Proteomics最新文献_第8页

Differential effects of physiological agonists on the proteome of platelet-derived extracellular vesicles 生理激动剂对血小板源性细胞外囊泡蛋白质组的不同影响。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-08-15 DOI: 10.1002/pmic.202400090

Clemens Gutmann, Manuel Mayr

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RETRACTION: Evaluation of Proteome Dynamics: Implications for Statistical Confidence in Mass Spectrometric Determination 返回：蛋白质组动态评估：对质谱测定的统计置信度的影响。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-08-15 DOI: 10.1002/pmic.202470135

{"title":"RETRACTION: Evaluation of Proteome Dynamics: Implications for Statistical Confidence in Mass Spectrometric Determination","authors":"","doi":"10.1002/pmic.202470135","DOIUrl":"10.1002/pmic.202470135","url":null,"abstract":"RETRACTION: I. Popova, E. Savelyeva, T. Degtyarevskaya, D. Babaskin, and A. Vokhmintsev, “Evaluation of Proteome Dynamics: Implications for Statistical Confidence in Mass Spectrometric Determination,” Proteomics 24, no. 14 (2024): 2300351, https://doi.org/10.1002/pmic.202300351.The above article, published online on 03 May 2024 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal Editor-in-Chief, Lucie Kalvodova; and Wiley-VCH GmbH. The retraction has been agreed due to a major unattributed overlap between the figures and figure legends of this article (Figures 2–7) and another article previously published elsewhere by a different group of authors [1]. Such publishing practice is against the journal's policy and Wiley's Best Practice Guidelines on Research Integrity and Publishing Ethics. The co-authors, I. Popova, T. Degtyarevskaya, D. Babaskin, and A. Vokhmintsev stated that they did not participate in the writing and submission of the article and gave no consent for publication. E. Savelyeva remained unresponsive.REFERENCES1. H. Boekweg, A. J. Guise, E. D. Plowey, R. T. Kelly, and S. Payne, “Calculating Sample Size Requirements for Temporal Dynamics in Single-Cell Proteomics,” Molecular & Cellular Proteomics 20, (2021): 100085, https://doi.org/10.1016/j.mcpro.2021.100085.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 17","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202470135","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987014","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}

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RETRACTION: Elevated GAPDH expression is associated with the proliferation and invasion of lung and esophageal squamous cell carcinomas 检索：GAPDH 表达升高与肺癌和食管鳞状细胞癌的增殖和侵袭有关。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-08-15 DOI: 10.1002/pmic.202470125

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Standard abbreviations 标准缩写。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-08-15 DOI: 10.1002/pmic.202470124

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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

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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":"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":"24 19","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202300491","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Diabetic retinopathy from the vitreous proteome perspective: The INSC94Y 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":"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":"24 20","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202300591","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":"OA","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

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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

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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":"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":"24 23-24","pages":""},"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}

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