Proteomics最新文献_第3页

Defining the Molecular Impacts of Humalite Application on Field-Grown Wheat (Triticum aestivum L.) Using Quantitative Proteomics 确定在大田小麦（Triticum aestivum L.）上施用腐殖石的分子效应使用定量蛋白质组学。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-06-23 DOI: 10.1002/pmic.13981

Lauren E. Grubb, Mohana Talasila, Linda Y. Gorim, Richard Glen Uhrig

{"title":"Defining the Molecular Impacts of Humalite Application on Field-Grown Wheat (Triticum aestivum L.) Using Quantitative Proteomics","authors":"Lauren E. Grubb, Mohana Talasila, Linda Y. Gorim, Richard Glen Uhrig","doi":"10.1002/pmic.13981","DOIUrl":"10.1002/pmic.13981","url":null,"abstract":"<p>Increasing global food production demands have resulted in increased fertilizer usage, causing detrimental environmental impacts. Biostimulants, such as humic substances, are currently being applied as a strategy to increase plant nutrient-use efficiency and minimize environmental impacts within cropping systems. One of these biostimulants is Humalite, which is a unique, naturally occurring coal-like substance found in deposits across southern Alberta. These deposits contain exceptionally high ratios of humic acids (>70%) and micronutrients due to their unique freshwater depositional environment. Humalite has begun to be applied to fields based on scientific data suggesting positive impacts on crop growth, yield, and nutrient usage; however, little is known about the underlying molecular mechanisms of Humalite. Here, as part of a larger field study, we report a quantitative proteomics approach to identify systems-level molecular changes induced by the addition of different Humalite application rates in field-grown wheat (<i>Triticum aestivum</i> L.) under three urea fertilizer application rates. In particular, we see wide-ranging abundance changes in proteins associated with several metabolic pathways and growth-related biological processes that suggest how Humalite modulates the plant molecular landscape. Overall, our results provide new, functional information that will help better inform agricultural producers on optimal biostimulant and fertilizer usage.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 14","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.13981","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144367638","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

Metaproteomic Dataset on Semi-Diurnal Variability of the Bacterioplankton Communities During a Spring Phytoplankton Bloom in the North Sea. 北海春季浮游植物繁殖期间浮游细菌群落半日变化的元蛋白质组学数据集。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-06-23 DOI: 10.1002/pmic.70001

Vaikhari Kale, Jürgen Bartel, Daniel Bartosik, Philip Berhard Lude, Chandni Sidhu, Hanno Teeling, Rudolf Amann, Thomas Schweder, Dörte Becher, Anke Trautwein-Schult

{"title":"Metaproteomic Dataset on Semi-Diurnal Variability of the Bacterioplankton Communities During a Spring Phytoplankton Bloom in the North Sea.","authors":"Vaikhari Kale, Jürgen Bartel, Daniel Bartosik, Philip Berhard Lude, Chandni Sidhu, Hanno Teeling, Rudolf Amann, Thomas Schweder, Dörte Becher, Anke Trautwein-Schult","doi":"10.1002/pmic.70001","DOIUrl":"https://doi.org/10.1002/pmic.70001","url":null,"abstract":"<p><p>Phytoplankton blooms create a substrate-rich environment that supports the growth of bacterial planktonic heterotrophs. Previously, we studied the dynamics of such bacterioplankton at a long-term ecological research site near the coast of Helgoland Island (North Sea) once a day. Here, we present a novel dataset (available under the PRIDE-ID: PXD055396) indicating significant differences at the protein level in a semi-diurnal analysis. Using metaproteomics, we studied changes in the free-living (0.2-3 µm) bacterial community that occurred between early (7 am) and late (9 pm) sampling over 3 days. The results highlight the sensitivity, robustness, and reproducibility of mass spectrometry-based metaproteomic analyses to assess changes in the activities of the bacterioplankton communities. Taxonomic analyses revealed significant changes in the abundance of 65 bacterial genera. Particularly, proteins from the flavobacterial genera Candidatus Prosiliicoccus and Aurantivirga were significantly more abundant in the late samples. This comprehensive dataset highlights semi-diurnal changes in bacterial community composition and metabolic activity during a phytoplankton bloom that would have remained undetected with a once-per-day sampling approach.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e70001"},"PeriodicalIF":3.4,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144367639","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

Sample Preparation for Multi-Omics Analysis: Considerations and Guidance for Identifying the Ideal Workflow. 多组学分析的样品制备：确定理想工作流程的考虑和指导。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-06-23 DOI: 10.1002/pmic.13983

