Molecular & Cellular Proteomics最新文献

{"title":"Anagrelide Remodels the PDE3A-SLFN12 Interactome to Associate with Translation Initiation Machinery in Cancer Cell Lines.","authors":"Sami Salmikangas, Iina Lindholm, Nasrin Sultana, Nanna Merikoski, Kirsi Toivanen, Xiaonan Liu, Markku Varjosalo, Tom Böhling, Tiina Vesterinen, Harri Sihto","doi":"10.1016/j.mcpro.2026.101663","DOIUrl":"10.1016/j.mcpro.2026.101663","url":null,"abstract":"<p><p>Phosphodiesterase 3A (PDE3A) modulators such as anagrelide induce complex formation between PDE3A and Schlafen 12 (SLFN12), selectively killing cancer cells that co-express both proteins. As PDE3A forms isoform- and cell type-specific signalosome complexes across multiple subcellular compartments, the effects of its modulation are expected to depend strongly on the surrounding protein interaction network. However, despite considerable preclinical and early clinical interest in PDE3A modulators, the cellular context in which these compounds act has remained poorly characterized. Using proximity-dependent biotinylation in two human cancer cell lines (SA-4, liposarcoma; HeLa, cervical adenocarcinoma), we mapped the interactomes of PDE3A, SLFN12, and the anagrelide-induced PDE3A-SLFN12 complex. Anagrelide induced 259 high-confidence interactions, most notably with ribosomal proteins and translation initiation factors, while suppressing 877 interactions, most prominently those associated with the proteasome, protein folding, and the ER membrane. Interactions were selectively induced with peripheral eukaryotic translation initiation factor 3 (eIF3) subunits eIF3A and eIF3B, while interactions with core eIF3 subunits eIF3H, eIF3L, and eIF3M were suppressed. These findings were validated by native co-immunoprecipitation across three cancer cell lines, and multiplex immunofluorescence confirmed accumulation and ribosomal redistribution of both PDE3A and SLFN12 following anagrelide treatment. AlphaFold modeling of the PDE3A-SLFN12 complex with a partial 43S pre-initiation complex predicted binding near eIF3B and the eIF2αβγ-tRNA ternary complex at the mRNA entry channel. By mapping the interactomes surrounding the drug-induced complex, our study provides important mechanistic context for how PDE3A modulators act within the cell. In our proposed model, anagrelide remodels the interactome of the PDE3A-SLFN12 complex, which relocalizes and accumulates near the mRNA entry channel of the 43S pre-initiation complex.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101663"},"PeriodicalIF":6.3,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149002133","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":"Protein Arginine Methylation of the Translation Initiation Factor eIF1A Increases Usage of a Near-Cognate Start Codon.","authors":"Rebecca Wegman, Michael Langberg, Haiteng Deng, Yuling Chen, Richoo B Davis, Xiaozhuo Liu, Minkui Luo, Michael C Yu, Sarah E Walker","doi":"10.1016/j.mcpro.2026.101661","DOIUrl":"10.1016/j.mcpro.2026.101661","url":null,"abstract":"<p><p>Protein arginine methylation has emerged as a key post-translational modification responsible for many facets of eukaryotic gene expression. To better understand the extent of this modification in cellular pathways, we carried out bioorthogonal methylation profiling in Saccharomyces cerevisiae to comprehensively identify the in vivo substrates of the major yeast protein arginine methyltransferase Hmt1. Gene ontology analysis of candidate substrates revealed an enrichment of proteins involved in the process of translation. We verified one such factor, eIF1A, by in vitro methylation. Three sites on eIF1A were found to be responsible for its methylation: R13, R14, and R62, with varied capacity by which each site contributed to the overall methylation capacity in vitro. To determine the role of methylation in eIF1A function, we used a battery of arginine-to-alanine substitution mutants to evaluate translation fidelity in these mutants. Our data show that substitution mutants at R13 and R14 in the N-terminal tail improved the fidelity of start codon recognition in an initiation fidelity assay. Overall, our data suggest that Hmt1-mediated methylation of eIF1A fine-tunes the fidelity of start codon recognition for proper translation initiation.