs.jproteome.4c0015810.1021/acs.jproteome.4c00158","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00158https://doi.org/10.1021/acs.jproteome.4c00158","url":null,"abstract":"Many shotgun proteomics experiments are negatively influenced by highly abundant proteins, such as those measuring residual host cell proteins (HCP) amidst highly abundant recombinant biotherapeutic or plasma proteins amidst albumin and immunoglobulins. While western blotting and ELISAs can reveal the presence of specific low abundance proteins from highly abundant background proteins, mass spectrometry approaches are required to define the low abundance protein composition in these scenarios. The challenge in detecting low abundance proteins in a high protein background by standard shotgun approaches is that spectra are often not triggered on their peptides in data dependent acquisition methods but rather on the highly abundant background peptides. Here, we use tandem mass tags (TMT) to introduce a carrier proteome approach to enhance the detection of proteins, such as from residual host cell proteomes amidst a highly abundant background. Using a mixture of bovine serum albumin (BSA) and E. coli as a mock high background/low abundance target protein formulation, we demonstrate proof-of-principle experiments allowing the improved detection of target proteins amidst a high protein background. While we observed significant coisolation interference, we mitigated it by using a spike-in interference detection TMT channel. Finally, we use the approach to identify 300 residual E. coli proteins from a protein A pulldown of a human IgG antibody, demonstrating that it may be applicable to analysis of HCPs in biotherapeutic protein formulations.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142560518","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

Achieving a 35-Plex Tandem Mass Tag Reagent Set through Deuterium Incorporation 通过氘结合实现 35 种复合串联质量标签试剂组合

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-10-09 DOI: 10.1021/acs.jproteome.4c0066810.1021/acs.jproteome.4c00668

Nathan R. Zuniga, Dustin C. Frost, Karsten Kuhn, Myungsun Shin, Rebecca L. Whitehouse, Ting-Yu Wei, Yuchen He, Shane L. Dawson, Ian Pike, Ryan D. Bomgarden, Steven P. Gygi* and Joao A. Paulo*,

{"title":"Achieving a 35-Plex Tandem Mass Tag Reagent Set through Deuterium Incorporation","authors":"Nathan R. Zuniga, Dustin C. Frost, Karsten Kuhn, Myungsun Shin, Rebecca L. Whitehouse, Ting-Yu Wei, Yuchen He, Shane L. Dawson, Ian Pike, Ryan D. Bomgarden, Steven P. Gygi* and Joao A. Paulo*, ","doi":"10.1021/acs.jproteome.4c0066810.1021/acs.jproteome.4c00668","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00668https://doi.org/10.1021/acs.jproteome.4c00668","url":null,"abstract":"Mass spectrometry-based sample multiplexing with isobaric tags permits the development of high-throughput and precise quantitative biological assays with proteome-wide coverage and minimal missing values. Here, we nearly doubled the multiplexing capability of the TMTpro reagent set to a 35-plex through the incorporation of one deuterium isotope into the reporter group. Substituting deuterium frequently results in suboptimal peak coelution, which can compromise the accuracy of reporter ion-based quantification. To counteract the deuterium effect on quantitation, we implemented a strategy that necessitated the segregation of nondeuterium and deuterium-containing channels into distinct subplexes during normalization procedures, with reassembly through a common bridge channel. This multiplexing strategy of “design independent sub-plexes but acquire together” (DISAT) was used to compare protein expression differences between human cell lines and in a cysteine-profiling (i.e., chemoproteomics) experiment to identify compounds binding to cysteine-113 of Pin1.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142560416","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

End-to-End Throughput Chemical Proteomics for Photoaffinity Labeling Target Engagement and Deconvolution 用于光亲和标记目标参与和解旋的端到端通量化学蛋白质组学

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-10-07 DOI: 10.1021/acs.jproteome.4c0044210.1021/acs.jproteome.4c00442

Sheldon T. Cheung*, Yongkang Kim, Ji-Hoon Cho, Kristoffer R. Brandvold, Brahma Ghosh, Amanda M. Del Rosario and Harris Bell-Temin*,

