Journal of Proteome Research最新文献_第5页

Maternal Plasma Proteins Associated with Birth Weight: A Longitudinal, Large Scale Proteomic Study. 与出生体重相关的母体血浆蛋白：一项纵向、大规模蛋白质组学研究。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-05 DOI: 10.1021/acs.jproteome.4c00940

Ina Jungersen Andresen, Ane Cecilie Westerberg, Marie Cecilie Paasche Roland, Manuela Zucknick, Trond Melbye Michelsen

{"title":"Maternal Plasma Proteins Associated with Birth Weight: A Longitudinal, Large Scale Proteomic Study.","authors":"Ina Jungersen Andresen, Ane Cecilie Westerberg, Marie Cecilie Paasche Roland, Manuela Zucknick, Trond Melbye Michelsen","doi":"10.1021/acs.jproteome.4c00940","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00940","url":null,"abstract":"Small infants for gestational age (SGA) and large infants for gestational age (LGA) have increased risk of complications during delivery and later in life. Prediction of the fetal weight is currently limited to biometric parameters obtained by ultrasound scans that can be imprecise. Biomarkers of fetal growth would be crucial for tailoring clinical management and optimizing outcomes for the mother and child. Seventy pregnant women participated in the current study, including 58, 7, and 5 giving birth to adequate for gestational age (AGA), SGA, and LGA infants, respectively. Maternal venous blood was drawn at gestational weeks 12-19, 21-27, and 28-34 and quantified for nearly 5000 proteins on the SomaLogic platform. We used machine learning algorithms with leave-one-out cross-validation to construct multiprotein models for prediction of birth weight groups. Random forest models using only 20 predefined proteins (selected by moderated t tests) were able to predict LGA with good discrimination (AUC > 0.8) at all three visits, while prediction of SGA was less successful. Protein differential abundance analysis revealed 148 proteins with higher abundance in LGA compared to AGA pregnancies, while only four proteins were differentially abundant between the SGA and AGA. The principal findings indicate that the maternal plasma proteome may hold potential biomarkers of LGA.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951228","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}

引用次数: 0

How to Train a Postprocessor for Tandem Mass Spectrometry Proteomics Database Search While Maintaining Control of the False Discovery Rate. 如何训练串联质谱法蛋白质组学数据库搜索的后处理器，同时保持对错误发现率的控制。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-02 Epub Date: 2025-03-31 DOI: 10.1021/acs.jproteome.4c00742

Jack Freestone, Lukas Käll, William Stafford Noble, Uri Keich

{"title":"How to Train a Postprocessor for Tandem Mass Spectrometry Proteomics Database Search While Maintaining Control of the False Discovery Rate.","authors":"Jack Freestone, Lukas Käll, William Stafford Noble, Uri Keich","doi":"10.1021/acs.jproteome.4c00742","DOIUrl":"10.1021/acs.jproteome.4c00742","url":null,"abstract":"Decoy-based methods are a popular choice for the statistical validation of peptide detection in tandem mass spectrometry and proteomics data. Such methods can achieve a substantial boost in statistical power when coupled with postprocessors such as Percolator that use auxiliary features to learn a better-discriminating scoring function. However, we recently showed that Percolator can struggle to control the false discovery rate (FDR) when reporting the list of discovered peptides. To address this problem, we introduce Percolator-RESET, which is an adaptation of our recently developed RESET meta-procedure to the peptide detection problem. Specifically, Percolator-RESET fuses Percolator's iterative SVM training procedure with RESET's general framework to provide valid false discovery rate control. Percolator-RESET operates in both a standard single-decoy mode and a two-decoy mode, with the latter requiring the generation of two decoys per target. We demonstrate that Percolator-RESET controls the FDR in both modes, both theoretically and empirically, while typically reporting only a marginally smaller number of discoveries than Percolator in the single-decoy mode. The two-decoy mode is marginally more powerful than both Percolator and the single-decoy mode and exhibits less variability than the latter.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"2266-2279"},"PeriodicalIF":3.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750274","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}