Breyer Woodland, Luke A Farrell, Lana Brockbals, Maria Rezcallah, Aiden Brennan, Emily J Sunnucks, Sam T Gould, Aleksandra M Stanczak, Matthew B O'Rourke, Matthew P Padula

引用次数: 0

Detergent Screening With Hybrid Detergents Increases Observable Number of Protein Identities in Bottom-Up Proteomics. 混合洗涤剂筛选增加了自下而上蛋白质组学中可观察到的蛋白质特征数量。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-06-20 DOI: 10.1002/pmic.70003

Jan-Simon Behnke, Andreas Hentschel, Maximilian Wolf, Virginia Wycisk, Albert Sickmann, Robert S Heyer, Leonhard H Urner

{"title":"Detergent Screening With Hybrid Detergents Increases Observable Number of Protein Identities in Bottom-Up Proteomics.","authors":"Jan-Simon Behnke, Andreas Hentschel, Maximilian Wolf, Virginia Wycisk, Albert Sickmann, Robert S Heyer, Leonhard H Urner","doi":"10.1002/pmic.70003","DOIUrl":"10.1002/pmic.70003","url":null,"abstract":"<p><p>Detergents are key reagents in bottom-up proteomics that create an apparent, yet underappreciated bias on observable proteomes. Maximizing the chemical diversity of detergents in parallelized screens is supposed to maximize observable proteomes if proteomics data sets of different detergents are combined. The aim of our work is to investigate the potential of fusing ionic and nonionic detergent headgroups into hybrid detergents for increasing the observable number of unique protein identities. Our data indicate that the solubilizing properties of hybrid detergents do not reflect an average of canonical detergents. The number of unique protein identities obtainable from an Escherichia coli screen increases from 1604 to 2169 when proteomics data sets from sodium dodecyl sulfate, dodecyltrimethylammonium bromide, dendritic triglycerol detergent, and related hybrid detergents are combined. Our data highlight the utility of cationic detergents and related hybrid detergents for enhancing observable proteomes. Detergent screening-based proteome reconstructions with canonical detergents and hybrid detergents present an interesting research direction towards improved proteome profiling applications.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e70003"},"PeriodicalIF":3.4,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144332220","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

Advancements in Ion Mobility-Based Diagnostics for Infectious Diseases 基于离子迁移率的传染病诊断研究进展

IF 3.4 4区生物学

Proteomics Pub Date : 2025-06-11 DOI: 10.1002/pmic.13976

Kimberly Y. Kartowikromo, Jessica S. Pizzo, Iffat Jerin, Ahmed M. Hamid

{"title":"Advancements in Ion Mobility-Based Diagnostics for Infectious Diseases","authors":"Kimberly Y. Kartowikromo, Jessica S. Pizzo, Iffat Jerin, Ahmed M. Hamid","doi":"10.1002/pmic.13976","DOIUrl":"10.1002/pmic.13976","url":null,"abstract":"<div>\u0000 \u0000 <p>Infectious diseases remain a leading global health concern, requiring rapid, precise, and cost-effective diagnostic approaches. Traditional diagnostic methods, such as culture-based techniques, serological assays, and molecular diagnostics, often have sensitivity, specificity, and time efficiency limitations. The emergence of mass spectrometry (MS)-based technologies, particularly matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS, has revolutionized clinical microbiology by enabling rapid microbial identification. However, MALDI-TOF MS has limitations, such as its limited ability to differentiate closely related species and database constraints, necessitating the development of more advanced methodologies. Ion mobility (IM)-MS has emerged as a promising analytical tool that enhances pathogen identification by separating ions based on their size, mass, shape, and charge. IM-MS has demonstrated significant potential in clinical microbiology by improving the characterization of bacterial, viral, and fungal infections. This review discusses the significance of infectious disease diagnosis in public health and the impact of timely and accurate identification on treatment outcomes. In addition, it provides a comprehensive analysis of IM-MS, detailing its principles, integration with omics technologies and machine learning, and its applications in infectious disease diagnosis. The review also explores the advantages of IM-MS over conventional techniques, highlights key studies demonstrating its effectiveness, and discusses future perspectives for enhancing its role in clinical diagnostics, precision medicine, and public health surveillance.</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 14","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144264970","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

Validation and Community Sharing of Ocean Spectral Libraries Generated by Machine Learning for Data Independent Acquisition Ocean Metaproteomic Analyses 基于机器学习的数据独立获取海洋元蛋白质组学分析海洋光谱库的验证与社区共享。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-06-11 DOI: 10.1002/pmic.13971

