Journal of Proteome Research最新文献_第3页

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 : 2025-04-07 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":"https://doi.org/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":""},"PeriodicalIF":3.8,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Temporal Proteome Profiling of Anterior Cruciate Ligament Tear Remnants: Secretory Proteins in the Acute Phase Potentially Promote Tissue Repair 前交叉韧带撕裂残余的时间蛋白质组分析：急性期分泌蛋白可能促进组织修复

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-07 DOI: 10.1021/acs.jproteome.4c0079210.1021/acs.jproteome.4c00792

Yiming Liu, Bin Li, Jun Zhang, Boming Zhao, Liaobin Chen* and Biao Chen*,

{"title":"Temporal Proteome Profiling of Anterior Cruciate Ligament Tear Remnants: Secretory Proteins in the Acute Phase Potentially Promote Tissue Repair","authors":"Yiming Liu, Bin Li, Jun Zhang, Boming Zhao, Liaobin Chen* and Biao Chen*, ","doi":"10.1021/acs.jproteome.4c0079210.1021/acs.jproteome.4c00792","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00792https://doi.org/10.1021/acs.jproteome.4c00792","url":null,"abstract":"Previous studies reported that preserving the anterior cruciate ligament (ACL) remnants following ACL rupture during reconstruction surgery could promote graft healing. However, the temporal proteomic expression of ACL remnants remains unclear. Based on previous reports, we have redefined the initial 6 weeks following ACL rupture as the acute phase and the subsequent 6 weeks to 6 months as the subacute phase. High-throughput proteomic sequencing on ACL remnants from the two groups was utilized. Our study unveiled a total of 381 differential expression proteins (DEPs), with 136 upregulated and 245 downregulated proteins in the acute phase. By intersecting these findings with secretory protein databases, we identified 26 upregulated secretory proteins and 19 downregulated in the acute phase. The upregulation of MMP9 and VTN and the downregulation of COL1A1 and POSTN in the acute phase were further confirmed by immunohistochemistry. These findings suggest that the elevated expression of secretory proteins in the acute phase may play crucial roles in promoting cell proliferation, angiogenesis, and tissue repair of the graft. This study not only enhances our understanding of repair mechanisms in ACL remnant preservation but also provides a theoretical foundation for guiding rational clinical surgical timing.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 5","pages":"2302–2313 2302–2313"},"PeriodicalIF":3.8,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143894166","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

Temporal Proteome Profiling of Anterior Cruciate Ligament Tear Remnants: Secretory Proteins in the Acute Phase Potentially Promote Tissue Repair. 前交叉韧带撕裂残余的时间蛋白质组分析：急性期分泌蛋白可能促进组织修复。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-07 DOI: 10.1021/acs.jproteome.4c00792

Yiming Liu, Bin Li, Jun Zhang, Boming Zhao, Liaobin Chen, Biao Chen

{"title":"Temporal Proteome Profiling of Anterior Cruciate Ligament Tear Remnants: Secretory Proteins in the Acute Phase Potentially Promote Tissue Repair.","authors":"Yiming Liu, Bin Li, Jun Zhang, Boming Zhao, Liaobin Chen, Biao Chen","doi":"10.1021/acs.jproteome.4c00792","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00792","url":null,"abstract":"Previous studies reported that preserving the anterior cruciate ligament (ACL) remnants following ACL rupture during reconstruction surgery could promote graft healing. However, the temporal proteomic expression of ACL remnants remains unclear. Based on previous reports, we have redefined the initial 6 weeks following ACL rupture as the acute phase and the subsequent 6 weeks to 6 months as the subacute phase. High-throughput proteomic sequencing on ACL remnants from the two groups was utilized. Our study unveiled a total of 381 differential expression proteins (DEPs), with 136 upregulated and 245 downregulated proteins in the acute phase. By intersecting these findings with secretory protein databases, we identified 26 upregulated secretory proteins and 19 downregulated in the acute phase. The upregulation of MMP9 and VTN and the downregulation of COL1A1 and POSTN in the acute phase were further confirmed by immunohistochemistry. These findings suggest that the elevated expression of secretory proteins in the acute phase may play crucial roles in promoting cell proliferation, angiogenesis, and tissue repair of the graft. This study not only enhances our understanding of repair mechanisms in ACL remnant preservation but also provides a theoretical foundation for guiding rational clinical surgical timing.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794081","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