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101661"},"PeriodicalIF":6.3,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148977157","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":"Kv11.1 (hERG) Protein Interaction Networks Connect Endocytic Trafficking to Polygenic Influences on Cardiac Repolarization.","authors":"Christian L Egly, Lea A Barny, Suah Woo, Devyn Mitchell, Matthew Ku, Björn C Knollmann, Lars Plate, Brett M Kroncke","doi":"10.1016/j.mcpro.2026.101656","DOIUrl":"10.1016/j.mcpro.2026.101656","url":null,"abstract":"<p><p>Polygenic scores (PGS) capture the combined effect of many common genetic variants on quantitative traits and disease risk, yet their functional consequences at the protein level remain poorly defined. Here, we integrated quantitative and interaction proteomics to resolve how polygenic liability for cardiac repolarization manifests in human cells. We studied human induced pluripotent stem cell-derived cardiomyocytes from donors with extreme PGS for QT interval duration, a clinically relevant electrophysiologic trait associated with arrhythmia risk. Global quantitative proteomics revealed increased abundance of mitochondrial proteins in high-PGS cardiomyocytes. To define protein network-level effects on a key repolarizing ion channel, we performed multiplexed affinity purification-mass spectrometry of Kv11.1. While mitochondrial changes did not directly explain Kv11.1-associated complexes, interactome analysis revealed increased association of Kv11.1 with myosin motor proteins and endosomal recycling machinery in high-PGS cells. These findings suggest altered channel trafficking dynamics of Kv11.1, distinct from the trafficking defects observed in monogenic Kv11.1 variants. Together, these data show that integrating global and interaction proteomics can resolve how polygenic variation reshapes protein networks. Future work using these methods could connect genomic risk to subcellular remodeling and our work provides a generalizable framework to probe the proteomic basis of complex traits. Significance Statement: Polygenic scores (PGS) predict disease risk, but how biological pathways are influenced by these common variants remains difficult to define. We generated human induced pluripotent stem cells from individuals with extreme high and low PGS for QT interval, a key electrocardiographic measure linked to arrhythmia risk. By combining global proteomics and interactomics for a common ion channel involved in regulating the QT interval (Kv11.1), we found potential mechanisms that are influenced by common genetic traits in patients. Our work provides an approach to connect polygenic scores to pathway-level molecular mechanisms in human cells and a general framework for uncovering how complex genetic architecture drives disease-relevant biology.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101656"},"PeriodicalIF":6.3,"publicationDate":"2026-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13682224/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148930518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-Center Study on Sample Preparation and Feature Selection Effects in Reproducible Mass Spectrometry Imaging for Clinical Translation.","authors":"Juliana P L Gonçalves, Marta Grzeski, Gentiane Krasniqi, Carsten Hopf, Oliver Klein, Kristina Schwamborn","doi":"10.1016/j.mcpro.2026.101658","DOIUrl":"10.1016/j.mcpro.2026.101658","url":null,"abstract":"<p><p>Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) provides spatially resolved proteomic information that is valuable for understanding disease development, identifying biomarkers, and predicting treatment responses. Despite this potential, MALDI-MSI has not yet been adopted as part of routine diagnostic workflows, primarily due to challenges in analytical validation and robustness. Although sample preparation workflows for MALDI-MSI generally follow the same core steps, there is still a lack of robust data-processing frameworks capable of minimizing technical artifacts, improving feature selection, and reducing inter-laboratory variability. To assess reproducibility and robustness of in situ proteomics across laboratories, we investigated formalin-fixed paraffin-embedded human tissue samples from spleen, intestine, and pancreas using MALDI-MSI. Two complementary workflows were evaluated: (i) decentralized sample preparation with data acquisition performed with one instrument and (ii) centralized sample preparation with data acquisition carried out on instruments across participating laboratories. Data analysis focused on evaluating strategies for feature selection that preserved morphological information. Our findings demonstrate that, with adherence to a standardized protocol, reproducible results across different laboratories can be achieved. Eventhough sample preparation remains a major source of variability, it can be mitigated through appropriate data analysis strategies, particularly in the choice of features used for analysis. Most importantly, biological differences between tissues were consistently identifiable across all datasets, further underscoring the reliability of the approach for clinical translation, especially when sources of variability are properly controlled.