Journal of Proteome Research最新文献

Proteomic Plasticity in the Coral Montipora capitata Gamete Bundles after Parent Thermal Bleaching.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-25 DOI: 10.1021/acs.jproteome.4c00946

Emma B Timmins-Schiffman, Rayhan Khanna, Tanya Brown, Jenna Dilworth, Brendan X MacLean, Miranda C Mudge, Samuel J White, Carly D Kenkel, Lisa J Rodrigues, Brook L Nunn, Jacqueline L Padilla-Gamiño

{"title":"Proteomic Plasticity in the Coral Montipora capitata Gamete Bundles after Parent Thermal Bleaching.","authors":"Emma B Timmins-Schiffman, Rayhan Khanna, Tanya Brown, Jenna Dilworth, Brendan X MacLean, Miranda C Mudge, Samuel J White, Carly D Kenkel, Lisa J Rodrigues, Brook L Nunn, Jacqueline L Padilla-Gamiño","doi":"10.1021/acs.jproteome.4c00946","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00946","url":null,"abstract":"Coral reefs are vital to marine biodiversity and human livelihoods, but they face significant threats from climate change. Increased ocean temperatures drive massive \"bleaching\" events, during which corals lose their symbiotic algae and the important metabolic resources those algae provide. Proteomics is a crucial tool for understanding coral function and tolerance to thermal stress, as proteins drive physiological processes and accurately represent cell functional phenotypes. We examined the physiological condition of coral (Montipora capitata) gametes from parents that either experienced thermal bleaching or were nonbleached controls by comparing data dependent (DDA) and data independent (DIA) acquisition methods and peptide quantification (spectral counting and area-under-the-curve, AUC) strategies. For DDA, AUC captured a broader dynamic range than spectral counting. DIA yielded better coverage of low abundance proteins than DDA and a higher number of proteins, making it the more suitable method for detecting subtle, yet biologically significant, shifts in protein abundance in gamete bundles. Gametes from bleached corals showed a broadscale decrease in metabolic proteins involved in carbohydrate metabolism, citric acid cycle, and protein translation. This metabolic plasticity could reveal how organisms and their offspring acclimatize and adapt to future environmental stress, ultimately shaping the resilience and dynamics of coral populations.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490332","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

Heterogeneities of Site-Specific N-Glycosylation in the Hippocampus of Depression-like Behavior Models in Mice Induced by Acute Stress and Chronic Stress.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-24 DOI: 10.1021/acs.jproteome.4c00655

Pengyu Ren, Longhui Fu, Xiaojuan Gong, Li Jia, Boqiang Lyu, Mengke Wang, Siyuan Zhang, Shisheng Sun, Na Zhao, Zongben Xu, Jie Zhu

{"title":"Heterogeneities of Site-Specific N-Glycosylation in the Hippocampus of Depression-like Behavior Models in Mice Induced by Acute Stress and Chronic Stress.","authors":"Pengyu Ren, Longhui Fu, Xiaojuan Gong, Li Jia, Boqiang Lyu, Mengke Wang, Siyuan Zhang, Shisheng Sun, Na Zhao, Zongben Xu, Jie Zhu","doi":"10.1021/acs.jproteome.4c00655","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00655","url":null,"abstract":"It is well established that acute and chronic stress contributes to the onset and progression of depression, but the underlying mechanisms have not been elucidated. Here an integrated N-glycoproteomic and proteomic analysis was performed to investigate heterogeneities of glycoprotein and site-specific glycosylation between the hippocampi of control, acute stress-affected (AS), and chronic mild stress-affected (CMS) mice. 1063 unique intact N-glycopeptides, 116 N-glycan compositions, and 512 glycosylation sites were identified. CMS and AS had significant effects on glycosylation. CMS reduced multiantenna glycosylation (N8H8 and N6H5F1S1) more strongly, while AS reduced multiantenna glycosylation (N5H3F1) more strongly. CMS inhibited high-mannose synthesis with high polymerization (N2H9 and N2H8), while AS inhibited high-mannose synthesis with low polymerization (N2H6, H2H5). Furthermore, 26 and 39 glycosylation-related genes (GRGs) were identified in the AS and CMS groups, separately. Functional enrichment analysis for GRGs in the AS and CMS groups exhibited that the up-regulated functions were leading edge membrane and cell adhesion molecule binding; meanwhile, the down-regulated functions were cAMP signaling pathways. Finally, tSNE analysis based on ScRNA-seq revealed that core GRGs were highly expressed in astrocytes. All of these findings improve our understanding of glycosylation in stress-related depression, providing valuable data resources for depression pathogenesis exploration and novel therapeutic target discovery.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490331","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

