Proteomics最新文献_第2页

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":"https://doi.org/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":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Automated multiplexed affinity-based enrichment of peptides for LC-MS/MS plasma proteomics. 用于 LC-MS/MS 血浆蛋白质组学的基于亲和力的多肽自动复用富集。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-08-27 DOI: 10.1002/pmic.202400049

Sergio Mosquim Junior, Fredrik Levander

{"title":"Automated multiplexed affinity-based enrichment of peptides for LC-MS/MS plasma proteomics.","authors":"Sergio Mosquim Junior, Fredrik Levander","doi":"10.1002/pmic.202400049","DOIUrl":"https://doi.org/10.1002/pmic.202400049","url":null,"abstract":"Plasma proteomics offers high potential for biomarker discovery, as plasma is collected through a minimally invasive procedure and constitutes the most complex human-derived proteome. However, the wide dynamic range poses a significant challenge. Here, we propose a semi-automated method based on the use of multiple single chain variable fragment antibodies, each enriching for peptides found in up to a few hundred proteins. This approach allows for the analysis of a complementary fraction compared to full proteome analysis. Proteins from pooled plasma were extracted and digested before testing the performance of 29 different antibodies with the aim of reproducibly maximizing peptide enrichment. Our results demonstrate the enrichment of 3662 peptides not detected in neat plasma or negative controls. Moreover, most antibodies were able to enrich for at least 155 peptides across different levels of abundance in plasma. To further reduce analysis time, a combination of antibodies was used in a multiplexed setting. Repeated sample analyses showed low coefficients of variation, and the method is flexible in terms of affinity binders. It does not impose drastic increases in instrument time, thus showing excellent potential for usage in large scale discovery projects.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142078670","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 16'24 编辑委员会：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.202470122

引用次数: 0

On the PhyloQuant protein expression profiles approach to the taxonomic problem 用 PhyloQuant 蛋白表达谱方法解决分类问题。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-08-15 DOI: 10.1002/pmic.202400117

Ayixon Sánchez Reyes, Cesar Ayala-Ruan

{"title":"On the PhyloQuant protein expression profiles approach to the taxonomic problem","authors":"Ayixon Sánchez Reyes, Cesar Ayala-Ruan","doi":"10.1002/pmic.202400117","DOIUrl":"10.1002/pmic.202400117","url":null,"abstract":"Inferring evolutionary relationships among organisms has been a fundamental problem in evolutionary biology. The current phylogenetic molecular methods serve as the baseline model to test new evolutionary hypotheses with taxonomic purposes. Leishmaniinae trypanosomatids subfamily includes protozoan parasites of clinical importance to humans. They have an intricate taxonomic history defined by morphological elements, host range, and molecular phylogenies. Unraveling the increasing diversity of this group has shown limitations in reconstructing the true evolutionary relationships among Trypanosomatidae species. Toward the goal of inferring evolutionary relationships that help to resolve phylogenetic and taxonomic controversies among parasites of the subfamily Leishmaniinae, Mule et al. propose the method PhyloQuant as a valuable approach, based on differential protein expression obtained from high throughput mass spectrometry data. Employing a pioneering methodological approach, Mule et al. assess the taxonomic problem for species hypothesis within Leishmaniinae, from quantitative phenetic protein expression profiles, in contrast to the standard multilocus phylogenetic approaches.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202400117","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987016","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

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

引用次数: 0

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

引用次数: 0

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

引用次数: 0

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":null,"pages":null},"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}

引用次数: 0