Comparison of N- and O-Glycosylation on Spike Glycoprotein 1 of SARS-CoV-1 and MERS-CoV. SARS-CoV-1和MERS-CoV刺突糖蛋白1 N-和o -糖基化的比较

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-07 DOI: 10.1021/acs.jproteome.4c00716

Yuan Tian, John F Cipollo

{"title":"Comparison of N- and O-Glycosylation on Spike Glycoprotein 1 of SARS-CoV-1 and MERS-CoV.","authors":"Yuan Tian, John F Cipollo","doi":"10.1021/acs.jproteome.4c00716","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00716","url":null,"abstract":"SARS-CoV-1 and MERS-CoV were the infective agents of the 2002 and 2012 coronavirus outbreaks, respectively. Here, we report a comparative liquid chromatography/mass spectrometry (LC/MS) Orbitrap N- and O-glycosylation glycoproteomics study of the recombinant S1 spike derived from these two viruses. The former was produced in HEK293 cells and the latter in both HEK293 and insect cells. Both proteins were highly glycosylated, with SARS-CoV-1 S1 having 13 and MERS-CoV S1 having 12 N-glycosites. Nearly all were occupied at 85% or more. Between 2 and 113 unique N-glycan compositions were detected at each N-glycosite across the three proteins. Complex N-glycans dominated in HEK293 cell-derived spike S1 proteins. While glycosylation differs between HEK293 and insect cells, the extent of glycan processing at glycosites was similar for the two MERS-CoV S1 forms. The HEK293-derived SARS-CoV-1 S1 N-glycans were more highly sialylated and fucosylated compared to MERS S1, while the latter had more high-mannose glycosides, particularly in the N-terminus and near the RBD. Seven and 8 O-glycosites were identified in SARS-CoV-1 S1 and MERS-CoV S1, respectively. Mapping of predicted antigenic and glycosylation sites reveals colocalization consistent with a role for glycosylation in immune system avoidance. Glycosylation patterns of these S1 proteins differ from those of other SARS-CoV-1 and MERS-CoV spike reported forms such as recombinant trimeric and virus-propagated forms, which has implications for virus research, including vaccine development, as glycosylation plays a role in spike function and epitope structure.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802035","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

Comparison of N- and O-Glycosylation on Spike Glycoprotein 1 of SARS-CoV-1 and MERS-CoV SARS-CoV-1和MERS-CoV刺突糖蛋白1 N-和o -糖基化的比较

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-07 DOI: 10.1021/acs.jproteome.4c0071610.1021/acs.jproteome.4c00716

Yuan Tian, and , John F. Cipollo*,

{"title":"Comparison of N- and O-Glycosylation on Spike Glycoprotein 1 of SARS-CoV-1 and MERS-CoV","authors":"Yuan Tian,  and , John F. Cipollo*, ","doi":"10.1021/acs.jproteome.4c0071610.1021/acs.jproteome.4c00716","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00716https://doi.org/10.1021/acs.jproteome.4c00716","url":null,"abstract":"SARS-CoV-1 and MERS-CoV were the infective agents of the 2002 and 2012 coronavirus outbreaks, respectively. Here, we report a comparative liquid chromatography/mass spectrometry (LC/MS) Orbitrap N- and O-glycosylation glycoproteomics study of the recombinant S1 spike derived from these two viruses. The former was produced in HEK293 cells and the latter in both HEK293 and insect cells. Both proteins were highly glycosylated, with SARS-CoV-1 S1 having 13 and MERS-CoV S1 having 12 N-glycosites. Nearly all were occupied at 85% or more. Between 2 and 113 unique N-glycan compositions were detected at each N-glycosite across the three proteins. Complex N-glycans dominated in HEK293 cell-derived spike S1 proteins. While glycosylation differs between HEK293 and insect cells, the extent of glycan processing at glycosites was similar for the two MERS-CoV S1 forms. The HEK293-derived SARS-CoV-1 S1 N-glycans were more highly sialylated and fucosylated compared to MERS S1, while the latter had more high-mannose glycosides, particularly in the N-terminus and near the RBD. Seven and 8 O-glycosites were identified in SARS-CoV-1 S1 and MERS-CoV S1, respectively. Mapping of predicted antigenic and glycosylation sites reveals colocalization consistent with a role for glycosylation in immune system avoidance. Glycosylation patterns of these S1 proteins differ from those of other SARS-CoV-1 and MERS-CoV spike reported forms such as recombinant trimeric and virus-propagated forms, which has implications for virus research, including vaccine development, as glycosylation plays a role in spike function and epitope structure.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 5","pages":"2256–2265 2256–2265"},"PeriodicalIF":3.8,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143894167","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 : 2025-04-07 DOI: 10.1021/acs.jproteome.4c0088410.1021/acs.jproteome.4c00884

