Proteomics最新文献

{"title":"EXPRESSION OF CONCERN: Binding of Insecticidal Lectin Colocasia esculenta Tuber Agglutinin (CEA) to Midgut Receptors of Bemisia tabaci and Lipaphis erysimi Provides Clues to its Insecticidal Potential.","authors":"Sampa Das","doi":"10.1002/pmic.70008","DOIUrl":"https://doi.org/10.1002/pmic.70008","url":null,"abstract":"","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e70008"},"PeriodicalIF":3.4,"publicationDate":"2025-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144574570","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}

{"title":"CoSpred: Machine Learning Workflow to Predict Tandem Mass Spectrum in Proteomics.","authors":"Liang Xue, Shivani Tiwary, Mykola Bordyuh, Robert Stanton","doi":"10.1002/pmic.70004","DOIUrl":"https://doi.org/10.1002/pmic.70004","url":null,"abstract":"<p><p>In mass spectrometry-based proteomics, the use of deep learning algorithms can help improve the identification rates of peptides and proteins through the generation of high-fidelity theoretical spectrum which can be used as the basis of a more complete spectral library than those presently available, especially for unobserved protein/genetic variants. Here we focus on providing an end-to-end user-friendly machine learning workflow, which we call Complete Spectrum Predictor (CoSpred). Using CoSpred users can create their own machine learning compatible training dataset and then train a machine learning model to predict both backbone and non-backbone ions. For the model a transformer encoder architecture is used to predict the complete MS/MS spectrum from a given peptide sequence. In addition to the transformer model provided in the package, the code is built modularly to allow for alternate ML models to be easily \"plugged in,\" allowing for spectrum prediction optimization given different experimental conditions. The CoSpred workflow (preprocessing→training→inference) provides a path for state-of-art ML capabilities to be more accessible to proteomics scientists.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e70004"},"PeriodicalIF":3.4,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525743","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}

{"title":"Issue Information: Proteomics 11–12'25","authors":"","doi":"10.1002/pmic.70002","DOIUrl":"https://doi.org/10.1002/pmic.70002","url":null,"abstract":"","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 11-12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.70002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144503145","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}

{"title":"Beyond Gravity: Leveraging Gene Plasticity to Mitigate Spaceflight-Induced Pathologies","authors":"Irina-Mihaela Matache","doi":"10.1002/pmic.202500087","DOIUrl":"https://doi.org/10.1002/pmic.202500087","url":null,"abstract":"<div>\u0000 \u0000 <p>As space exploration becomes increasingly accessible, understanding the molecular and pathophysiological consequences of spaceflight on the human body becomes crucial. Space-induced modifications could disrupt multiple signaling pathways, with significant implications for the functional integrity of cardiovascular, nervous, and musculoskeletal systems, among others. In a recent study, Bourdakou et al. have focused on alterations in gene expression profiles linked to cardiovascular disease (CVD), using human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) undergoing spaceflight and subsequent postflight conditions. Genes with known associations with CVD and nuclear factor erythroid 2-related factor 2 (NRF2) oxidative stress regulatory network have been identified to present consistent directional expression changes in both spaceflight and postflight. A computational drug repurposing analysis identified ten candidate agents with the potential to reverse observed transcriptomic modifications in spaceflight-exposed cardiomyocytes. These findings highlight the importance of molecular studies and emphasize the need for integrative, multi-omic research efforts to protect human health during and beyond spaceflight.</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 11-12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144503147","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}

{"title":"Multi-Disciplinary and Omics-Driven Approaches to Advance Personalized Medicine in Cardiovascular and Chronic Kidney Disease","authors":"Griet Glorieux,&nbsp;Julie Klein,&nbsp;Agnieszka Latosinska","doi":"10.1002/pmic.202500093","DOIUrl":"https://doi.org/10.1002/pmic.202500093","url":null,"abstract":"","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 11-12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144503146","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}

{"title":"Quantitative Proteomics of Cochlear Tissues: Bilateral Comparisons in Guinea Pigs and Rats","authors":"Motahare Khorrami,&nbsp;Paul A. Haynes,&nbsp;Christopher Pastras,&nbsp;Mohsen Asadnia","doi":"10.1002/pmic.13977","DOIUrl":"10.1002/pmic.13977","url":null,"abstract":"<p>The cochlea, an incredibly sensitive sensory system, detects sound waves and converts them into electrical signals the brain recognizes as sound. Damage to cochlear hair cells can release proteins, triggering biological responses that may impair hearing. Mass spectrometry-based proteomics offers insights into protein expression changes in cochlear tissues, improving our understanding of inner ear diseases. In this study, we performed a comprehensive proteomics analysis of whole cochlear tissue extracted from healthy guinea pigs and rats. The study optimized protein extraction protocols and analyzed cochlear protein expression using three biological replicates for each animal model. The results included the identification of 1841 proteins in guinea pigs and 3423 proteins in rats, with a high overlap in cochlear protein expression between the left and right ears—93% in guinea pigs and 89% in rats. The findings validate the assumption that the cochlear tissues from both sides of the ears can be considered biologically equivalent. This experiment provides a comprehensive cochlear proteome for guinea pigs and rats, supporting future studies on inner ear disorders.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 13","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.13977","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144367640","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}