Margaret Mars Brisbin, Matthew R. McIlvin, Damien Beau Wilburn, Jaclyn K. Saunders, Natalie R. Cohen, Maya Bhatia, Elizabeth Kujawinski, Brian C. Searle, Mak A. Saito

{"title":"Validation and Community Sharing of Ocean Spectral Libraries Generated by Machine Learning for Data Independent Acquisition Ocean Metaproteomic Analyses","authors":"Margaret Mars Brisbin, Matthew R. McIlvin, Damien Beau Wilburn, Jaclyn K. Saunders, Natalie R. Cohen, Maya Bhatia, Elizabeth Kujawinski, Brian C. Searle, Mak A. Saito","doi":"10.1002/pmic.13971","DOIUrl":"10.1002/pmic.13971","url":null,"abstract":"<div>\u0000 \u0000 <p>Ocean metaproteomics provides valuable insights into the structure and function of marine microbial communities. Yet, ocean samples are challenging due to their extensive biological diversity, which results in a very large number of peptides with a large dynamic range. This study characterized the capabilities of data independent acquisition (DIA) mode for use in ocean metaproteomic samples. Spectral libraries were constructed from discovered peptides and proteins using machine learning (ML) algorithms to remove the incorporation of false positives in the libraries. When compared with 1-dimensional and 2-dimensional data dependent acquisition analyses (DDA), DIA outperformed DDA both with and without gas phase fractionation. We found that larger discovered protein spectral libraries performed better, regardless of the geographic distance between where samples were collected for library generation and where the test samples were collected. Moreover, the spectral library containing all unique proteins present in the Ocean Protein Portal (OPP) outperformed smaller libraries generated from individual sampling campaigns. However, a spectral library constructed from all open reading frames (ORFs) in a metagenome was found to be too large to be workable, resulting in low peptide identifications due to challenges in maintaining a low false discovery rate with such a large database size. Given sufficient sequencing depth and validation studies, spectral libraries generated from previously discovered proteins can serve as a community resource, saving resequencing efforts. The spectral libraries generated in this study are available at the OPP to enable future ocean proteomic studies.</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 13","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144264971","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

Multi-Omics Identification of Extracellular Components of the Fetal Monkey and Human Neocortex 猴胎和人新皮层细胞外成分的多组学鉴定。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-06-09 DOI: 10.1002/pmic.202400385

Felipe Vilicich, Dhanya Vettiatil, Seth Kattapong-Graber, Nadiya Nawsheen, Neel Patel, Alexandra Quezada, Elizabeth Gurney, Emma Smith, Hallie N. Nelson, Susan Pesci, Jessica Atrio, Nadjeda Moreno, Aragorn Jones, Melinda Murphy, Nerys Benfield, Jon Hennebold, Nita Solanky, Steven Lisgo, Ian Glass, Birth Defects Research Laboratory (BDRL), Simone Sidoli

{"title":"Multi-Omics Identification of Extracellular Components of the Fetal Monkey and Human Neocortex","authors":"Felipe Vilicich, Dhanya Vettiatil, Seth Kattapong-Graber, Nadiya Nawsheen, Neel Patel, Alexandra Quezada, Elizabeth Gurney, Emma Smith, Hallie N. Nelson, Susan Pesci, Jessica Atrio, Nadjeda Moreno, Aragorn Jones, Melinda Murphy, Nerys Benfield, Jon Hennebold, Nita Solanky, Steven Lisgo, Ian Glass, Birth Defects Research Laboratory (BDRL), Simone Sidoli","doi":"10.1002/pmic.202400385","DOIUrl":"10.1002/pmic.202400385","url":null,"abstract":"<div>\u0000 \u0000 <p>During development, precursor cells are continuously and intimately interacting with their extracellular environment, which guides their ability to generate functional tissues and organs. Much is known about the development of the neocortex in mammals. This information has largely been derived from histological analyses, heterochronic cell transplants, and genetic manipulations in mice, and to a lesser extent from transcriptomic and histological analyses in humans. However, these approaches have not led to a characterization of the extracellular composition of the developing neocortex in any species. Here, using a combination of single-cell transcriptomic analyses from published datasets and our proteomics and immunohistofluorescence analyses, we provide a more comprehensive and unbiased picture of the early developing fetal neocortex in humans and non-human primates. Our findings provide a starting point for further hypothesis-driven studies on structural and signaling components in the developing cortex that had previously not been identified.</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 13","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144245396","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