Enhancing Proteomics Quality Control: Insights from the Visualization Tool QCeltis. 加强蛋白质组学质量控制：可视化工具 QCeltis 的启示。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-24 DOI: 10.1021/acs.jproteome.4c00777

Manasa Vegesna, Niveda Sundararaman, Ajay Bharadwaj, Kirstin Washington, Rakhi Pandey, Ali Haghani, Blandine Chazarin, Aleksandra Binek, Qin Fu, Susan Cheng, David Herrington, Jennifer E Van Eyk

{"title":"Enhancing Proteomics Quality Control: Insights from the Visualization Tool QCeltis.","authors":"Manasa Vegesna, Niveda Sundararaman, Ajay Bharadwaj, Kirstin Washington, Rakhi Pandey, Ali Haghani, Blandine Chazarin, Aleksandra Binek, Qin Fu, Susan Cheng, David Herrington, Jennifer E Van Eyk","doi":"10.1021/acs.jproteome.4c00777","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00777","url":null,"abstract":"Large-scale mass-spectrometry-based proteomics experiments are complex and prone to analytical variability, requiring rigorous quality checks across each step in the workflow: sample preparation, chromatography, mass spectrometry, and the bioinformatics stages. This includes quality control (QC) measures that address biological and technical variation. Most QC approaches involve detecting sample outliers and monitoring parameters related to sample preparation and mass spectrometer performance. Evaluating these parameters regularly is essential for reliable downstream analysis and proteomics research. Here, we introduce \"QCeltis\", a Python package designed to facilitate automated QC analysis across the proteomics workflow, aiding in the identification of technical biases and consistency verification. QCeltis is a versatile tool for detecting QC issues in large-scale data-independent acquisition proteomics experiments by not only identifying sample preparation and acquisition issues but also aiding in differentiating between QC issues vs batch effects. QCeltis is available for command-line use in Windows and Linux environments. We present three case studies showcasing QCeltis's capabilities across different data sets, including depleted plasma, whole blood vs plasma, and dried blood spot samples, emphasizing its potential impact on large-scale proteomics projects. This package can be used to enhance data reliability and enable nuanced downstream analysis and interpretation for proteomics studies.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481731","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

A Scalable, Web-Based Platform for Proteomics Data Processing, Result Storage and Analysis.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-21 DOI: 10.1021/acs.jproteome.4c00871

Markus Schneider, Daniel P Zolg, Patroklos Samaras, Samia Ben Fredj, Dulguun Bold, Agnes Guevende, Alexander Hogrebe, Michelle T Berger, Michael Graber, Vishal Sukumar, Lizi Mamisashvili, Igor Bronsthein, Layla Eljagh, Siegfried Gessulat, Florian Seefried, Tobias Schmidt, Martin Frejno

{"title":"A Scalable, Web-Based Platform for Proteomics Data Processing, Result Storage and Analysis.","authors":"Markus Schneider, Daniel P Zolg, Patroklos Samaras, Samia Ben Fredj, Dulguun Bold, Agnes Guevende, Alexander Hogrebe, Michelle T Berger, Michael Graber, Vishal Sukumar, Lizi Mamisashvili, Igor Bronsthein, Layla Eljagh, Siegfried Gessulat, Florian Seefried, Tobias Schmidt, Martin Frejno","doi":"10.1021/acs.jproteome.4c00871","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00871","url":null,"abstract":"The exponential increase in proteomics data presents critical challenges for conventional processing workflows. These pipelines often consist of fragmented software packages, glued together using complex in-house scripts or error-prone manual workflows running on local hardware, which are costly to maintain and scale. The MSAID Platform offers a fully automated, managed proteomics data pipeline, consolidating formerly disjointed functions into unified, API-driven services that cover the entire process from raw data to biological insights. Backed by the cloud-native search algorithm CHIMERYS, as well as scalable cloud compute instances and data lakes, the platform facilitates efficient processing of large data sets, automation of processing via the command line, systematic result storage, analysis, and visualization. The data lake supports elastically growing storage and unified query capabilities, facilitating large-scale analyses and efficient reuse of previously processed data, such as aggregating longitudinally acquired studies. Users interact with the platform via a web interface, CLI client, or API, providing flexible, automated access. Readily available tools for accessing result data include browser-based interrogation and one-click visualizations for statistical analysis. The platform streamlines research processes, making advanced and automated proteomic workflows accessible to a broader range of scientists. The MSAID Platform is globally available via https://platform.msaid.io.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143471994","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

