Proteomics最新文献_第3页

Contents: Proteomics 16'24 内容：蛋白质组学 16'24

IF 3.4 4区生物学

Proteomics Pub Date : 2024-08-15 DOI: 10.1002/pmic.202470123

引用次数: 0

TermineR: Extracting information on endogenous proteolytic processing from shotgun proteomics data. TermineR：从枪弹蛋白质组学数据中提取内源性蛋白质分解处理信息。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-08-10 DOI: 10.1002/pmic.202300491

Miguel Cosenza-Contreras, Adrianna Seredynska, Daniel Vogele, Niko Pinter, Eva Brombacher, Ruth Fiestas Cueto, Thien-Ly Julia Dinh, Patrick Bernhard, Manuel Rogg, Junwei Liu, Patrick Willems, Simon Stael, Pitter F Huesgen, E Wolfgang Kuehn, Clemens Kreutz, Christoph Schell, Oliver Schilling

{"title":"TermineR: Extracting information on endogenous proteolytic processing from shotgun proteomics data.","authors":"Miguel Cosenza-Contreras, Adrianna Seredynska, Daniel Vogele, Niko Pinter, Eva Brombacher, Ruth Fiestas Cueto, Thien-Ly Julia Dinh, Patrick Bernhard, Manuel Rogg, Junwei Liu, Patrick Willems, Simon Stael, Pitter F Huesgen, E Wolfgang Kuehn, Clemens Kreutz, Christoph Schell, Oliver Schilling","doi":"10.1002/pmic.202300491","DOIUrl":"https://doi.org/10.1002/pmic.202300491","url":null,"abstract":"State-of-the-art mass spectrometers combined with modern bioinformatics algorithms for peptide-to-spectrum matching (PSM) with robust statistical scoring allow for more variable features (i.e., post-translational modifications) being reliably identified from (tandem-) mass spectrometry data, often without the need for biochemical enrichment. Semi-specific proteome searches, that enforce a theoretical enzymatic digestion to solely the N- or C-terminal end, allow to identify of native protein termini or those arising from endogenous proteolytic activity (also referred to as \"neo-N-termini\" analysis or \"N-terminomics\"). Nevertheless, deriving biological meaning from these search outputs can be challenging in terms of data mining and analysis. Thus, we introduce TermineR, a data analysis approach for the (1) annotation of peptides according to their enzymatic cleavage specificity and known protein processing features, (2) differential abundance and enrichment analysis of N-terminal sequence patterns, and (3) visualization of neo-N-termini location. We illustrate the use of TermineR by applying it to tandem mass tag (TMT)-based proteomics data of a mouse model of polycystic kidney disease, and assess the semi-specific searches for biological interpretation of cleavage events and the variable contribution of proteolytic products to general protein abundance. The TermineR approach and example data are available as an R package at https://github.com/MiguelCos/TermineR.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141910947","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

Diabetic retinopathy from the vitreous proteome perspective: The INS^C94Y transgenic pig model study. 从玻璃体蛋白质组的角度看糖尿病视网膜病变：INSC94Y 转基因猪模型研究。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-08-09 DOI: 10.1002/pmic.202300591

Roxane L Degroote, Adrian Schmalen, Simone Renner, Eckhard Wolf, Stefanie M Hauck, Cornelia A Deeg

{"title":"Diabetic retinopathy from the vitreous proteome perspective: The INSC94Y transgenic pig model study.","authors":"Roxane L Degroote, Adrian Schmalen, Simone Renner, Eckhard Wolf, Stefanie M Hauck, Cornelia A Deeg","doi":"10.1002/pmic.202300591","DOIUrl":"https://doi.org/10.1002/pmic.202300591","url":null,"abstract":"INSC94Y transgenic pigs represent a model for mutant insulin gene-induced diabetes of youth, with impaired insulin secretion and beta cell loss, leading to elevated fasting blood glucose levels. A key complication of diabetes mellitus is diabetic retinopathy (DR), characterized by hyperglycemia-induced abnormalities in the retina. Adjacent to the retina lies the vitreous, a gelatinous matrix vital for ocular function. It harbors proteins and signaling molecules, offering insights into vitreous biology and ocular health. Moreover, as a reservoir for secreted molecules, the vitreous illuminates molecular processes within intraocular structures, especially under pathological conditions. To uncover the proteomic profile of porcine vitreous and explore its relevance to DR, we employed discovery proteomics to compare vitreous samples from INSC94Y transgenic pigs and wild-type controls. Our analysis identified 1404 proteins, with 266 showing differential abundance in INSC94Y vitreous. Notably, the abundances of ITGB1, COX2, and GRIFIN were significantly elevated in INSC94Y vitreous. Gene Set Enrichment Analysis unveiled heightened MYC and mTORC1 signaling in INSC94Y vitreous, shedding light on its biological significance in diabetes-associated ocular pathophysiology. These findings deepen our understanding of vitreous involvement in DR and provide valuable insights into potential therapeutic targets. Raw data are accessible via ProteomeXchange (PXD038198).","PeriodicalId":224,"journal":{"name":"Proteomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141910946","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

