静电排斥-亲水相互作用色谱法的肽保留时间预测。

IF 3.8 2区 化学 Q1 BIOCHEMICAL RESEARCH METHODS Journal of Chromatography A Pub Date : 2024-10-02 DOI:10.1016/j.chroma.2024.465414
{"title":"静电排斥-亲水相互作用色谱法的肽保留时间预测。","authors":"","doi":"10.1016/j.chroma.2024.465414","DOIUrl":null,"url":null,"abstract":"<div><div>Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) is one of the legacy separation tools developed by Dr. Andrew Alpert and has been used for developing unique separation methods of hydrophilic compounds, including peptides. In the past it has been studied using designed peptide libraries to elucidate major features of its separation mechanism, while comprehensive peptide retention modeling for ERLIC is still lacking. In this work we employed a proteomics-derived ∼170,000 peptide retention datasets to evaluate major ERLIC retention features using the framework of our Sequence-Specific Retention Calculator model. The separation conditions were adjusted to obtain a wider proteome coverage, particularly for non-modified peptides, resulting in a superior separation orthogonality for a 2D LC combination with reversed-phase C18 LC-MS in the second dimension. The SSRCalc ERLIC model presents a consistent theme with the existing ERLIC retention mechanism, reflecting a dependence on peptide orientation and the position of charged and hydrophilic residues across the peptide backbone. R<sup>2</sup> values of 0.935 and 0.955 accuracy were demonstrated for the standard interpretable SSRCalc model and machine learning algorithm, respectively. The effects of various PTMs on peptide retention were evaluated in this study, covering spontaneous (oxidation, deamidation) and enzymatic (N-terminal acetylation, phosphorylation, glycosylation) modifications.</div></div>","PeriodicalId":347,"journal":{"name":"Journal of Chromatography A","volume":null,"pages":null},"PeriodicalIF":3.8000,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Peptide retention time prediction for electrostatic repulsion-hydrophilic interaction chromatography\",\"authors\":\"\",\"doi\":\"10.1016/j.chroma.2024.465414\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><div>Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) is one of the legacy separation tools developed by Dr. Andrew Alpert and has been used for developing unique separation methods of hydrophilic compounds, including peptides. In the past it has been studied using designed peptide libraries to elucidate major features of its separation mechanism, while comprehensive peptide retention modeling for ERLIC is still lacking. In this work we employed a proteomics-derived ∼170,000 peptide retention datasets to evaluate major ERLIC retention features using the framework of our Sequence-Specific Retention Calculator model. The separation conditions were adjusted to obtain a wider proteome coverage, particularly for non-modified peptides, resulting in a superior separation orthogonality for a 2D LC combination with reversed-phase C18 LC-MS in the second dimension. The SSRCalc ERLIC model presents a consistent theme with the existing ERLIC retention mechanism, reflecting a dependence on peptide orientation and the position of charged and hydrophilic residues across the peptide backbone. R<sup>2</sup> values of 0.935 and 0.955 accuracy were demonstrated for the standard interpretable SSRCalc model and machine learning algorithm, respectively. The effects of various PTMs on peptide retention were evaluated in this study, covering spontaneous (oxidation, deamidation) and enzymatic (N-terminal acetylation, phosphorylation, glycosylation) modifications.</div></div>\",\"PeriodicalId\":347,\"journal\":{\"name\":\"Journal of Chromatography A\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.8000,\"publicationDate\":\"2024-10-02\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Chromatography A\",\"FirstCategoryId\":\"1\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S002196732400788X\",\"RegionNum\":2,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOCHEMICAL RESEARCH METHODS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chromatography A","FirstCategoryId":"1","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S002196732400788X","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0

摘要

静电斥力-亲水相互作用色谱法(ERLIC)是安德鲁-阿尔伯特博士开发的传统分离工具之一,一直用于开发包括肽在内的亲水性化合物的独特分离方法。过去,人们利用设计的肽库对其进行研究,以阐明其分离机制的主要特征,但仍缺乏针对 ERLIC 的全面的肽保留模型。在这项工作中,我们利用蛋白质组学衍生的 17 万个肽段保留数据集,在序列特异性保留计算模型的框架内评估了 ERLIC 的主要保留特征。对分离条件进行了调整,以获得更广泛的蛋白质组覆盖范围,特别是非修饰肽段,从而使二维液相色谱与反相 C18 LC-MS 在二维中的分离正交性更优越。SSRCalc ERLIC 模型与现有的 ERLIC 保留机制呈现出一致的主题,反映了肽的取向以及肽骨架上带电和亲水残基位置的依赖性。标准可解释 SSRCalc 模型和机器学习算法的 R2 值分别为 0.935 和 0.955。本研究评估了各种 PTM 对肽保留的影响,包括自发修饰(氧化、脱氨基)和酶修饰(N 端乙酰化、磷酸化、糖基化)。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
Peptide retention time prediction for electrostatic repulsion-hydrophilic interaction chromatography
Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) is one of the legacy separation tools developed by Dr. Andrew Alpert and has been used for developing unique separation methods of hydrophilic compounds, including peptides. In the past it has been studied using designed peptide libraries to elucidate major features of its separation mechanism, while comprehensive peptide retention modeling for ERLIC is still lacking. In this work we employed a proteomics-derived ∼170,000 peptide retention datasets to evaluate major ERLIC retention features using the framework of our Sequence-Specific Retention Calculator model. The separation conditions were adjusted to obtain a wider proteome coverage, particularly for non-modified peptides, resulting in a superior separation orthogonality for a 2D LC combination with reversed-phase C18 LC-MS in the second dimension. The SSRCalc ERLIC model presents a consistent theme with the existing ERLIC retention mechanism, reflecting a dependence on peptide orientation and the position of charged and hydrophilic residues across the peptide backbone. R2 values of 0.935 and 0.955 accuracy were demonstrated for the standard interpretable SSRCalc model and machine learning algorithm, respectively. The effects of various PTMs on peptide retention were evaluated in this study, covering spontaneous (oxidation, deamidation) and enzymatic (N-terminal acetylation, phosphorylation, glycosylation) modifications.
求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Journal of Chromatography A
Journal of Chromatography A 化学-分析化学
CiteScore
7.90
自引率
14.60%
发文量
742
审稿时长
45 days
期刊介绍: The Journal of Chromatography A provides a forum for the publication of original research and critical reviews on all aspects of fundamental and applied separation science. The scope of the journal includes chromatography and related techniques, electromigration techniques (e.g. electrophoresis, electrochromatography), hyphenated and other multi-dimensional techniques, sample preparation, and detection methods such as mass spectrometry. Contributions consist mainly of research papers dealing with the theory of separation methods, instrumental developments and analytical and preparative applications of general interest.
期刊最新文献
Fingerprinting analyses of low molecular weight heparin with an orthogonal MHC 2D LC-MS system Custom GC×GC configuration for the selective isolation or removal of compounds from complex samples Analysis of volatile compound metabolic profiles during the fermentation of filler tobacco leaves through integrated E-nose, GC–MS, GC-IMS, and sensory evaluation Sampling efficiency of flow-through air sampler: Effect of sampling rate Boronic acid functionalized of covalent organic framework for high performance capture of trace phthalates
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1