{"title":"End-to-End Throughput Chemical Proteomics for Photoaffinity Labeling Target Engagement and Deconvolution","authors":"Sheldon T. Cheung*, Yongkang Kim, Ji-Hoon Cho, Kristoffer R. Brandvold, Brahma Ghosh, Amanda M. Del Rosario and Harris Bell-Temin*, ","doi":"10.1021/acs.jproteome.4c0044210.1021/acs.jproteome.4c00442","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00442https://doi.org/10.1021/acs.jproteome.4c00442","url":null,"abstract":"Photoaffinity labeling (PAL) methodologies have proven to be instrumental for the unbiased deconvolution of protein–ligand binding events in physiologically relevant systems. However, like other chemical proteomic workflows, they are limited in many ways by time-intensive sample manipulations and data acquisition techniques. Here, we describe an approach to address this challenge through the innovation of a carboxylate bead-based protein cleanup procedure to remove excess small-molecule contaminants and couple it to plate-based, proteomic sample processing as a semiautomated solution. The analysis of samples via label-free, data-independent acquisition (DIA) techniques led to significant improvements on a workflow time per sample basis over current standard practices. Experiments utilizing three established PAL ligands with known targets, (+)-JQ-1, lenalidomide, and dasatinib, demonstrated the utility of having the flexibility to design experiments with a myriad of variables. Data revealed that this workflow can enable the confident identification and rank ordering of known and putative targets with outstanding protein signal-to-background enrichment sensitivity. This unified end-to-end throughput strategy for processing and analyzing these complex samples could greatly facilitate efficient drug discovery efforts and open up new opportunities in the chemical proteomics field.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142560418","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

Defining Alzheimer’s Disease through Proteomic CSF Profiling 通过脑脊液蛋白质组分析确定阿尔茨海默病

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-10-07 DOI: 10.1021/acs.jproteome.4c0059010.1021/acs.jproteome.4c00590

Carmen Peña-Bautista, Lourdes Álvarez-Sánchez, Ángel Balaguer, Luis Raga, Lorena García-Vallés, Miguel Baquero and Consuelo Cháfer-Pericás*,

{"title":"Defining Alzheimer’s Disease through Proteomic CSF Profiling","authors":"Carmen Peña-Bautista, Lourdes Álvarez-Sánchez, Ángel Balaguer, Luis Raga, Lorena García-Vallés, Miguel Baquero and Consuelo Cháfer-Pericás*, ","doi":"10.1021/acs.jproteome.4c0059010.1021/acs.jproteome.4c00590","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00590https://doi.org/10.1021/acs.jproteome.4c00590","url":null,"abstract":"Alzheimer disease (AD) is the main cause of dementia, and its complexity is not yet completely understood. Proteomic profiles can provide useful information to explore the pathways involved and the heterogeneity among AD patients. A proteomic analysis was performed in cerebrospinal fluid (CSF) samples from mild cognitive impairment due to AD (MCI-AD) and control individuals; both groups were classified by amyloid β42/amyloid β40 levels in CSF (data available in BioStudies database (S-BSST1456)). The analysis based on PLS regression and volcano plot identified 7 proteins (FOLR2, PPP3CA, SMOC2, STMN1, TAGLN3, TMEM132B, and UCHL1) mainly related to protein phosphorylation, structure maintenance, inflammation, and protein degradation. Enrichment analysis revealed the involvement of different biological processes related to neuronal mechanisms and synapses, lipid and carbohydrate metabolism, immune system and inflammation, vascular, hormones, and response to stimuli, and cell signaling and adhesion. In addition, the proteomic profile showed some association with the levels of AD biomarkers in CSF. Regarding the subtypes, two MCI-AD subgroups were identified: one could be related to synapsis and neuronal functions and the other to innate immunity. The study of the proteomic profile in the CSF of AD patients reflects the heterogeneity of biochemical pathways involved in AD.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142571031","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

Time-Resolved Multiomics Illustrates Host and Gut Microbe Interactions during Salmonella Infection 时间分辨多组学图解沙门氏菌感染过程中宿主与肠道微生物的相互作用