引用次数: 0

NA_mCNN: Classification of Sodium Transporters in Membrane Proteins by Integrating Multi-Window Deep Learning and ProtTrans for Their Therapeutic Potential. NA_mCNN：基于多窗口深度学习和ProtTrans的膜蛋白钠转运蛋白分类研究

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-02 Epub Date: 2025-04-07 DOI: 10.1021/acs.jproteome.4c00884

Muhammad Shahid Malik, Van The Le, Yu-Yen Ou

{"title":"NA_mCNN: Classification of Sodium Transporters in Membrane Proteins by Integrating Multi-Window Deep Learning and ProtTrans for Their Therapeutic Potential.","authors":"Muhammad Shahid Malik, Van The Le, Yu-Yen Ou","doi":"10.1021/acs.jproteome.4c00884","DOIUrl":"10.1021/acs.jproteome.4c00884","url":null,"abstract":"Sodium transporters maintain cellular homeostasis by transporting ions, minerals, and nutrients across the membrane, and Na+/K+ ATPases facilitate the cotransport of solutes in neurons, muscle cells, and epithelial cells. Sodium transporters are important for many physiological processes, and their dysfunction leads to diseases such as hypertension, diabetes, neurological disorders, and cancer. The NA_mCNN computational method highlights the functional diversity and significance of sodium transporters in membrane proteins using protein language model embeddings (PLMs) and multiple-window scanning deep learning models. This work investigates PLMs that include Tape, ProtTrans, ESM-1b-1280, and ESM-2-128 to achieve more accuracy in sodium transporter classification. Five-fold cross-validation and independent testing demonstrate ProtTrans embedding robustness. In cross-validation, ProtTrans achieved an AUC of 0.9939, a sensitivity of 0.9829, and a specificity of 0.9889, demonstrating its ability to distinguish positive and negative samples. In independent testing, ProtTrans maintained a sensitivity of 0.9765, a specificity of 0.9991, and an AUC of 0.9975, which indicates its high level of discrimination. This study advances the understanding of sodium transporter diversity and function, as well as their role in human pathophysiology. Our goal is to use deep learning techniques and protein language models for identifying sodium transporters to accelerate identification and develop new therapeutic interventions.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"2324-2335"},"PeriodicalIF":3.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12053934/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802041","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}

引用次数: 0

Proteomic Insights into the Adaptation of Acidithiobacillus ferridurans to Municipal Solid Waste Incineration Residues for Enhanced Bioleaching Efficiency. 酸性铁硫杆菌适应城市生活垃圾焚烧残渣以提高生物浸出效率的蛋白质组学研究。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-02 Epub Date: 2025-04-09 DOI: 10.1021/acs.jproteome.4c00527

Jiri Kucera, Klemens Kremser, Pavel Bouchal, David Potesil, Tomas Vaculovic, Dalibor Vsiansky, Georg M Guebitz, Martin Mandl

