Journal of Proteome Research最新文献_第3页

Quantitative Proteome Analysis of Plasma Extracellular Vesicles Identifies Three Proteins with Potential Diagnostic Value for Mycobacterium bovis Infection in Cows. 血浆细胞外囊泡定量蛋白质组学分析鉴定出三种可能诊断牛分枝杆菌感染的蛋白质。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-15 DOI: 10.1021/acs.jproteome.5c00143

Hangfan Zhou, Wenhui Wu, Qilong Zhang, Tao Zhang, Songhao Jiang, Hui Liu, Yuan Ma, Lei Chang, Yuping Xie, Jiaqiang Zhu, Degang Zhou, Yao Zhang, Ping Xu

{"title":"Quantitative Proteome Analysis of Plasma Extracellular Vesicles Identifies Three Proteins with Potential Diagnostic Value for Mycobacterium bovis Infection in Cows.","authors":"Hangfan Zhou, Wenhui Wu, Qilong Zhang, Tao Zhang, Songhao Jiang, Hui Liu, Yuan Ma, Lei Chang, Yuping Xie, Jiaqiang Zhu, Degang Zhou, Yao Zhang, Ping Xu","doi":"10.1021/acs.jproteome.5c00143","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00143","url":null,"abstract":"Bovine tuberculosis (bTB) is a zoonotic disease that affects cattle and human health. Although the tuberculin skin test (TST) is the main detection method, there is a need for simpler on-farm tests using fluid samples. This study analyzed plasma extracellular vesicles (EVs) from two cow groups (Cohort A, 15 negative, 22 positive; Cohort B, 28 negative, 40 positive) to explore bTB indicators using proteome profiling. Among the 756 proteins, 217 (Cohort A) and 233 (Cohort B) showed differences between healthy and infected cows, with 47 consistently dysregulated in both groups. These proteins were related to tuberculosis, neutrophil extracellular trap formation, and antigen processing and presentation pathways. Notably, three proteins, HSPA8, B2M, and HRG, were confirmed as bTB indicators using multiple methods, including least absolute shrinkage and selection operator (Lasso) regression selection, western blot (WB), and enzyme-linked immunosorbent assay (ELISA) validation with an independent cohort (Cohort C). This study identifies plasma EV biomarkers for bTB infection, offering insights for bTB detection.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144074897","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

Glycoproteomics of Gastrointestinal Cancers and Its Use in Clinical Diagnostics. 胃肠道肿瘤的糖蛋白组学及其在临床诊断中的应用。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-14 DOI: 10.1021/acs.jproteome.5c00095

Tomas Bertok, Andrea Pinkeova, Lenka Lorencova, Anna Datkova, Michal Hires, Eduard Jane, Jan Tkac

引用次数: 0

Technical Evaluation of Plasma Proteomics Technologies. 血浆蛋白质组学技术评价

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-14 DOI: 10.1021/acs.jproteome.5c00221

William F Beimers, Katherine A Overmyer, Pavel Sinitcyn, Noah M Lancaster, Scott T Quarmby, Joshua J Coon

{"title":"Technical Evaluation of Plasma Proteomics Technologies.","authors":"William F Beimers, Katherine A Overmyer, Pavel Sinitcyn, Noah M Lancaster, Scott T Quarmby, Joshua J Coon","doi":"10.1021/acs.jproteome.5c00221","DOIUrl":"10.1021/acs.jproteome.5c00221","url":null,"abstract":"Plasma proteomics technologies are rapidly evolving and of critical importance to the field of biomedical research. Here, we report a technical evaluation of six notable plasma proteomics technologies─unenriched (Neat), acid depletion, PreOmics ENRICHplus, Mag-Net, Seer Proteograph XT, and Olink Explore HT. The methods were compared on proteomic depth, reproducibility, linearity, tolerance to lipid interference, and limit of detection/quantification. In total, we performed 618 LC-MS/MS experiments and 93 Olink Explore HT assays. The Seer method achieved the greatest proteomic depth (∼4500 proteins detected), while Olink detected ∼2600 proteins. Other MS-based methods ranged from ∼500-2200 proteins detected. In our analysis, Neat, Mag-Net, Seer, and Olink had good reproducibility, while PreOmics and Acid had higher variability (>20% median coefficient of variation). All MS methods showed good linearity with spiked-in C-reactive protein (CRP); CRP was surprisingly not in the Olink assay. None of the methods were affected by lipid interference. Seer produced the highest number of quantifiable proteins with a measurable LOD (4407) and LOQ (2696). Olink had the next highest number of quantifiable proteins, with 2002 having an LOD and 1883 having an LOQ. Finally, we tested the applicability of these methods for detecting differences between healthy and cancer groups in a nonsmall cell lung cancer (NSCLC) cohort. All six methods detected differentially abundant proteins between the cancer and healthy samples but disagreed on which proteins were significant, highlighting the contrast between each method.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143954578","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