Muhammad Shahid Malik, Van The Le and 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 and Yu-Yen Ou*, ","doi":"10.1021/acs.jproteome.4c0088410.1021/acs.jproteome.4c00884","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00884https://doi.org/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":"24 5","pages":"2324–2335 2324–2335"},"PeriodicalIF":3.8,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jproteome.4c00884","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143894093","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

Increasing Proteome Coverage Through a Reduction in Analyte Complexity in Single-Cell Equivalent Samples. 通过降低单细胞等效样本的分析复杂度提高蛋白质组覆盖率

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-04 Epub Date: 2024-06-04 DOI: 10.1021/acs.jproteome.4c00062

Marion Pang, Jeff J Jones, Ting-Yu Wang, Baiyi Quan, Nicole J Kubat, Yanping Qiu, Michael L Roukes, Tsui-Fen Chou

{"title":"Increasing Proteome Coverage Through a Reduction in Analyte Complexity in Single-Cell Equivalent Samples.","authors":"Marion Pang, Jeff J Jones, Ting-Yu Wang, Baiyi Quan, Nicole J Kubat, Yanping Qiu, Michael L Roukes, Tsui-Fen Chou","doi":"10.1021/acs.jproteome.4c00062","DOIUrl":"10.1021/acs.jproteome.4c00062","url":null,"abstract":"The advancement of sophisticated instrumentation in mass spectrometry has catalyzed an in-depth exploration of complex proteomes. This exploration necessitates a nuanced balance in experimental design, particularly between quantitative precision and the enumeration of analytes detected. In bottom-up proteomics, a key challenge is that oversampling of abundant proteins can adversely affect the identification of a diverse array of unique proteins. This issue is especially pronounced in samples with limited analytes, such as small tissue biopsies or single-cell samples. Methods such as depletion and fractionation are suboptimal to reduce oversampling in single cell samples, and other improvements on LC and mass spectrometry technologies and methods have been developed to address the trade-off between precision and enumeration. We demonstrate that by using a monosubstrate protease for proteomic analysis of single-cell equivalent digest samples, an improvement in quantitative accuracy can be achieved, while maintaining high proteome coverage established by trypsin. This improvement is particularly vital for the field of single-cell proteomics, where single-cell samples with limited number of protein copies, especially in the context of low-abundance proteins, can benefit from considering analyte complexity. Considerations about analyte complexity, alongside chromatographic complexity, integration with data acquisition methods, and other factors such as those involving enzyme kinetics, will be crucial in the design of future single-cell workflows.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1528-1538"},"PeriodicalIF":3.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141236702","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 Reveals Neuroblastoma Molecular Signature Predicting Risk Stratification and Tumor Microenvironment Differences. 多组学分析揭示神经母细胞瘤分子特征预测风险分层和肿瘤微环境差异。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-04 Epub Date: 2025-01-06 DOI: 10.1021/acs.jproteome.4c00882

Xing Zhou, Zhaokai Zhou, Xiaohan Qin, Jian Cheng, Yongcheng Fu, Yuanyuan Wang, Jingyue Wang, Pan Qin, Da Zhang