{"title":"Proteomic Insights into the Adaptation of Acidithiobacillus ferridurans to Municipal Solid Waste Incineration Residues for Enhanced Bioleaching Efficiency.","authors":"Jiri Kucera, Klemens Kremser, Pavel Bouchal, David Potesil, Tomas Vaculovic, Dalibor Vsiansky, Georg M Guebitz, Martin Mandl","doi":"10.1021/acs.jproteome.4c00527","DOIUrl":"10.1021/acs.jproteome.4c00527","url":null,"abstract":"Acidithiobacillus spp. have traditionally been utilized to extract metals from mineral ores through bioleaching. This process has recently expanded to include artificial ores, such as those derived from municipal solid waste incineration (MSWI) residues. Previous studies have indicated that microbial adaptation enhances bioleaching efficiency, prompting this study to identify proteins involved in the adaptation of A. ferridurans to MSWI residues. We employed data-independent acquisition-parallel accumulation serial fragmentation to determine the proteomic response of A. ferridurans DSM 583 to three distinct materials: bottom ash (BA), kettle ash (KA), and filter ash (FA), which represent typical MSWI residues. Our findings indicate that, irrespective of the residue type, a suite of membrane transporters, porins, efflux pumps, and specific electron and cation transfer proteins was notably upregulated. The upregulation of certain proteins involved in anaerobic pathways suggested the development of a spontaneous microaerobic environment, which minimally impacted the bioleaching efficiency. Additionally, the adaptation was most efficient at half the target FA concentration, marked by a significant increase in the detoxification and efflux systems required by microorganisms to tolerate high heavy metal concentrations. Given that metal recovery peaked at lower FA concentrations for most metals of interest, further adaptation at the level of protein expression may not be warranted for improved bioleaching outcomes.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"2243-2255"},"PeriodicalIF":3.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12053936/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810093","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}

引用次数: 0

Online Alkaline-pH Reversed-Phase Nanoelectrospray-Tandem Mass Spectrometry Complements Traditional Phosphoproteomic Analysis via Influencing Charge State Distribution of Phosphopeptides. 在线碱性- ph反相纳米电喷雾串联质谱法通过影响磷酸肽的电荷态分布来补充传统的磷酸蛋白质组学分析。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-02 Epub Date: 2025-04-10 DOI: 10.1021/acs.jproteome.4c01091

Yuqiu Wang, Jing Gao, Wenfan Xie, Minchu Tang, Xin Chen, Lv Chen, Hongxu Chen, Zhicheng Yang, Qiang Gao, Yansheng Liu, Hu Zhou

{"title":"Online Alkaline-pH Reversed-Phase Nanoelectrospray-Tandem Mass Spectrometry Complements Traditional Phosphoproteomic Analysis via Influencing Charge State Distribution of Phosphopeptides.","authors":"Yuqiu Wang, Jing Gao, Wenfan Xie, Minchu Tang, Xin Chen, Lv Chen, Hongxu Chen, Zhicheng Yang, Qiang Gao, Yansheng Liu, Hu Zhou","doi":"10.1021/acs.jproteome.4c01091","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01091","url":null,"abstract":"Phosphorylation (O-linked and N-linked) plays an important role in biological functions and cell signaling. Here, we employed a one-dimensional online alkaline-pH reversed-phase nanoelectrospray-tandem mass spectrometry (alkaline-pH-MS/MS) for the investigation of global phosphorylation. In this method, phosphopeptides were separated on a nanoflow C18 column with an alkaline-pH gradient and directly introduced to the mass spectrometer through nanoelectrospray ionization. Although the phosphosites and phosphopeptides identified by alkaline-pH-MS/MS were slightly lower than those of traditional online low-pH reversed-phase tandem MS (low-pH-MS/MS), these two methods were highly complementary to each other. This alkaline-pH-MS/MS may affect the actual polarity and CSD of phosphopeptides, consequently improving the identification of multiply phosphorylated peptides. Moreover, alkaline-pH-MS/MS was compatible with other peptide fractionation and phosphopeptide enrichment techniques, such as offline high-pH or low-pH reversed-phase liquid chromatography fractionation. The complementarity of alkaline-pH-MS/MS and low-pH-MS/MS was further demonstrated by the tandem mass tag (TMT)-based quantitative phosphoproteomic analysis of five pairs of hepatocellular carcinoma (HCC) tumors and normal adjacent tissues (NATs). Furthermore, unique information on significantly changed phosphosites was observed by alkaline-pH-MS/MS. This study provided an alternative and complementary tool for global analysis of both O- and N-phosphoproteome, which may be beneficial for the discovery of phosphoproteins with significant biological functions.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 5","pages":"2443-2453"},"PeriodicalIF":3.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143952728","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}