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101658"},"PeriodicalIF":6.3,"publicationDate":"2026-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148930545","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":"SIMPATICO-Streamlined Isolation of the N-Terminome via Phosphonate Tagging and Coordination-Based Depletion.","authors":"Piero Giansanti, Adnan Fojnica, Andreas Pichlmair","doi":"10.1016/j.mcpro.2026.101660","DOIUrl":"10.1016/j.mcpro.2026.101660","url":null,"abstract":"<p><p>Protein processing is critical for regulating cellular functions. Therefore, there is considerable interest in developing effective proteome-wide strategies to identify protease cleavage products to enhance our understanding of proteolytic pathways and their perturbation in diseases. Here, we present a streamlined N-termini proteome analysis leveraging N-Hydroxysuccinimide (NHS) ester chemistry. At the protein level, N-terminal amines (naturally occurring protein N-termini, lysines, or protease-generated N-termini) are blocked directly in the cell lysate, and tryptic digestion is performed straight after, without the need for any buffer exchange. The internal tryptic peptides are tagged with a phosphonate moiety and subsequently depleted via metal-based coordination, keeping exclusively N-blocked terminal peptides for analysis by mass spectrometry. We demonstrate the applicability of this approach by monitoring proteolytic events induced by intrinsic apoptotic pathway. Our approach identified more than 690 aspartyl-cleaved proteins in response to Staurosporine-induced apoptosis, including many previously unknown substrates and cleavage sites. The presented approach is, therefore, a straightforward and robust method for mass spectrometry-based identification of caspase-generated cleavage products. Although demonstrated here in the context of caspase-mediated proteolysis, the underlying workflow is not restricted to this protease class and should be broadly applicable to the study of other proteolytic events.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101660"},"PeriodicalIF":6.3,"publicationDate":"2026-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13673259/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148930569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global Proteomic Profiling of Cerebral Malaria-Infected Erythrocytes Reveals a Specific PfEMP1 Expression Pattern.","authors":"Jérémy Fraering, Virginie Salnot, Valentin Joste, Bertin Vianou, Nicolas Argy, Romain Coppée, Florence Migot-Nabias, Emilie-Fleur Gautier, Gwladys Irénée Bertin","doi":"10.1016/j.mcpro.2026.101659","DOIUrl":"10.1016/j.mcpro.2026.101659","url":null,"abstract":"<p><p>Cerebral malaria (CM) is the most lethal complication of malaria, causing severe impairment of brain function. Although the precise mechanisms leading to CM remain unknown, the adhesion of infected erythrocytes to the cerebral endothelium, mediated by Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) proteins, is considered a key factor. These proteins, encoded by var genes, are divided into several groups and contain specific domain cassettes (DCs) already known to be associated with CM. In this study, we compared the human and parasite proteomes of Plasmodium falciparum-infected erythrocytes from 19 samples from the NeuroCM cohort, consisting of 10 children with uncomplicated malaria and 9 with CM from Benin. We used data-independent acquisition mass spectrometry with trapped ion mobility spectrometry and parallel accumulation serial fragmentation coupled to recent PfEMP1 databases to analyze our samples. Our results identified over 7000 proteins, including both host and parasite proteins. Analysis of the host proteome revealed an increased abundance of reticulocyte-specific proteins in CM cases, suggesting a possible parasite preference for invading erythroid precursors. On the parasite side, an increase in membrane proteins (PHIST, RIFIN, and STEVOR) was observed in CM cases. Moreover, PfEMP1 proteins containing DC8 and DC13 were significantly more abundant in CM patients. These results provide protein-level confirmation of the association between DC8/DC13 of PfEMP1 and CM, supporting the hypothesis of an enhanced parasite adhesion mechanism in CM. Our study highlights the importance of proteomic analysis in understanding the pathogenesis of CM and may contribute to the development of novel therapeutic strategies.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101659"},"PeriodicalIF":6.3,"publicationDate":"2026-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13682175/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148920293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative Lactylomic Profiling Unveils Dynamic Reprogramming of Post-translational Lactylation Landscapes During Human Sperm Capacitation.","authors":"Guohui Zhang, Yuhong Zhao, Yu Lei, Weiwei Zhi, Wenming Xu, Jiuzhi Zeng, Li Wang, Fangyi Long, Juncen Guo, Weixin Liu","doi":"10.1016/j.mcpro.2026.101657","DOIUrl":"10.1016/j.mcpro.2026.101657","url":null,"abstract":"<p><p>Lactylation, a novel post-translational modification involving lactate conjugation to lysine residues, bridges metabolic flux and epigenetic regulation and has emerged as a conserved regulatory mechanism across eukaryotes and prokaryotes, governing cell proliferation, immune responses, and metabolic reprogramming via a \"Writer-Eraser\" system. Despite the established