Journal of Proteome Research最新文献

{"title":"Unraveling Cecal Alterations in <i>Clostridioides difficile</i> Colonized Mice through Comprehensive Metabolic Profiling.","authors":"Olga Deda, Emily G Armitage, Thomai Mouskeftara, Melina Kachrimanidou, Ioannis Zervos, Andigoni Malousi, Neil J Loftus, Ioannis Taitzoglou, Helen Gika","doi":"10.1021/acs.jproteome.4c00578","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00578","url":null,"abstract":"<p><p>The disruption of gut microbiota caused by antibiotics favors the intestinal colonization of <i>Clostridioides difficile</i> - a Gram-positive, spore-forming anaerobic bacterium that causes potentially fatal gastrointestinal infections. In an endeavor to elucidate the complexities of the gut-brain axis in the context of <i>Clostridium difficile</i> infection (CDI), a murine model has been used to investigate the potential effects of antibiotic administration and subsequent colonization by <i>C. difficile</i>, as well as the impact of three different 10-day treatments (metronidazole, probiotics, and fecal microbiota transplantation), on the cecal metabolome for the first time. This follows our previous research which highlighted the metabolic effect of CDI and these treatments in the brain and employs the same four different metabolomics-based methods (targeted GC-MS/MS, targeted HILIC-MS/MS, untargeted RP-LC-HRMS/MS and untargeted GC-MS). A total of 286 unique metabolites have been identified in the mouse cecal profiles and statistical analysis revealed that CDI, as well as the subsequent treatments, significantly alters cecal metabolites and lipids implicated in various biochemical pathways centered around amino acid metabolism, glycerophospholipid metabolism, and central carbon metabolism. To our knowledge, this study represents the first exploration of the effects of <i>C. difficile</i>-induced colitis and potential treatments on the cecal tissue metabolome.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Variability of 7K and 11K SomaScan Plasma Proteomics Assays.","authors":"Julián Candia, Giovanna Fantoni, Francheska Delgado-Peraza, Nader Shehadeh, Toshiko Tanaka, Ruin Moaddel, Keenan A Walker, Luigi Ferrucci","doi":"10.1021/acs.jproteome.4c00667","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00667","url":null,"abstract":"<p><p>SomaScan is an aptamer-based proteomics assay designed for the simultaneous measurement of thousands of human proteins with a broad range of endogenous concentrations. The 7K SomaScan assay has recently been expanded into the new 11K version. Following up on our previous assessment of the 7K assay, here, we expand our work on technical replicates from donors enrolled in the Baltimore Longitudinal Study of Aging. By generating SomaScan data from a second batch of technical replicates in the 7K version as well as additional intra- and interplate replicate measurements in the new 11K version using the same donor samples, this work provides useful precision benchmarks for the SomaScan user community. Beyond updating our previous technical assessment of the 7K assay with increased statistics, here, we estimate interbatch variability, assess inter- and intraplate variability in the new 11K assay, compare the observed variability between the 7K and 11K assays (leveraging the use of overlapping pairs of technical replicates), and explore the potential effects of sample storage time (ranging from 2 to 30 years) in the assays' precision.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phosphorylation in the <i>Plasmodium falciparum</i> Proteome: A Meta-Analysis of Publicly Available Data Sets.","authors":"Oscar J M Camacho, Kerry A Ramsbottom, Ananth Prakash, Zhi Sun, Yasset Perez Riverol, Emily Bowler-Barnett, Maria Martin, Jun Fan, Eric W Deutsch, Juan Antonio Vizcaíno, Andrew R Jones","doi":"10.1021/acs.jproteome.4c00418","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00418","url":null,"abstract":"<p><p>Malaria is a deadly disease caused by Apicomplexan parasites of the <i>Plasmodium</i> genus. Several species of the <i>Plasmodium</i> genus are known to be infectious to humans, of which <i>P. falciparum</i> is the most virulent. Post-translational modifications (PTMs) of proteins coordinate cell signaling and hence regulate many biological processes in <i>P. falciparum</i> homeostasis and host infection, of which the most highly studied is phosphorylation. Phosphosites on proteins can be identified by tandem mass spectrometry (MS) performed on enriched samples (phosphoproteomics), followed by downstream computational analyses. We have performed a large-scale meta-analysis of 11 publicly available