引用次数: 0

Impact of Static Myoblast Loading on Protein Secretion Linked to Tenocyte Migration. 静态肌母细胞负载对与小细胞迁移相关的蛋白质分泌的影响。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-02 Epub Date: 2025-04-09 DOI: 10.1021/acs.jproteome.5c00068

Junhong Li, Xin Zhou, Jialin Chen, Shaochun Zhu, Andre Mateus, Pernilla Eliasson, Paul J Kingham, Ludvig J Backman

{"title":"Impact of Static Myoblast Loading on Protein Secretion Linked to Tenocyte Migration.","authors":"Junhong Li, Xin Zhou, Jialin Chen, Shaochun Zhu, Andre Mateus, Pernilla Eliasson, Paul J Kingham, Ludvig J Backman","doi":"10.1021/acs.jproteome.5c00068","DOIUrl":"10.1021/acs.jproteome.5c00068","url":null,"abstract":"Exercise has been shown to promote wound healing, including tendon repair. Myokines released from the exercised muscles are believed to play a significant role in this process. In our previous study, we used an in vitro coculture and loading model to demonstrate that 2% static loading of myoblasts increased the migration and proliferation of cocultured tenocytes─two crucial aspects of wound healing. IGF-1, released from myoblasts in response to 2% static loading, was identified as a contributor to the increased proliferation. However, the factors responsible for the enhanced migration remained unknown. In the current study, we subjected myoblasts in single culture conditions to 2, 5, and 10% static loading and performed proteomic analysis of the cell supernatants. Gene Ontology (GO) analysis revealed that 2% static loading induced the secretion of NBL1, C5, and EFEMP1, which is associated with cell migration and motility. Further investigation by adding exogenous recombinant proteins to human tenocytes showed that NBL1 increased tenocyte migration but not proliferation. This effect was not observed with treatments using C5 and EFEMP1.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"2529-2541"},"PeriodicalIF":3.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12053940/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810089","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}

引用次数: 0

Alteration of Ubiquitination in the Brain of ENOPH1 Knockout Mice after Early Ischemic Stroke. 早期缺血性脑卒中后ENOPH1基因敲除小鼠脑内泛素化的改变。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-02 Epub Date: 2025-04-01 DOI: 10.1021/acs.jproteome.4c00913

Yike Wu, Ping Tang, Zhengzheng Huang, Dayong Gu, Dewen Yan, Li Su, Yuan Zhang

{"title":"Alteration of Ubiquitination in the Brain of ENOPH1 Knockout Mice after Early Ischemic Stroke.","authors":"Yike Wu, Ping Tang, Zhengzheng Huang, Dayong Gu, Dewen Yan, Li Su, Yuan Zhang","doi":"10.1021/acs.jproteome.4c00913","DOIUrl":"10.1021/acs.jproteome.4c00913","url":null,"abstract":"Enolase-phosphatase 1 (ENOPH1) is a newly identified enzyme associated with stress responses and neurodevelopmental disorders. Our previous study found that ENOPH1 mediates cerebral cell apoptosis and blood-brain barrier (BBB) dysfunction during early cerebral ischemia. Ubiquitination has been identified in neuronal damage and the neuroinflammatory response in ischemic stroke. However, whether ENOPH1 regulates ischemia-induced protein ubiquitination alteration is yet unclear. Hence, the present study explored changes in the ubiquitinomic in early ischemic brain tissues between wildtype and ENOPH1 knockout mice using a comprehensive quantitative analysis. Our results showed that 4000 ubiquitination-modified sites in 1613 proteins were quantified, with 772 ubiquitinated sites in 464 proteins significantly decreasing or increasing after ENOPH1 knockout (fold change >1.5 or <1/1.5, p < 0.05). When compared to our previous parallel proteome profiles, common differential proteins FKBP5 and Claudin-11 were observed and further validated. ENOPH1 regulates the degradation of FKBP5 and the promotion of Claudin-11 by ubiquitination mediation, leading to the activation or inhibition of nuclear-initiated steroid signaling and transendothelial migration pathways. These findings, for the first time, identified ubiquitinomic features of early ischemic brain tissues after ENOPH1 knockout, suggesting that ENOPH1 may regulate neuroinflammatory stress and barrier function by modifying FKBP5 and Claudin-11 protein ubiquitination.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"2349-2357"},"PeriodicalIF":3.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762475","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}