Multiomics Analysis of Liver Molecular Dysregulation Leading to Nonviral-Related Hepatocellular Carcinoma Development.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-21 DOI: 10.1021/acs.jproteome.4c00729

Hikaru Nakahara, Atsushi Ono, C Nelson Hayes, Yuki Shirane, Ryoichi Miura, Yasutoshi Fujii, Yosuke Tamura, Shinsuke Uchikawa, Hatsue Fujino, Takashi Nakahara, Eisuke Murakami, Masami Yamauchi, Tomokazu Kawaoka, Daiki Miki, Masataka Tsuge, Tsuyoshi Kobayashi, Hideki Ohdan, Koji Arihiro, Shiro Oka

{"title":"Multiomics Analysis of Liver Molecular Dysregulation Leading to Nonviral-Related Hepatocellular Carcinoma Development.","authors":"Hikaru Nakahara, Atsushi Ono, C Nelson Hayes, Yuki Shirane, Ryoichi Miura, Yasutoshi Fujii, Yosuke Tamura, Shinsuke Uchikawa, Hatsue Fujino, Takashi Nakahara, Eisuke Murakami, Masami Yamauchi, Tomokazu Kawaoka, Daiki Miki, Masataka Tsuge, Tsuyoshi Kobayashi, Hideki Ohdan, Koji Arihiro, Shiro Oka","doi":"10.1021/acs.jproteome.4c00729","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00729","url":null,"abstract":"Chronic liver diseases exhibit diverse backgrounds, and it is believed that numerous factors contribute to progression to cancer. To achieve effective prevention of nonviral hepatocellular carcinoma, it is imperative to identify fundamental molecular abnormalities at the patient level. Utilizing cancer-adjacent liver tissues obtained from hepatocellular carcinoma patients (chronic liver disease), we conducted RNA-Seq and metabolome analyses. In the chronic liver disease cohort, upregulation of inflammation-associated signals was observed, concomitant with accumulation of acylcarnitine and fatty acid and depletion of NADP+, gamma-tocopherol, and dehydroisoandrosterone-3-sulfate-1 (DHEAS). To minimize heterogeneity, we performed multiomics clustering, successfully categorizing the chronic liver disease cases into two distinct subtypes. Subtype 1 demonstrated elevated inflammatory levels, whereas Subtype 2 included a disproportionately high proportion of elderly cases. Furthermore, RNA-Seq analysis revealed upregulation of inflammatory signals in Subtype 1, while both subtypes exhibited downregulation of fatty acid metabolism. Metabolome analysis indicated a tendency of increased acylcarnitine levels in Subtype 1 and augmented fatty acid accumulation in Subtype 2. Validation of differentially expressed genes using the Gene Expression Omnibus (GEO) data set revealed the potential for amelioration through supplementation with antioxidants such as epigallocatechin gallate (EGCG).","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466570","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

Modified Decision Tree with Custom Splitting Logic Improves Generalization across Multiple Brains' Proteomic Data Sets of Alzheimer's Disease.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-21 DOI: 10.1021/acs.jproteome.4c00677

Mark V Ivanov, Anna S Kopeykina, Elizaveta M Kazakova, Irina A Tarasova, Zhao Sun, Valeriy I Postoenko, Jinghua Yang, Mikhail V Gorshkov

{"title":"Modified Decision Tree with Custom Splitting Logic Improves Generalization across Multiple Brains' Proteomic Data Sets of Alzheimer's Disease.","authors":"Mark V Ivanov, Anna S Kopeykina, Elizaveta M Kazakova, Irina A Tarasova, Zhao Sun, Valeriy I Postoenko, Jinghua Yang, Mikhail V Gorshkov","doi":"10.1021/acs.jproteome.4c00677","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00677","url":null,"abstract":"Many factors negatively affect a generalization of the findings in discovery proteomics. They include differentiation between patient cohorts, a variety of experimental conditions, etc. We presented a machine-learning-based workflow for proteomics data analysis, aiming at improving generalizability across multiple data sets. In particular, we customized the decision tree model by introducing a new parameter, min_groups_leaf, which regulates the presence of the samples from each data set inside the model's leaves. Further, we analyzed a trend for the feature importance's curve as a function of the novel parameter for feature selection to a list of proteins with significantly improved generalization. The developed workflow was tested using five proteomic data sets obtained for post-mortem human brain samples of Alzheimer's disease. The data sets consisted of 535 LC-MS/MS acquisition files. The results were obtained for two different pipelines of data processing: (1) MS1-only processing based on DirectMS1 search engine and (2) a standard MS/MS-based one. Using the developed workflow, we found seven proteins with expression patterns that were unique for asymptomatic Alzheimer patients. Two of them, Serotransferrin TRFE and DNA repair nuclease APEX1, may be potentially important for explaining the lack of dementia in patients with the presence of neuritic plaques and neurofibrillary tangles.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143471995","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