Dynamic Changes in Lymphocyte Subsets and Inflammation-Immune-Related Proteins in Patients with Thyroid Papillary Carcinoma before and after Radioactive Iodine Therapy. 放射性碘治疗前后甲状腺乳头状癌患者淋巴细胞亚群和炎症免疫相关蛋白的动态变化

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-14 DOI: 10.1021/acs.jproteome.5c00128

Junyu Zhang, Lulu Shi, Zhilin Zhang, Wanshu Peng, Peifen Chen, Jiaxin Cao, Jing Liu, Jin Zhang, Keyi Lu, Zhifang Wu, Haiyan Liu, Sijin Li

{"title":"Dynamic Changes in Lymphocyte Subsets and Inflammation-Immune-Related Proteins in Patients with Thyroid Papillary Carcinoma before and after Radioactive Iodine Therapy.","authors":"Junyu Zhang, Lulu Shi, Zhilin Zhang, Wanshu Peng, Peifen Chen, Jiaxin Cao, Jing Liu, Jin Zhang, Keyi Lu, Zhifang Wu, Haiyan Liu, Sijin Li","doi":"10.1021/acs.jproteome.5c00128","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00128","url":null,"abstract":"Radioactive iodine therapy (RAIT) is one of the main treatment methods for patients with papillary thyroid carcinoma (PTC). Peripheral blood samples were collected from 29 PTC patients who underwent total thyroidectomy 1-2 days before RAIT (RAIT-0), 30 days after (RAIT-30), and 90 days after (RAIT-90). Flow cytometry was used to detect the absolute counts of peripheral blood lymphocyte subpopulations, and the Proximity Extension Assay (PEA) was used for targeted proteome quantification. We found that after RAIT, peripheral blood lymphocyte subpopulations and the abundance of inflammation-related proteins in PTC patients changed and did not return to pretreatment levels for a long time. The immune pathway \"Cytokine-cytokine receptor interaction\" related to cytokine signaling may be activated. In addition, there were two types of protein trends that were similar to the lymphocyte count trends. The five proteins with the greatest degree of trend change were MCP-1, TRAIL, TGF-alpha, Flt3L, and IL15. In RAIT-30 vs RAIT-0, B cells were significantly negatively correlated with protein Flt3L, and Th17 cells were significantly positively correlated with protein CRTAM. MCP-1, TRAIL, IL15, Flt3L, TGF-alpha, and CRTAM may be potential marker proteins for immune recovery in PTC patients after RAIT.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951184","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

Upregulations of SNAT2 and GLS-1 Are Key Osmoregulatory Responses of Human Corneal Epithelial Cells to Hyperosmotic Stress. 人角膜上皮细胞对高渗应激的关键渗透调节反应是上调SNAT2和GLS-1。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-13 DOI: 10.1021/acs.jproteome.4c01046

Kenrick Kai-Yuen Chan, Alan Chun-Kit Lee, Shing-Yan Roy Chung, Man-Sau Wong, Chi-Wai Do, Thomas Chuen Lam, Hang-Kin Kong

{"title":"Upregulations of SNAT2 and GLS-1 Are Key Osmoregulatory Responses of Human Corneal Epithelial Cells to Hyperosmotic Stress.","authors":"Kenrick Kai-Yuen Chan, Alan Chun-Kit Lee, Shing-Yan Roy Chung, Man-Sau Wong, Chi-Wai Do, Thomas Chuen Lam, Hang-Kin Kong","doi":"10.1021/acs.jproteome.4c01046","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01046","url":null,"abstract":"Dry eye syndrome (DES) affects millions of people worldwide. However, as the cellular responses of the corneal epithelium under hyperosmotic stress remain unclear, this study investigated the proteomic changes between human corneal epithelial cells (HCECs) cultured with isosmotic and hyperosmotic media. Under hyperosmotic stress, HCECs increased expressions of sodium-coupled neutral amino acid transporter (SNAT2), glutaminase (GLS-1), and a few isoforms of heat shock protein and aldo-keto reductase family 1. The expressions of SNAT2 and GLS-1 were increased after 6 h of exposure to hyperosmotic stress but not by glutamine deprivation. The hyperosmotic stress increased intracellular levels of glutamine, mitochondrial superoxide, and mitochondrial membrane potential and induced mitochondrial fission in HCECs. Thus, the intracellular level of glutamine was elevated in the hyperosmotic stressed HCECs via the upregulation of SNAT2. Glutamine can act as an osmolyte to regulate the osmolarity of HCECs or be converted to glutamate by GLS-1 for the tricarboxylic acid cycle and oxidative phosphorylation to maintain ATP production under the hyperosmotic stress-induced mitochondrial fission. Thus, the increases in the expressions of SNAT2 and GLS-1 are key osmoregulations in HCECs upon the hyperosmotic stress and may act as corneal biomarkers for monitoring DES progression.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143955723","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