Contents: Proteomics 15'24 内容：蛋白质组学 15'24

IF 3.4 4区生物学

Proteomics Pub Date : 2024-08-02 DOI: 10.1002/pmic.202470113

引用次数: 0

Editorial Board: Proteomics 15'24 编辑委员会：蛋白质组学 15'24

IF 3.4 4区生物学

Proteomics Pub Date : 2024-08-02 DOI: 10.1002/pmic.202470112

引用次数: 0

Deep phosphotyrosine characterisation of primary murine T cells using broad spectrum optimisation of selective triggering. 利用选择性触发的广谱优化技术深入分析原代小鼠 T 细胞的磷酸酪氨酸特征。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-08-01 DOI: 10.1002/pmic.202400106

Aurora Callahan, Xien Yu Chua, Alijah A Griffith, Tobias Hildebrandt, Guoping Fu, Mengzhou Hu, Renren Wen, Arthur R Salomon

{"title":"Deep phosphotyrosine characterisation of primary murine T cells using broad spectrum optimisation of selective triggering.","authors":"Aurora Callahan, Xien Yu Chua, Alijah A Griffith, Tobias Hildebrandt, Guoping Fu, Mengzhou Hu, Renren Wen, Arthur R Salomon","doi":"10.1002/pmic.202400106","DOIUrl":"https://doi.org/10.1002/pmic.202400106","url":null,"abstract":"Sequencing the tyrosine phosphoproteome using MS-based proteomics is challenging due to the low abundance of tyrosine phosphorylation in cells, a challenge compounded in scarce samples like primary cells or clinical samples. The broad-spectrum optimisation of selective triggering (BOOST) method was recently developed to increase phosphotyrosine sequencing in low protein input samples by leveraging tandem mass tags (TMT), phosphotyrosine enrichment, and a phosphotyrosine-loaded carrier channel. Here, we demonstrate the viability of BOOST in T cell receptor (TCR)-stimulated primary murine T cells by benchmarking the accuracy and precision of the BOOST method and discerning significant alterations in the phosphoproteome associated with receptor stimulation. Using 1 mg of protein input (about 20 million cells) and BOOST, we identify and precisely quantify more than 2000 unique pY sites compared to about 300 unique pY sites in non-BOOST control samples. We show that although replicate variation increases when using the BOOST method, BOOST does not jeopardise quantitative precision or the ability to determine statistical significance for peptides measured in triplicate. Many pY previously uncharacterised sites on important T cell signalling proteins are quantified using BOOST, and we identify new TCR responsive pY sites observable only with BOOST. Finally, we determine that the phase-spectrum deconvolution method on Orbitrap instruments can impair pY quantitation in BOOST experiments.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141873751","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

Data acquisition approaches for single cell proteomics. 单细胞蛋白质组学的数据采集方法。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-08-01 DOI: 10.1002/pmic.202400022

Gautam Ghosh, Ariana E Shannon, Brian C Searle

引用次数: 0

Integration of metagenomics and metaproteomics in the intestinal lavage fluids benefits construction of discriminative model and discovery of biomarkers for HBV liver diseases. 整合肠道灌洗液中的元基因组学和元蛋白组学有利于构建鉴别模型和发现 HBV 肝病的生物标记物。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-07-23 DOI: 10.1002/pmic.202400002

Hongkai Xu, Jiangguo Zhang, Fang Wang, Yiyang Chen, Hao Chen, Yang Feng, Guixue Hou, Jin Zi, Meiping Zhang, Jinfeng Zhou, Le Deng, Liang Lin, Xiaoyin Zhang, Siqi Liu