引用次数: 0

Identification of Salivary Biomarkers in Colorectal Cancer by Integrating Olink Proteomics and Metabolomics. 结合Olink蛋白质组学和代谢组学鉴定结直肠癌唾液生物标志物。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-02 Epub Date: 2025-04-04 DOI: 10.1021/acs.jproteome.5c00091

Hairong Su, Xiangyu Gu, Weizheng Zhang, Fengye Lin, Xinyi Lu, Xuan Zeng, Chuyang Wang, Weicheng Chen, Wofeng Liu, Ping Tan, Liaonan Zou, Bing Gu, Qubo Chen

{"title":"Identification of Salivary Biomarkers in Colorectal Cancer by Integrating Olink Proteomics and Metabolomics.","authors":"Hairong Su, Xiangyu Gu, Weizheng Zhang, Fengye Lin, Xinyi Lu, Xuan Zeng, Chuyang Wang, Weicheng Chen, Wofeng Liu, Ping Tan, Liaonan Zou, Bing Gu, Qubo Chen","doi":"10.1021/acs.jproteome.5c00091","DOIUrl":"10.1021/acs.jproteome.5c00091","url":null,"abstract":"Identifying novel biomarkers is crucial for early detection of colorectal cancer (CRC). Saliva, as a noninvasive sample, holds promise for CRC detection. Here, we used Olink proteomics and untargeted metabolomics to analyze saliva samples from CRC patients and healthy controls with the aim of identifying candidate biomarkers in CRC saliva. Univariate and multivariate analyses revealed 16 differentially expressed proteins (DEPs) and 40 differentially accumulated metabolites (DAMs). Pathway enrichment showed DEPs were mainly involved in cancer transcriptional dysregulation, Toll-like receptor signaling, and chemokine signaling. Metabolomics analysis highlighted significant changes in amino acid metabolites, particularly in pathways such as arginine biosynthesis, histidine metabolism, and cysteine and methionine metabolism. Random forest analysis and ELISA validation identified four potential biomarkers: succinate, l-methionine, GZMB, and MMP12. A combined protein-metabolite diagnostic model was developed using logistic regression, achieving an area under the curve of 0.933 (95% CI: 0.871-0.996) for the discovery cohort and 0.969 (95% CI: 0.918-1.000) for the validation cohort, effectively distinguishing CRC patients from healthy individuals. In conclusion, our study identified and validated a panel of noninvasive saliva-based biomarkers that could improve CRC screening and provide new insights into clinical CRC diagnosis.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"2542-2552"},"PeriodicalIF":3.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12054530/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778609","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}

引用次数: 0

Effects of In Vitro Hemolysis and Repeated Freeze-Thaw Cycles in Protein Abundance Quantification Using the SomaScan and Olink Assays. 体外溶血和反复冻融循环对SomaScan和Olink测定蛋白丰度的影响。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-02 Epub Date: 2025-04-18 DOI: 10.1021/acs.jproteome.5c00069

Julián Candia, Giovanna Fantoni, Ruin Moaddel, Francheska Delgado-Peraza, Nader Shehadeh, Toshiko Tanaka, Luigi Ferrucci