ProteoPlotter: An Executable Proteomics Visualization Tool Compatible with Perseus. ProteoPlotter：一个可执行的蛋白质组可视化工具与珀尔修斯兼容。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-13 DOI: 10.1021/acs.jproteome.4c00963

Esther Olabisi-Adeniyi, Jason A McAlister, Daniela Ferretti, Juergen Cox, Jennifer Geddes-McAlister

{"title":"ProteoPlotter: An Executable Proteomics Visualization Tool Compatible with Perseus.","authors":"Esther Olabisi-Adeniyi, Jason A McAlister, Daniela Ferretti, Juergen Cox, Jennifer Geddes-McAlister","doi":"10.1021/acs.jproteome.4c00963","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00963","url":null,"abstract":"Mass spectrometry-based proteomics experiments produce complex data sets requiring robust statistical testing and effective visualization tools to ensure meaningful conclusions are drawn. The publicly available proteomics data analysis platform, Perseus, is extensively used to perform such tasks, but opportunities to enhance visualization tools and promote accessibility of the data exist. In this study, we developed ProteoPlotter, a user-friendly, executable tool to complement Perseus for visualization of proteomics data sets. ProteoPlotter is built on the Shiny framework for R programming and enables illustration of multidimensional proteomics data. ProteoPlotter supports mapping of one-dimensional enrichment analyses, enhanced adaptability of volcano plots through incorporation of Gene Ontology terminology, visualization of 95% confidence intervals in principal component analysis plots using data ellipses, and customizable features. ProteoPlotter is designed for intuitive use by biological and computational researchers alike, providing descriptive instructions (i.e., Help Guide) for preparing and uploading Perseus output files. Herein, we demonstrate the application of ProteoPlotter toward microbial proteome remodeling under altered nutrient conditions and highlight the diversity of visualizations enabled with the platform for enhanced biological insights. Through its comprehensive data visualization capabilities, linked to the power of Perseus data handling and statistical analyses, ProteoPlotter facilitates enhanced visualization of proteomics data to drive new biological discoveries.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951075","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

Comprehensive Comparison of Methods for Isolation of Extracellular Vesicles from Human Plasma. 人血浆细胞外囊泡分离方法的综合比较。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-12 DOI: 10.1021/acs.jproteome.5c00149

Patil Shivprasad Suresh, Qibin Zhang

{"title":"Comprehensive Comparison of Methods for Isolation of Extracellular Vesicles from Human Plasma.","authors":"Patil Shivprasad Suresh, Qibin Zhang","doi":"10.1021/acs.jproteome.5c00149","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00149","url":null,"abstract":"Extracellular vesicles (EVs) are a vital component in cell-cell communication and hold significant potential as biomarkers and therapeutic carriers. Having a reproducible and simple EV isolation method for small volumes of human plasma is essential for biomarker discovery. Although combining multiple methods has been a recent trend in its ability to minimize contamination, it is not ideal for clinical specimens due to the large sample number and small sample volume. This study compared EVs isolated from 100 μL of plasma by nine commonly used methods based on different principles, including centrifugation, polymer precipitation, size exclusion, electrostatic interaction, and affinity enrichment. The isolated EVs were characterized by particle size and number using nanoparticle tracking analysis, purity, and contaminants using Simple Western and overall proteomic profiles using bottom-up proteomics. Despite the same EV enrichment principle, individual methods isolated EVs exhibited distinct characteristics, likely due to variations in the physicochemical properties of materials used and specific protocols. Overall, all of the methods evaluated are reproducible. MagNet and MagCap methods result in purer EVs with the narrowest size distribution and the highest proteome coverage but modest yield. This is the first report on isolating EVs from 100 μL of plasma using nine different methods with detailed characterization.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144042183","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

To Fly, or Not to Fly, That Is the Question: A Deep Learning Model for Peptide Detectability Prediction in Mass Spectrometry. 飞，还是不飞，这是一个问题：质谱中肽可检测性预测的深度学习模型。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-09 DOI: 10.1021/acs.jproteome.4c00973

Naim Abdul-Khalek, Mario Picciani, Omar Shouman, Reinhard Wimmer, Michael Toft Overgaard, Mathias Wilhelm, Simon Gregersen Echers