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-10-07 DOI: 10.1021/acs.jproteome.4c0017210.1021/acs.jproteome.4c00172

Yongseok Kim, Katherine Kokkinias, Anice Sabag-Daigle, Ikaia Leleiwi, Mikayla Borton, Michael Shaffer, Maryam Baniasad, Rebecca Daly, Brian M. M. Ahmer, Kelly C. Wrighton and Vicki H. Wysocki*,

{"title":"Time-Resolved Multiomics Illustrates Host and Gut Microbe Interactions during Salmonella Infection","authors":"Yongseok Kim, Katherine Kokkinias, Anice Sabag-Daigle, Ikaia Leleiwi, Mikayla Borton, Michael Shaffer, Maryam Baniasad, Rebecca Daly, Brian M. M. Ahmer, Kelly C. Wrighton and Vicki H. Wysocki*, ","doi":"10.1021/acs.jproteome.4c0017210.1021/acs.jproteome.4c00172","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00172https://doi.org/10.1021/acs.jproteome.4c00172","url":null,"abstract":"Salmonella infection, also known as Salmonellosis, is one of the most common food-borne illnesses. Salmonella infection can trigger host defensive functions, including an inflammatory response. The provoked-host inflammatory response has a significant impact on the bacterial population in the gut. In addition, Salmonella competes with other gut microorganisms for survival and growth within the host. Compositional and functional alterations in gut bacteria occur because of the host immunological response and competition between Salmonella and the gut microbiome. Host variation and the inherent complexity of the gut microbial community make understanding commensal and pathogen interactions particularly difficult during a Salmonella infection. Here, we present metabolomics and lipidomics analyses along with the 16S rRNA sequence analysis, revealing a comprehensive view of the metabolic interactions between the host and gut microbiota during Salmonella infection in a CBA/J mouse model. We found that different metabolic pathways were altered over the four investigated time points of Salmonella infection (days −2, +2, +6, and +13). Furthermore, metatranscriptomics analysis integrated with metabolomics and lipidomics analysis facilitated an understanding of the heterogeneous response of mice, depending on the degree of dysbiosis.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142560417","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

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

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-10-07 DOI: 10.1021/acs.jproteome.4c0018010.1021/acs.jproteome.4c00180

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

{"title":"DiDBiT-TMT: A Novel Method to Quantify Changes in the Proteomic Landscape Induced by Neural Plasticity","authors":"Mariam Gamaleldin, Nam-Kyung Yu, Jolene K Diedrich, Yuanhui Ma, Anne Wienand, Daniel B. McClatchy, Anders Nykjaer, Sadegh Nabavi* and John R. Yates III*, ","doi":"10.1021/acs.jproteome.4c0018010.1021/acs.jproteome.4c00180","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00180https://doi.org/10.1021/acs.jproteome.4c00180","url":null,"abstract":"Direct detection of biotinylated proteins (DiDBiT) is a proteomic method that can enrich and detect newly synthesized proteins (NSPs) labeled with bio-orthogonal amino acids with 20-fold improved detectability compared to conventional methods. However, DiDBiT has currently been used to compare only two conditions per experiment. Here, we present DiDBiT-TMT, a method that can be used to quantify NSPs across many conditions and replicates in the same experiment by combining isobaric tandem mass tagging (TMT) with DiDBiT. We applied DiDBiT-TMT to brain slices to determine changes in the de novo proteome that occur after inducing chemical long-term potentiation (cLTP) or treatment with the neuromodulator norepinephrine. We successfully demonstrated DiDBiT-TMT’s capacity to quantitatively compare up to 9 samples in parallel. We showed that there is a minimal overlap among NSPs that are differentially expressed in cLTP-treated organotypic brain slices, norepinephrine-treated organotypic brain slices, and organotypic slices undergoing combinatorial treatment with norepinephrine and cLTP. Our results point to the possible divergence of the molecular mechanisms underlying these treatments and showcase the applicability of DiDBiT-TMT for studying neurobiology.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142571108","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