{"title":"Effects of In Vitro Hemolysis and Repeated Freeze-Thaw Cycles in Protein Abundance Quantification Using the SomaScan and Olink Assays.","authors":"Julián Candia, Giovanna Fantoni, Ruin Moaddel, Francheska Delgado-Peraza, Nader Shehadeh, Toshiko Tanaka, Luigi Ferrucci","doi":"10.1021/acs.jproteome.5c00069","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00069","url":null,"abstract":"SomaScan and Olink are affinity-based platforms that aim to estimate the relative abundance of thousands of human proteins with a broad range of endogenous concentrations. In this study, we investigated the effects of in vitro hemolysis and repeated freeze-thaw cycles in protein abundance quantification across 10,776 (11 K SomaScan) and 1472 (Olink Explore 1536) analytes, respectively. Using SomaScan, we found two distinct groups, each one consisting of 4% of all aptamers, affected by either hemolysis or freeze-thaw cycles. Using Olink, we found 6% of analytes affected by freeze-thaw cycles and nearly half of all measured probes significantly impacted by hemolysis. Moreover, we observed that Olink probes affected by hemolysis target proteins with a larger number of annotated protein-protein interactions. We found that Olink probes affected by hemolysis were significantly associated with the erythrocyte proteome, whereas SomaScan probes were not. Given the extent of the observed nuisance effects, we propose that unbiased, quantitative methods of evaluating hemolysis, such as the hemolysis index successfully implemented in many clinical laboratories, should be adopted in proteomics studies. We provide detailed results for each SomaScan and Olink probe in the form of extensive Supporting Information files to be used as resources for the growing user communities of both platforms.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 5","pages":"2517-2528"},"PeriodicalIF":3.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12053949/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951422","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}

引用次数: 0

Lipidomics Atlas Tracks Alterations Associated with Deltamethrin-Induced Developmental Neurotoxicity in Embryonic Zebrafish. 脂质组学图谱追踪与溴氰菊酯诱导的胚胎斑马鱼发育神经毒性相关的改变。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-02 Epub Date: 2025-04-03 DOI: 10.1021/acs.jproteome.4c00779

Longhua Gao, Jingwen Hao, Zhengyi Hua, Changchun Zeng, Jia Li, Jun Zeng

{"title":"Lipidomics Atlas Tracks Alterations Associated with Deltamethrin-Induced Developmental Neurotoxicity in Embryonic Zebrafish.","authors":"Longhua Gao, Jingwen Hao, Zhengyi Hua, Changchun Zeng, Jia Li, Jun Zeng","doi":"10.1021/acs.jproteome.4c00779","DOIUrl":"10.1021/acs.jproteome.4c00779","url":null,"abstract":"Deltamethrin (DM) is a widely used pyrethroid pesticide associated with childhood neurodevelopmental disorders. However, the specific impact of DM exposure during distinct early life stages remains unclear. Here, zebrafish embryos were exposed to DM at different stages: before (10-16 hpf), at the onset of (16-24 hpf), at the peak of (24-36 hpf) hypothalamic neurogenesis, and continuously from 10 to 120 hpf (subchronic exposure), using different dosages (1, 100, and 250 nM). Exposure to middle/high-dose DM at 24-36 and 10-120 hpf significantly reduced zebrafish locomotor activities and increased apoptotic cells in the spinal cord. As a pivotal factor in central nervous system disorder progression, altered lipid metabolism was investigated using nontargeted lipidomic analysis. DM exposure at 10-16 and 24-36 hpf led to the most significant lipidome reprogramming. Despite exhibiting a dose-dependent trend, even low-dose DM changed the lipidome. Cer 40:2;2 and PG 44:12 showed potential in identifying DM exposure effects. Significant changes in sphingolipid, cardiolipin, phosphatidylglycerol, and glycerolipid pathways were linked to DM-induced developmental neurotoxicity, indicating impaired membrane function, mitochondrial damage, and disrupted energy metabolism. Our study sheds new light on assessing early neurodevelopmental disturbances and identifying intervention targets, emphasizing sensitivity to DM during the critical early phase of neurodevelopment.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"2280-2290"},"PeriodicalIF":3.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143770742","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}

引用次数: 0