phosphoproteomics data sets to build a comprehensive atlas of phosphosites in the <i>P. falciparum</i> proteome, using robust pipelines aimed at strict control of false identifications. We identified a total of 26,609 phosphorylated sites on <i>P. falciparum</i> proteins, split across three categories of data reliability (gold/silver/bronze). We identified significant sequence motifs, likely indicative of different groups of kinases responsible for different groups of phosphosites. Conservation analysis identified clusters of phosphoproteins that are highly conserved and others that are evolving faster within the <i>Plasmodium</i> genus, and implicated in different pathways. We were also able to identify over 180,000 phosphosites within <i>Plasmodium</i> species beyond <i>falciparum</i>, based on orthologue mapping. We also explored the structural context of phosphosites, identifying a strong enrichment for phosphosites on fast-evolving (low conservation) intrinsically disordered regions (IDRs) of proteins. In other species, IDRs have been shown to have an important role in modulating protein-protein interactions, particularly in signaling, and thus warranting further study for their roles in host-pathogen interactions. All data have been made available via UniProtKB, PRIDE, and PeptideAtlas, with visualization interfaces for exploring phosphosites in the context of other data on <i>Plasmodium</i> proteins.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural Analysis of the 20S Proteasome Using Native Mass Spectrometry and Ultraviolet Photodissociation.","authors":"Jada N Walker, Amit K S Gautam, Andreas Matouschek, Jennifer S Brodbelt","doi":"10.1021/acs.jproteome.4c00568","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00568","url":null,"abstract":"<p><p>Owing to the role of the 20S proteasome in a wide spectrum of pathologies, including neurodegenerative disorders, proteasome-associated autoinflammatory syndromes (PRAAS), and cardiovascular diseases, understanding how its structure and composition contribute to dysfunction is crucial. As a 735 kDa protein assembly, the 20S proteasome facilitates normal cellular proteostasis by degrading oxidized and misfolded proteins. Declined proteasomal activity, which can be attributed to perturbations in the structural integrity of the 20S proteasome, is considered one of the main contributors to multiple proteasome-related diseases. Devising methods to characterize the structures of 20S proteasomes provides necessary insight for the development of drugs and inhibitors that restore proper proteasomal function. Here, native mass spectrometry was combined with multiple dissociation techniques, including ultraviolet photodissociation (UVPD), to identify the protein subunits comprising the 20S proteasome. UVPD, demonstrating an ability to uncover structural features of large (>300 kDa) macromolecular complexes, provided complementary information to conventional collision-based methods. Additionally, variable-temperature electrospray ionization was combined with UV photoactivation to study the influence of solution temperature on the stability of the 20S proteasome.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antitumoral Activity and Metabolic Signatures of Dichloroacetate, 6-Aminonicotinamide and Etomoxir in Breast-Tumor-Educated Macrophages.","authors":"Ana S Dias, Catarina R Almeida, Luisa Helguero, Iola F Duarte","doi":"10.1021/acs.jproteome.4c00654","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00654","url":null,"abstract":"<p><p>Pharmacological targeting of metabolic pathways represents an appealing strategy to selectively kill cancer cells while promoting antitumor functions of stromal cells. In this study, we assessed the effectiveness of 13 metabolic drugs (MDs) in steering <i>in vitro</i> generated breast tumor-educated macrophages (TEMs) toward an antitumoral phenotype. For that, the production of vascular endothelial growth factor (VEGF) and tumor necrosis factor α (TNF-α), two important regulators of tumor progression, was evaluated. Notably, dichloroacetate (DCA), 6-aminonicotinamide (6-AN), and etomoxir decreased VEGF production and enhanced TNF-α release. Hence, we further clarified their impact on TEM metabolism using an untargeted NMR-based metabolomics approach. DCA downregulated glycolysis and enhanced the utilization of extracellular substrates like lactate while reconfiguring lipid metabolism. Several DCA-induced changes significantly correlated with heightened TNF-α production in response to pro-inflammatory stimulation. The inhibition of the pentose phosphate pathway by 6-AN was accompanied by enhanced glutaminolysis, which correlated with a decreased level of VEGF production. In etomoxir-treated TEM, inhibition of fatty acid oxidation was compensated through upregulation of glycolysis, catabolism of intracellular amino acids, and consumption of extracellular branched chain alpha-ketoacids (BCKA) and citrate. Overall, our results offer a comprehensive view of the metabolic signature of each MD in breast TEM and highlight putative correlations with phenotypic effects.