γ Irradiation Alters the Staphylococcus aureus Proteome and Enhances Pathogenicity.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-20 DOI: 10.1021/acs.jproteome.4c01018

Jingjing Liu, Xinghua Jin, Jingxin Zhu, Jundong Feng, Jian Zhao, Yixuan Wang, Quan Wang, Xiaofeng Song

{"title":"γ Irradiation Alters the Staphylococcus aureus Proteome and Enhances Pathogenicity.","authors":"Jingjing Liu, Xinghua Jin, Jingxin Zhu, Jundong Feng, Jian Zhao, Yixuan Wang, Quan Wang, Xiaofeng Song","doi":"10.1021/acs.jproteome.4c01018","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01018","url":null,"abstract":"Staphylococcus aureus (S. aureus) infection has become one of the most common and severe complications among cancer patients. The impact of γ radiation from radiotherapy on S. aureus's growth and virulence is not yet fully understood. In this study, S. aureus was exposed to γ radiation at a dose of 100 Gy, and its descendants were cultured under normal conditions. Proteome alternations of unirradiated, irradiated, and descendants of irradiated S. aureus were identified by using data-independent acquisition (DIA) proteomic technology. To investigate the consequences of proteome alternations induced by γ irradiation in S. aureus, functional enrichment analysis, pathway enrichment analysis, and protein-protein interaction network analysis were performed. Differentially expressed proteins (DEPs) in the irradiated S. aureus and its descendants were primarily enriched in lipoteichoic acid biosynthesis, S. aureus infection, two-component system, and cationic antimicrobial peptide resistance, suggesting an enhanced infection ability. A strong infection ability is typically associated with increased biofilm formation. Both the proteome study and the biofilm assay indicate that γ irradiation enhances the infection ability of S. aureus, likely resulting in increased pathogenicity.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456251","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

Proteomics Reveals That Vitamin D Deficiency Leads to Immunoglobulin Abnormalities and Immune Dysregulation in Patients with Post-COVID-19 Condition.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-20 DOI: 10.1021/acs.jproteome.4c01120

Wenrui Ji, Xiaomin Xie, Guirong Bai, Yalei Fan, Yanting He, Li Zhang, Haiyan Zhou, Ling Li, Huan Li

{"title":"Proteomics Reveals That Vitamin D Deficiency Leads to Immunoglobulin Abnormalities and Immune Dysregulation in Patients with Post-COVID-19 Condition.","authors":"Wenrui Ji, Xiaomin Xie, Guirong Bai, Yalei Fan, Yanting He, Li Zhang, Haiyan Zhou, Ling Li, Huan Li","doi":"10.1021/acs.jproteome.4c01120","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01120","url":null,"abstract":"Vitamin D (VD) levels are closely related to the occurrence of post-COVID-19 conditions (PCCs), but the specific mechanism is still unclear. Here, a total of 50 PCC patient serum samples were divided into the VD sufficient group (VD ≥ 30 ng/mL), the VD insufficient group (20 ng/mL ≤ VD < 30 ng/mL), and the VD deficiency group (VD < 20 ng/mL) and then subjected to proteomic analysis. We identified 15 differential abundance proteins (DAPs) between the VD sufficient and VD insufficient groups, including 5 immunoglobulin proteins (JCHAJN, IGHV4-28, GHV4-34, IGHM, and IGLV2-11), which were significantly negatively correlated with VD levels in PCC patients. These DAPs were primarily enriched in immune-related pathways such as the TNF signaling pathway and the B cell receptor signaling pathway. Compared with the VD insufficient group, VD deficiency resulted in 4 proteins being upregulated and 8 proteins being downregulated. The declined abundance of IGLV1-47 negatively correlated with serum VD levels. Albumin (ALB) was in the center of the protein-protein interaction (PPI) network map of all DAPs and was negatively correlated with serum VD levels. In conclusion, VD insufficiency/deficiency leads to abnormalities in immunoglobulin heavy, light, and J chains, resulting in PCC syndrome. VD supplementation may be a potential therapeutic strategy to alleviate the symptoms of PCC.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466571","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