Liquid Y2H-Seq, a Rapid and Data-Rich Alternative to Conventional Yeast Two-Hybrid Screening 液体Y2H-Seq，快速和数据丰富的替代传统酵母双杂交筛选。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-06-08 DOI: 10.1002/pmic.13970

Yanping Qi, Chunlei Zhang, Shan Yuan, Xin Xu, Shi Sun, Lixin Zhang, Luping Liu, Tingting Wu, Tianfu Han, Cunxiang Wu, Bingjun Jiang

引用次数: 0

A Survey of Annotated smORF-Encoded Polypeptides in Bacteria Interacting With Eukaryotic Hosts 细菌与真核宿主相互作用中带注释的smorf编码多肽研究进展。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-06-02 DOI: 10.1002/pmic.202400464

Gonzalo Zapata, Ezequiel G. Mogro, Abril L. Pagnutti, Macarena Algañaras, Pilar Cañameras, Walter O. Draghi, Antonio Lagares, Daniela Bottero, Mauricio J. Lozano

{"title":"A Survey of Annotated smORF-Encoded Polypeptides in Bacteria Interacting With Eukaryotic Hosts","authors":"Gonzalo Zapata, Ezequiel G. Mogro, Abril L. Pagnutti, Macarena Algañaras, Pilar Cañameras, Walter O. Draghi, Antonio Lagares, Daniela Bottero, Mauricio J. Lozano","doi":"10.1002/pmic.202400464","DOIUrl":"10.1002/pmic.202400464","url":null,"abstract":"<div>\u0000 \u0000 <p>smORF encoded polypeptides (SEPs) are difficult to predict due to their small size. While modern genome annotation tools are capable of identifying smORFs, their reliability is often uncertain. Furthermore, experimental validation of smORFs has primarily focused on a limited set of model organisms. Here, we conduct a comprehensive analysis of annotated smORFs in a diverse range of bacteria interacting with eukaryotic hosts. Our analysis revealed that bacterial genomes typically harbor between 100 and 300 annotated smORFs, predominantly encoding SEPs exceeding 40 residues and annotated as hypothetical proteins. We show that functional annotation of SEPs can be improved to some extent with the currently available resources, and that SEPs exhibit distinct functional profiles in bacteria associated with different host types (plant vs. animal). We also found that most of the experimentally validated SEPs are conserved and that all the annotated SEPs begin with methionine, although that is not always the case for the experimentally validated ones. Our findings underscore the need for improved annotation methods and further experimental characterization to fully understand the functional roles and evolutionary significance of smORFs in bacteria-host interactions.</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 13","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144197892","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

Tissue-Specific Regulation of Fatty Acid Metabolism in a Mouse Model of Isolated Complex I Deficiency 孤立性复合物I缺乏小鼠模型中脂肪酸代谢的组织特异性调节。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-06-01 DOI: 10.1002/pmic.13969

Sibonelo Glen Khumalo, Jeremie Zander Lindeque, Marianne Venter

{"title":"Tissue-Specific Regulation of Fatty Acid Metabolism in a Mouse Model of Isolated Complex I Deficiency","authors":"Sibonelo Glen Khumalo, Jeremie Zander Lindeque, Marianne Venter","doi":"10.1002/pmic.13969","DOIUrl":"10.1002/pmic.13969","url":null,"abstract":"<p>Isolated complex I deficiency (ICD) is commonly associated with mitochondrial diseases and closely mimics subacute necrotising encephalomyelopathy. This disorder is characterised by metabolic perturbations that affect energy metabolism pathways, including fatty acid metabolism. Here, we examined the tissue-specific changes in fatty acid metabolism in the <i>Ndufs4</i> KO mice by employing mass-spectrometry-based proteomics as a hypothesis-generating approach. We investigated proteomic changes in six tissues, including brain regions (brainstem, cerebellum, olfactory bulb), heart, kidney and liver, focusing on proteins involved in fatty acid metabolism. Although it is expected that most tissues, except for the brain, will utilise fatty acids as alternative energy sources when oxidative phosphorylation (OXPHOS) is deficient, our data revealed a more complex response. In the liver, fatty acid consumption (oxidation) was favoured as expected, but in the heart, fatty acid synthesis was favoured. In the kidney, proteins involved in almost all fatty acid metabolic processes (oxidation and synthesis) were downregulated. Our data demonstrate that metabolic adaptations in fatty acid metabolism to ICD were tissue-specific and often in opposing directions. Understanding the differential adaptations across tissues could inform future treatment targets for mitochondrial disorders.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 13","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.13969","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144197893","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