{"title":"Integration of metagenomics and metaproteomics in the intestinal lavage fluids benefits construction of discriminative model and discovery of biomarkers for HBV liver diseases.","authors":"Hongkai Xu, Jiangguo Zhang, Fang Wang, Yiyang Chen, Hao Chen, Yang Feng, Guixue Hou, Jin Zi, Meiping Zhang, Jinfeng Zhou, Le Deng, Liang Lin, Xiaoyin Zhang, Siqi Liu","doi":"10.1002/pmic.202400002","DOIUrl":"https://doi.org/10.1002/pmic.202400002","url":null,"abstract":"Intestinal lavage fluid (IVF) containing the mucosa-associated microbiota instead of fecal samples was used to study the gut microbiota using different omics approaches. Focusing on the 63 IVF samples collected from healthy and hepatitis B virus-liver disease (HBV-LD), a question is prompted whether omics features could be extracted to distinguish these samples. The IVF-related microbiota derived from the omics data was classified into two enterotype sets, whereas the genomics-based enterotypes were poorly overlapped with the proteomics-based one in either distribution of microbiota or of IVFs. There is lack of molecular features in these enterotypes to specifically recognize healthy or HBV-LD. Running machine learning against the omics data sought the appropriate models to discriminate the healthy and HBV-LD IVFs based on selected genes or proteins. Although a single omics dataset is basically workable in such discrimination, integration of the two datasets enhances discrimination efficiency. The protein features with higher frequencies in the models are further compared between healthy and HBV-LD based on their abundance, bringing about three potential protein biomarkers. This study highlights that integration of metaomics data is beneficial for a molecular discriminator of healthy and HBV-LD, and reveals the IVF samples are valuable for microbiome in a small cohort.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141750689","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

Whole proteome analysis of germinating and outgrowing Bacillus subtilis 168 发芽和生长期枯草芽孢杆菌 168 的全蛋白质组分析。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-07-23 DOI: 10.1002/pmic.202400031

Jiří Pospíšil, Alice Sax, Martin Hubálek, Libor Krásný, Jiří Vohradský

引用次数: 0

Combining SDS-PAGE to capillary zone electrophoresis-tandem mass spectrometry for high-resolution top-down proteomics analysis of intact histone proteoforms 将 SDS-PAGE 与毛细管区带电泳-串联质谱相结合，对完整的组蛋白蛋白形式进行高分辨率自上而下的蛋白质组学分析。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-07-17 DOI: 10.1002/pmic.202300650

Fei Fang, Guangyao Gao, Qianyi Wang, Qianjie Wang, Liangliang Sun

{"title":"Combining SDS-PAGE to capillary zone electrophoresis-tandem mass spectrometry for high-resolution top-down proteomics analysis of intact histone proteoforms","authors":"Fei Fang, Guangyao Gao, Qianyi Wang, Qianjie Wang, Liangliang Sun","doi":"10.1002/pmic.202300650","DOIUrl":"10.1002/pmic.202300650","url":null,"abstract":"Mass spectrometry (MS)-based top-down proteomics (TDP) analysis of histone proteoforms provides critical information about combinatorial post-translational modifications (PTMs), which is vital for pursuing a better understanding of epigenetic regulation of gene expression. It requires high-resolution separations of histone proteoforms before MS and tandem MS (MS/MS) analysis. In this work, for the first time, we combined SDS-PAGE-based protein fractionation (passively eluting proteins from polyacrylamide gels as intact species for mass spectrometry, PEPPI-MS) with capillary zone electrophoresis (CZE)-MS/MS for high-resolution characterization of histone proteoforms. We systematically studied the histone proteoform extraction from SDS-PAGE gel and follow-up cleanup as well as CZE-MS/MS, to determine an optimal procedure. The optimal procedure showed reproducible and high-resolution separation and characterization of histone proteoforms. SDS-PAGE separated histone proteins (H1, H2, H3, and H4) based on their molecular weight and CZE provided additional separations of proteoforms of each histone protein based on their electrophoretic mobility, which was affected by PTMs, for example, acetylation and phosphorylation. Using the technique, we identified over 200 histone proteoforms from a commercial calf thymus histone sample with good reproducibility. The orthogonal and high-resolution separations of SDS-PAGE and CZE made our technique attractive for the delineation of histone proteoforms extracted from complex biological systems.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202300650","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141632126","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