Swift Universal Glycan Acquisition (SUGA) Enables Quantitative Glycan Profiling across Diverse Sample Types.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-20 DOI: 10.1021/acs.jproteome.4c00657

Christopher Ashwood, Cecilia Voelcker, Richard D Cummings

{"title":"Swift Universal Glycan Acquisition (SUGA) Enables Quantitative Glycan Profiling across Diverse Sample Types.","authors":"Christopher Ashwood, Cecilia Voelcker, Richard D Cummings","doi":"10.1021/acs.jproteome.4c00657","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00657","url":null,"abstract":"The ability to rapidly analyze complex mixtures of glycans derived from glycoproteins is important, but techniques are often laborious and require multiple glycan derivatization steps. Here, we describe an approach termed Swift Universal Glycan Acquisition (SUGA) in which the total released, nonreduced N-glycan samples are analyzed following direct injection and electrospray ionization in a mass spectrometer with a rapid 3 min run time for each sample. As electrospray ionization (ESI) can generate multiple charge states and adducts for the same glycan composition (MS1), deconvolution is performed to yield the relative intensity profile for each detected glycan composition; each annotated composition is supported by an annotated MS2 spectrum. This combination of MS1 and MS2 data enables confident glycan identification. The data obtained by SUGA are comparable to those obtained using permethylated N-glycans analyzed by matrix-assisted laser desorption/ionization (MALDI)-MS. The SUGA approach was applied to the analyses of several purified glycoproteins and N-glycans derived from cells and compared to spectra obtained following permethylation and analysis by MALDI-MS. This new approach will facilitate the rapid and high-throughput analysis of N-glycans from diverse biological samples.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466572","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

Quantitative Proteome and Phosphoproteome Profiling across Three Cell Lines Revealed Potential Proteins Relevant to Nasopharyngeal Carcinoma Metastasis.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-19 DOI: 10.1021/acs.jproteome.4c01002

Jie Song, Yi Shen, Zhen Wu, Lin Huang, Yun Deng, Wei Yu, Xiaoshen Wang, Xumin Zhang

{"title":"Quantitative Proteome and Phosphoproteome Profiling across Three Cell Lines Revealed Potential Proteins Relevant to Nasopharyngeal Carcinoma Metastasis.","authors":"Jie Song, Yi Shen, Zhen Wu, Lin Huang, Yun Deng, Wei Yu, Xiaoshen Wang, Xumin Zhang","doi":"10.1021/acs.jproteome.4c01002","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01002","url":null,"abstract":"Despite the substantial reduction in the mortality rates of nasopharyngeal carcinoma (NPC), metastasis remains the primary cause of death in NPC cases. To explore metastasis-related proteins, we conducted proteomic and phosphoproteomic analyses of three NPC cell lines: SUNE1 and its subclones, 5-8F (high metastatic potential) and 6-10B (low metastatic potential). Using TMT-based quantification, we identified 1231, 1524, and 166 differentially regulated proteins (DRPs), as well as 177, 270, and 20 differentially regulated phosphoproteins (DRpPs) in 5-8F/SUNE1, 6-10B/SUNE1 and 5-8F/6-10B, respectively. These were enriched in cancer metastasis-related pathways, including cell migration and PPAR and PI3K pathways. Notably, 5-8F and 6-10B showed greater proteomic and phosphoproteomic similarity. To identify key proteins involved in NPC metastasis, we focused on the top 10 DRPs in 5-8F/6-10B. Knockdown experiments revealed that eight of these proteins, CRABP2, DNAJC15, NACAD, MYL9, DPYSL3, MAOA, MCAM, and S100A2, significantly influenced cell migration or invasion, with CRABP2, NACAD, and DPYSL3 dramatically enhancing these processes. Notably, DNAJC15 and NACAD are identified for the first time as novel metastasis-related proteins. Our findings demonstrate the effectiveness of this approach in identifying NPC metastasis biomarker candidates and offer new insights into underlying metastasis mechanisms, thus laying the groundwork for future research endeavors.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456249","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