roles of lactylation in energy metabolism, its function in male reproduction remains unexplored. This study investigates the lactylation modification dynamics during human sperm capacitation, a process requiring metabolic reprogramming for hyperactivated motility. Through 4D FastDIA-based quantitative dynamic profiling, we first conducted the comprehensive characterization of lysine lactylation modifications during sperm capacitation, systematically mapping differential lactylation patterns at the pathway, proteomic, and site-specific levels. We identified 2030 quantifiable lactylated proteins, revealing significant capacitation-dependent modulation: 115 proteins with 133 sites demonstrated upregulated lactylation, while 287 proteins containing 471 sites showed downregulation (p < 0.05, Fold Change >1.5). Notably, 30 proteins exhibited bidirectional regulatory patterns with coexisting upregulated and downregulated sites, and a predominant proportion of modified proteins (263 of 372) displayed single-site differential lactylation. A marked reduction in lactylation levels of mitochondrial respiratory chain proteins was observed after sperm capacitation, indicating heightened ATP requirements. Moreover, proteins with differential lactylation were enriched in biological processes including fertilization, sperm capacitation, β-oxidation, and microtubule dynamics. Strikingly, the presence of known lactylation regulatory enzymes including Alanine-tRNA ligase 1 (AARS1), Sirtuin (SIRT) 2/3, and Histone deacetylase (HDAC) 1/2/6 were detected in the sperm proteome, revealing a 1.6-fold upregulation of SIRT3, implicating its role in delactylation regulation during capacitation. Collectively, these findings delineate a lactylation-coordinated mechanism governing mitochondrial oxidative phosphorylation optimization and cytoskeletal architecture remodeling. This work substantiates a trinity regulatory mechanism integrating \"metabolism-epigenetics-function\" axes through lactylation circuitry, which may have implications for understanding male infertility.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101657"},"PeriodicalIF":6.3,"publicationDate":"2026-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148912866","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":"Galectin-1 Modulates Cell Adhesions, Cavin-1 Phosphorylation, and Vascular Permeability in Kidney Endothelial Cells-Insights From Proteomics, Phosphoproteomics, and Functional Studies.","authors":"Alex Boshart, Sofia Farkona, Shravanthi Rajasekar, Chiara Pastrello, Maya Allen, Stefan Petrovic, Kieran Manion, Slaghaniya Neupane, Sergi Clotet-Freixas, Hong Sang Choi, Anne-Marie Bulboaca, Rohan John, Allen Duong, Stephen Juvet, Milica Radisic, Juan Manuel Pérez Sáez, Gabriel A Rabinovich, Sara Deir, Boyang Zhang, Igor Jurisica, Ana Konvalinka","doi":"10.1016/j.mcpro.2026.101655","DOIUrl":"10.1016/j.mcpro.2026.101655","url":null,"abstract":"<p><p>Microvascular inflammation and endothelial injury, triggered by interferon-gamma (IFNγ), are hallmarks of antibody-mediated rejection (ABMR), the leading cause of premature kidney allograft loss. Glomerular extracellular matrix (ECM) remodeling and endothelial caveolae formation are important aspects of chronic ABMR. We found galectin-1, an immunomodulatory protein that interacts with the ECM, to be increased in the glomeruli of patients with ABMR, while its gene (LGALS1) expression was decreased by IFNγ stimulation in glomerular endothelial cells. Mechanisms underlying endothelial dysfunction in ABMR, its links to ECM remodeling, and the role of immunomodulatory proteins such as galectin-1 remain incompletely understood. We studied the effects of galectin-1 modulation in glomerular microvascular endothelial cells (GMECs) in vitro. We demonstrated that galectin-1 was mainly expressed by glomerular endothelial cells in ABMR kidneys. To model aspects of endothelial injury in ABMR, we knocked down LGALS1 in GMECs, followed by stimulation with IFNγ and label-free quantitative proteomic and phosphoproteomic profiling of GMECs. Proteomic analysis identified 5446 proteins (FDR < 0.01), of which 236, 827, and 267 were differentially expressed in response to LGALS1 knockdown, IFNγ treatment, and their interaction, respectively (FDR < 0.05). Both LGALS1 knockdown and the interaction between treatments significantly altered expression of adhesion proteins (FDR < 0.01), particularly integrin subunit β5, which was validated. Phosphoproteomic profiling identified 2727 phosphopeptides (FDR < 0.01), with 28 differentially phosphorylated across LGALS1 knockdown, IFNγ treatment, and their interaction (p < 0.01). Phosphorylation of caveolae-associated protein 1 and colocalization with its partner CAV1, critical for caveolar formation, were decreased in GMECs upon LGALS1 knockdown, IFNγ stimulation, or both. In a microfluidic model of the glomerular microvasculature, the addition of recombinant galectin-1 increased endothelial permeability and secretion of proinflammatory cytokines in LGALS1-silenced GMECs. Thus, endothelial signaling pathways regulated by inflammatory cues and galectin-1 contribute to endothelial injury and may affect caveolae formation, highlighting a potential link between galectin-1 and ABMR.