{"title":"To Fly, or Not to Fly, That Is the Question: A Deep Learning Model for Peptide Detectability Prediction in Mass Spectrometry.","authors":"Naim Abdul-Khalek, Mario Picciani, Omar Shouman, Reinhard Wimmer, Michael Toft Overgaard, Mathias Wilhelm, Simon Gregersen Echers","doi":"10.1021/acs.jproteome.4c00973","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00973","url":null,"abstract":"Identifying detectable peptides, known as flyers, is key in mass spectrometry-based proteomics. Peptide detectability is strongly related to peptide sequences and their resulting physicochemical properties. Moreover, the high variability in MS data challenges the development of a generic model for detectability prediction, underlining the need for customizable tools. We present Pfly, a deep learning model developed to predict peptide detectability based solely on peptide sequence. Pfly is a versatile and reliable state-of-the-art tool, offering high performance, accessibility, and easy customizability for end-users. This adaptability allows researchers to tailor Pfly to specific experimental conditions, improving accuracy and expanding applicability across various research fields. Pfly is an encoder-decoder with an attention mechanism, classifying peptides as flyers or non-flyers, and providing both binary and categorical probabilities for four distinct classes defined in this study. The model was initially trained on a synthetic peptide library and subsequently fine-tuned with a biological dataset to mitigate bias toward synthesizability, improving predictive capacity and outperforming state-of-the-art predictors in benchmark comparisons across different human and cross-species datasets. The study further investigates the influence of protein abundance and rescoring, illustrating the negative impact on peptide identification due to misclassification. Pfly has been integrated into the DLOmix framework and is accessible on GitHub at https://github.com/wilhelm-lab/dlomix.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951442","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

Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer. 使用三重四极杆质谱仪进行靶向蛋白质组学分析的数据独立采集。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-06 DOI: 10.1021/acs.jproteome.5c00016

Deanna L Plubell, Eric Huang, Sandra E Spencer, Kathleen L Poston, Thomas J Montine, Michael J MacCoss

{"title":"Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer.","authors":"Deanna L Plubell, Eric Huang, Sandra E Spencer, Kathleen L Poston, Thomas J Montine, Michael J MacCoss","doi":"10.1021/acs.jproteome.5c00016","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00016","url":null,"abstract":"Mass spectrometry based targeted proteomics methods provide a sensitive and high-throughput analysis of selected proteins. To develop a targeted bottom-up proteomics assay, peptides must be evaluated as proxies for the measurement of a protein or proteoform in a biological matrix. Candidate peptide selection typically relies on predetermined biochemical properties, data from semistochastic sampling, or empirical measurements. These strategies require extensive testing and method refinement due to the difficulties associated with prediction of the peptide response in the biological matrix of interest. Gas-phase fractionated (GPF) narrow window data-independent acquisition (DIA) aids in the development of reproducible selected reaction monitoring (SRM) assays by providing matrix-specific information on peptide detectability and quantification by mass spectrometry. To demonstrate the suitability of DIA data for selecting peptide targets, we reimplement a portion of an existing assay to measure 98 Alzheimer's disease proteins in cerebrospinal fluid (CSF). Peptides were selected from GPF-DIA based on signal intensity and reproducibility. The resulting SRM assay exhibits a quantitative precision similar to that of published data, despite the inclusion of different peptides between the assays. This workflow enables development of new assays without additional upfront data acquisition, demonstrated here through generation of a separate assay for an unrelated set of proteins in CSF from the same data set.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951565","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

Do-It-Yourself De Novo Antibody Sequencing Workflow that Achieves Complete Accuracy of the Variable Regions. 自己动手从头抗体测序工作流程，实现完全准确的可变区域。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-05 DOI: 10.1021/acs.jproteome.5c00210

Meng-Ting He, Ning Li, Jian-Hua Wang, Zhi-Zhong Wei, Jie Feng, Wen-Ting Li, Jian-Hua Sui, Niu Huang, Meng-Qiu Dong

{"title":"Do-It-Yourself De Novo Antibody Sequencing Workflow that Achieves Complete Accuracy of the Variable Regions.","authors":"Meng-Ting He, Ning Li, Jian-Hua Wang, Zhi-Zhong Wei, Jie Feng, Wen-Ting Li, Jian-Hua Sui, Niu Huang, Meng-Qiu Dong","doi":"10.1021/acs.jproteome.5c00210","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00210","url":null,"abstract":"Antibodies are widely used as research tools or therapeutic agents. Knowing the sequences of the variable regions of an antibody─both the heavy chain and the light chain─is a prerequisite for the production of recombinant antibodies. Mass spectrometry-based de novo sequencing is a frequently used, and sometimes the only approach to gaining this information. Here, we describe a workflow that enables accurate sequence determination of monoclonal antibodies based on mass spectrometry data and freely available software tools. This workflow, which we developed using a homemade anti-FLAG monoclonal antibody as a reference sample, achieved 100% accuracy of the variable regions with clear distinction between leucine (L) and isoleucine (I). Using this workflow, we successfully decoded a monoclonal anti-HA antibody, for which we had no prior knowledge of its sequence. Based on the de novo sequencing result, we generated a recombinant anti-HA antibody, and demonstrated that it has the same specificity, sensitivity, and affinity as the commercial antibody.","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":"143952028","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