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hybrid Quadrupole Mass Filter-Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics.","authors":"Philip M Remes, Cristina C Jacob, Lilian R Heil, Nicholas Shulman, Brendan X MacLean, Michael J MacCoss","doi":"10.1021/acs.jproteome.4c00599","DOIUrl":"10.1021/acs.jproteome.4c00599","url":null,"abstract":"<p><p>Targeted mass spectrometry (MS) methods are powerful tools for the selective and sensitive analysis of peptides identified in global discovery experiments. Selected reaction monitoring (SRM) is the most widely accepted clinical MS method due to its reliability and performance. However, SRM and parallel reaction monitoring (PRM) are limited in throughput and are typically used for assays with around 100 targets or fewer. Here we introduce a new MS platform featuring a quadrupole mass filter, collision cell, and linear ion trap architecture, capable of targeting 5000-8000 peptides per hour. This high multiplexing capability is facilitated by acquisition rates of 70-100 Hz and real-time chromatogram alignment. We present a Skyline external software tool for building targeted methods based on data-independent acquisition chromatogram libraries or unscheduled analysis of heavy labeled standards. Our platform demonstrates ∼10× lower limits of quantitation (LOQs) than traditional SRM on a triple quadrupole instrument for highly multiplexed assays, due to parallel product ion accumulation. Finally, we explore how analytical figures of merit vary with method duration and the number of analytes, providing insights into optimizing assay performance.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomic Analysis of Microsomal Proteins Reveals That MVP Is Crucial for the Secretion of GDF-15, Which in Turn Promotes the Neuroendocrine Differentiation of PCa Cells.","authors":"Sandhya Venkata Lakshmi Pampana, Biswajit Biswas, Saikiran Jajula, Srikanth Rapole, Ramesh Ummanni","doi":"10.1021/acs.jproteome.4c00694","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00694","url":null,"abstract":"<p><p>Neuroendocrine prostate cancer (NEPC) is an aggressive androgen-independent PCa (AIPC) that tends to resist treatment. Understanding its progression and resistance could improve survival outcomes. Previous studies on PCa cells highlighted microsomal proteins' role in PCa progression, but their role in the progression of NEPC remains unclear. Thus, we investigated microsomal proteins in <i>in vitro</i> differentiated NE-LNCaP cells and their role in NED of PCa. Microsomal proteomics revealed two cancer-associated proteins GDF-15 and MVP as elevated in NE-LNCaP cells with GDF-15 among the top 5 upregulated proteins. MVP is elevated in NE-LNCaP and is also increased in NCI-H660 microsomes compared to LNCaP. GO and protein network analysis showed that different molecular networks are affected by microsomal protein enrichment, and MVP and GDF-15 are mapped to functional subnetworks associated with cancer. Remarkably, GDF-15 and MVP are essential for LNCaP cell differentiation when stimulated with Forskolin. Interestingly, AKT and MAPK/ERK signaling pathways are significantly upregulated in NE-LNCaP and NCI-H660 cells with the direct involvement of GDF-15. In summary, we have uncovered that GDF-15 and MVP are involved in NED, with MVP being essential for GDF-15 secretion, promoting NED in PCa cells. These findings provide insights into NED mechanisms and suggest potential therapeutic targets or biomarkers for NEPC.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiomics Profiling of Plasma Reveals Molecular Alterations Prior to a Diagnosis with Stroke Among Chinese Hypertension Patients.","authors":"Jingjing Zeng, Changyi Wang, Jiamin Guo, Tian Zhao, Han Wang, Ruijie Zhang, Liyuan Pu, Huiqun Yang, Jie Liang, Liyuan Han, Lei Li","doi":"10.1021/acs.jproteome.4c00559","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00559","url":null,"abstract":"<p><p>We aimed to investigate the correlation between plasma proteins and metabolites and the occurrence of future strokes using mass spectrometry and bioinformatics as well as to identify other biomarkers that could predict stroke risk in hypertensive patients. In a