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101655"},"PeriodicalIF":6.3,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148888125","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":"H-NOX and NosP Regulate Flagellar Protein and Virulence Factor Production in Vibrio Cholerae.","authors":"Thathmi Wathsara Herath Pathiranage, Md Shariful Islam, Cedar Stellon, Michelle D Cherne, Daniel Valencia, Diane Bimczok, Erik T Yukl","doi":"10.1016/j.mcpro.2026.101654","DOIUrl":"10.1016/j.mcpro.2026.101654","url":null,"abstract":"<p><p>The ability of Vibrio cholerae to transition between motile and sessile forms in the environment and in the host is critical to its survival and virulence. The molecular cues, sensor proteins, and signaling pathways mediating these transitions are highly complex and often overlapping. Nevertheless, a detailed understanding of them is critical for understanding the persistence and pathogenesis of this deadly pathogen. Nitric oxide functions as an important signaling molecule in many bacteria, affecting biofilm formation, motility, and virulence, often through interaction with heme protein sensors. The genome of V. cholerae encodes two such sensors called H-NOX and NosP. Here we constructed a Δhnox/nosP mutant and employed a multiomics methodology that combines tandem mass tag-based quantitative proteomics, phosphoproteomics, and targeted metabolomics to investigate the function of these sensors. A set of 258 proteins was differentially expressed in the mutant that included many proteins involved in flagellar biosynthesis and motility as well as critical virulence factors, iron acquisition systems, and metabolic enzymes. Many of the identified genes are also part of the ferric uptake regulator regulon and iron-dependent transcriptional repression of several ferric uptake regulator targets was disrupted. Phosphoproteomics analysis also revealed proteins involved in motility and virulence as differentially phosphorylated in the mutant strain. In most cases, these phosphoproteins have not been previously observed and provide a wealth of new targets for investigating mechanisms of V. cholerae signaling. Taken together, this work illustrates a role for H-NOX and NosP in promoting factors important for infection while suppressing those important for environmental survival, suggesting a function in priming the organism for infection and/or maintaining the infectious phenotype.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101654"},"PeriodicalIF":6.3,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13654575/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148888099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fusion Entrapment Enables Unbiased Assessment of False Discovery Rate Control in Cascaded Database Searches.","authors":"Xinpei Yi, Yan Fu","doi":"10.1016/j.mcpro.2026.101636","DOIUrl":"10.1016/j.mcpro.2026.101636","url":null,"abstract":"<p><p>Cascaded database searches boost identification sensitivity in vast proteomic search spaces but challenge false discovery rate (FDR) control. The standard target-decoy approach to FDR control relies on decoy matches providing an exchangeable and properly scaled representation of incorrect target matches. This assumption can be disrupted when protein-level filtering is used to define a reduced search space, because target and decoy entries may no longer undergo symmetric retention during database reduction. Although entrapment provides an external benchmark for assessing FDR control, conventional separate-entrapment implementations can become invalid in cascaded searches because entrapment sequences may be disproportionately discarded during protein-level filtering. Here we introduce Fusion Entrapment, a strategy that computationally fuses entrapment sequences with target proteins to preserve identical selection pressure during database reduction. Simulations show that this strategy provides accurate entrapment-based false discovery proportion (FDP) estimation in cascaded searches involving protein-level filtering. Applying Fusion Entrapment to human gut metaproteomic datasets, we further observed that conventional separate target-decoy database reduction led to substantial inflation of the entrapment-estimated FDP relative to the reported FDR threshold. In contrast, fusion target-decoy reduction maintained empirical FDR control under Fusion Entrapment assessment while retaining substantial sensitivity gains over single-step analysis.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101636"},"PeriodicalIF":6.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13563576/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148707065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}