{"title":"Multiomics Analysis Reveals Neuroblastoma Molecular Signature Predicting Risk Stratification and Tumor Microenvironment Differences.","authors":"Xing Zhou, Zhaokai Zhou, Xiaohan Qin, Jian Cheng, Yongcheng Fu, Yuanyuan Wang, Jingyue Wang, Pan Qin, Da Zhang","doi":"10.1021/acs.jproteome.4c00882","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00882","url":null,"abstract":"Neuroblastoma (NB) remains associated with high mortality and low initial response rate, especially for high-risk patients, thus warranting exploration of molecular markers for precision risk classifiers. Through integrating multiomics profiling, we identified a range of hub genes involved in cell cycle and associated with dismal prognosis and malignant cells. Single-cell transcriptome sequencing revealed that a subset of malignant cells, subcluster 1, characterized by high proliferation and dedifferentiation, was strongly correlated with the hub gene signature and orchestrated an immunosuppressive tumor microenvironment (TME). Furthermore, we constructed a robust malignant subcluster 1 related signature (MSRS), which was an independent prognostic factor and superior to other clinical characteristics and published signatures. Besides, TME differences conferred remarkably distinct therapeutic responses between high and low MSRS groups. Notably, polo-like kinase-1 (PLK1) was one of the most crucial contributors to MSRS and remarkably correlated with malignant subcluster 1, and PLK1 inhibition was effective for NB treatment as demonstrated by in silico analysis and in vitro experiments. Overall, our study constructs a novel molecular model to further guide the clinical classification and individualized treatment of NB.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 4","pages":"1606-1623"},"PeriodicalIF":3.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778610","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

pyOpenMS-viz: Streamlining Mass Spectrometry Data Visualization with pandas. pyOpenMS-viz：使用 pandas 简化质谱数据可视化。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-04 Epub Date: 2025-02-28 DOI: 10.1021/acs.jproteome.4c00873

Justin Cyril Sing, Joshua Charkow, Axel Walter, Mingxuan Gao, Tom David Müller, Wout Bittremieux, Timo Sachsenberg, Hannes Luc Röst

引用次数: 0

A Comparison of Derivatives of Alanine and d-Alanine Used in Gas Chromatography-Mass Spectrometry Analysis for Protein Kinetics. 丙氨酸和d-丙氨酸衍生物在蛋白质动力学气相色谱-质谱分析中的应用比较。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-04 Epub Date: 2025-03-16 DOI: 10.1021/acs.jproteome.4c01004

Yihong Kaufmann, Rick Williams, Matthew Cotter, Arny Ferrando, Elisabet Børsheim

{"title":"A Comparison of Derivatives of Alanine and d-Alanine Used in Gas Chromatography-Mass Spectrometry Analysis for Protein Kinetics.","authors":"Yihong Kaufmann, Rick Williams, Matthew Cotter, Arny Ferrando, Elisabet Børsheim","doi":"10.1021/acs.jproteome.4c01004","DOIUrl":"10.1021/acs.jproteome.4c01004","url":null,"abstract":"Stable isotope techniques serve as invaluable tools for kinetic measurements in metabolic research. In particular, deuterated water (D2O) administration is increasingly being applied in human health research. For use in protein kinetic studies, this includes measurements on gas chromatography-mass spectrometry (GC-MS) analysis of alanine (ALA) and deuterium-labeled alanines (d-ALAs) coming from D2O administration. However, the choice of the derivative of ALA and d-ALAs used in such analyses has not been evaluated thoroughly. Hence, we conducted a comprehensive head-to-head comparison to determine the most effective and reliable derivative. Two derivatization reagents, N,N-dimethylformamide dimethyl acetal (methyl-8 reagent) and N-methyl-N-tert-butyldimethylsilyltrifluoroacetamide (MtBSTFA), were considered as candidates. Using chemical standards and available rodent muscle tissue, both reagents underwent testing, including the standard curve linear regression fit, sensitivity, reproducibility, and, importantly, column effectiveness. Our findings indicate that both reagents were suitable for ALA/d-ALAs analyses. However, the MtBSTFA derivative exhibited a better linear regression fit, higher sensitivity, and greater reproducibility than methyl-8. More importantly, the methyl-8 derivative resulted in severe column damage. In conclusion, our study highlights the MtBSTFA derivative as a preferred choice for ALA and d-ALAs GC-MS analysis, contributing to a reliable and sensitive analytical method for D2O administration studies for measurements of in vivo metabolic rates.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1983-1991"},"PeriodicalIF":3.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11970985/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143646538","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