nested case-control study, baseline plasma samples were collected from 50 hypertensive subjects who developed stroke and 50 gender-, age- and body mass index-matched controls. Plasma untargeted metabolomics and data independent acquisition-based proteomics analysis were performed in hypertensive patients, and 19 metabolites and 111 proteins were found to be differentially expressed. Integrative analyses revealed that molecular changes in plasma indicated dysregulation of protein digestion and absorption, salivary secretion, and regulation of actin cytoskeleton, along with significant metabolic suppression. C4BPA, Caprolactam, Col15A1, and HBB were identified as predictors of stroke occurrence, and the Support Vector Machines (SVM) model was determined to be the optimal predictive model by integrating six machine-learning classification models. The SVM model showed strong performance in both the internal validation set (area under the curve [AUC]: 0.977, 95% confidence interval [CI]: 0.941-1.000) and the external independent validation set (AUC: 0.973, 95% CI: 0.921-0.999).</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Construction of Protein Sequence Databases for Metaproteomics: A Review of the Current Tools and Databases.","authors":"Muzaffer Arıkan, Başak Atabay","doi":"10.1021/acs.jproteome.4c00665","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00665","url":null,"abstract":"<p><p>In metaproteomics studies, constructing a reference protein sequence database that is both comprehensive and not overly large is critical for the peptide identification step. Therefore, the availability of well-curated reference databases and tools for custom database construction is essential to enhance the performance of metaproteomics analyses. In this review, we first provide an overview of metaproteomics by presenting a concise historical background, outlining a typical experimental and bioinformatics workflow, emphasizing the crucial step of constructing a protein sequence database for metaproteomics. We then delve into the current tools available for building such databases, highlighting their individual approaches, utility, and advantages and limitations. Next, we examine existing protein sequence databases, detailing their scope and relevance in metaproteomics research. Then, we provide practical recommendations for constructing protein sequence databases for metaproteomics, along with an overview of the current challenges in this area. We conclude with a discussion of anticipated advancements, emerging trends, and future directions in the construction of protein sequence databases for metaproteomics.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combining Quantitative Proteomics and Interactomics for a Deeper Insight into Molecular Differences between Human Cell Lines.","authors":"Anna A Bakhtina, Helisa H Wippel, Juan D Chavez, James E Bruce","doi":"10.1021/acs.jproteome.4c00503","DOIUrl":"10.1021/acs.jproteome.4c00503","url":null,"abstract":"<p><p>In modern biomedical research, cultivable cell lines are an indispensable tool, and the selection of cell lines that exhibit specific functional profiles is often critical to success. Cellular functional pathways have evolved through the selection of protein intra- and intermolecular interactions collectively referred to as the interactome. In the present work, quantitative in vivo protein cross-linking and mass spectrometry were used to probe large-scale protein interactome differences among three commonly employed human cell lines, namely, HEK293, MCF-7, and HeLa cells. These data illustrated highly reproducible quantitative interactome levels with <i>R</i>² values larger than 0.8 for all biological replicates. Proteome abundance levels were also measured using data-independent acquisition quantitative proteomics methods. Combining quantitative interactome and proteome information allowed the visualization of cell type-specific interactome changes mediated by proteome level adaptations and independently regulated interactome changes to gain deeper insight into possible drivers of these changes. Among the largest detected alterations in protein interactions and conformations are changes in cytoskeletal proteins, RNA-binding proteins, chromatin remodeling complexes, mitochondrial proteins, and others. Overall, these data demonstrate the utility and reproducibility of quantitative cross-linking to study system-level interactome variations. Moreover, these results illustrate how combined quantitative interactomics and proteomics can provide unique insight into cellular functional landscapes.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}