{"title":"Covalent Inhibition of the Peptidyl-Prolyl Isomerase Pin1 by Sulfopin Results in a Broad Impact on the Phosphoproteome of Human Osteosarcoma U2-OS Cells","authors":"Scott E. Roffey,&nbsp;Owen Hovey,&nbsp;Kristina Jurcic,&nbsp;Kun Ping Lu,&nbsp;Xiao Zhen Zhou,&nbsp;David W. Litchfield","doi":"10.1002/pmic.13980","DOIUrl":"10.1002/pmic.13980","url":null,"abstract":"&lt;div&gt;\u0000 \u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;p&gt;Peptidyl-prolyl isomerase, NIMA-interacting protein 1-(Pin1) catalyses the &lt;i&gt;cis&lt;/i&gt;–&lt;i&gt;trans&lt;/i&gt; interconversion of the inflexible bond between serine or threonine residues and proline at the +1 position (pSer/pThr-Pro). Although initially discovered as an essential regulator of cell division, Pin1 has since been identified as a regulator of many biological processes and is associated with numerous malignancies and neurodegenerative disorders. Pin1 has been shown to influence phosphorylation by modulating phosphatase accessibility. However, it can also indirectly regulate phosphorylation by isomerizing peptidyl-prolyl bonds on kinases, affecting their subcellular localization and/or substrate specificity. Here, SILAC-based mass spectrometry was employed to identify proteomic and phosphoproteomic changes in human osteosarcoma human osteosarcoma cell line (U2-OS) cells in response to treatment with the selective covalent Pin1 inhibitor Sulfopin. We confirmed that Sulfopin covalently binds Pin1 and profiled Pin1-dependent changes to the proteome and phosphoproteome, identifying 803 phosphosites that underwent significant Sulfopin-dependent changes. The identified phosphosites include substrates for a number of distinct kinases, including protein kinase B (AKT1), aurora kinase A (AURKA), cyclin-dependent kinase (CDK)1 and CK2. Overall, this study reveals the broad impact of Sulfopin on the phosphoproteome, improving our understanding of how Pin1 modulates complex regulatory kinase networks in living cells.&lt;/p&gt;\u0000 &lt;/section&gt;\u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;h3&gt; Summary&lt;/h3&gt;\u0000 \u0000 &lt;div&gt;\u0000 &lt;ul&gt;\u0000 \u0000 &lt;li&gt;\u0000 &lt;p&gt;The peptidyl-prolyl isomerase (PPIase) Pin1 has emerged as a potential therapeutic target for numerous malignancies and neurodegenerative disorders based on its altered expression in several diseases.&lt;/p&gt;\u0000 &lt;/li&gt;\u0000 \u0000 &lt;li&gt;\u0000 &lt;p&gt;As the activity of Pin1 is phosphorylation-dependent, it is intimately involved with constituents of regulatory kinase networks within cells.&lt;/p&gt;\u0000 &lt;/li&gt;\u0000 \u0000 &lt;li&gt;\u0000 &lt;p&gt;To elucidate how Pin1 orchestrates regulatory signalling within cells, we performed quantitative proteomic and phosphoproteomic profiling of SILAC-labelled human osteosarcoma U2-OS cells treated with Sulfopin, a highly selective covalent Pin1 inhibitor.&lt;/p&gt;\u0000 &lt;/li&gt;\u0000 \u0000 &lt;li&gt;\u0000 &lt;p&gt;In addition to demonstrating that Pin1 inhibition alters the abundance and phosphorylation of proteins involved in a variety of fundamental cellular processes, these studies revealed that Pin1 inhibition modulates the ","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.13980","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144367637","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}

{"title":"Defining the Molecular Impacts of Humalite Application on Field-Grown Wheat (Triticum aestivum L.) Using Quantitative Proteomics","authors":"Lauren E. Grubb,&nbsp;Mohana Talasila,&nbsp;Linda Y. Gorim,&nbsp;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 (&gt;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}

{"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}

{"title":"Sample Preparation for Multi-Omics Analysis: Considerations and Guidance for Identifying the Ideal Workflow.","authors":"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","doi":"10.1002/pmic.13983","DOIUrl":"10.1002/pmic.13983","url":null,"abstract":"<p><p>Advances in methodologies and technologies over the past decade have led to an unprecedented depth of analysis of a cell's biomolecules, with entire genomes able to be sequenced in hours and up to 10,000 transcripts or ORF products (proteins) able to be quantified from a single cell. Methods for analysing individual omes are now optimised, reliable and robust but are often performed in isolation with other biomolecules considered contaminants. However, there is a growing body of systems biology studies that aim to study multiple omes from the same sample. This review details the current state of the \"multi-omics\" field, trying to define what the field is, the methodologies employed and the challenges facing researchers in this field. It also critically evaluates whether these approaches are \"fit-for-purpose\" and how the field needs to evolve to enhance our understanding of how biomolecules from distinct omes interact with one another to alter cellular phenotype in response to change.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e13983"},"PeriodicalIF":3.4,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144367641","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}