• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法,用中文像聊天一样搜索,搜遍4000万医学文献。AI智能推荐,让科研检索更轻松。

立即免费搜索

文件翻译

保留排版,准确专业,支持PDF/Word/PPT等文件格式,支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述,25分钟生成高质量综述,智能提取关键信息,辅助科研写作。

立即免费体验

天际线生态系统:定量质谱蛋白质组学信息学。

The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics.

机构信息

Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington.

出版信息

Mass Spectrom Rev. 2020 May;39(3):229-244. doi: 10.1002/mas.21540. Epub 2017 Jul 9.

DOI:10.1002/mas.21540
PMID:28691345
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5799042/
Abstract

Skyline is a freely available, open-source Windows client application for accelerating targeted proteomics experimentation, with an emphasis on the proteomics and mass spectrometry community as users and as contributors. This review covers the informatics encompassed by the Skyline ecosystem, from computationally assisted targeted mass spectrometry method development, to raw acquisition file data processing, and quantitative analysis and results sharing.

摘要

Skyline 是一个免费的、开源的 Windows 客户端应用程序,用于加速靶向蛋白质组学实验,重点是将蛋白质组学和质谱社区作为用户和贡献者。这篇综述涵盖了 Skyline 生态系统所包含的信息学,从计算辅助靶向质谱方法开发,到原始采集文件数据处理,以及定量分析和结果共享。

相似文献

1
The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics.天际线生态系统:定量质谱蛋白质组学信息学。
Mass Spectrom Rev. 2020 May;39(3):229-244. doi: 10.1002/mas.21540. Epub 2017 Jul 9.
2
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.Skyline:用于创建和分析靶向蛋白质组学实验的开源文档编辑器。
Bioinformatics. 2010 Apr 1;26(7):966-8. doi: 10.1093/bioinformatics/btq054. Epub 2010 Feb 9.
3
A framework for installable external tools in Skyline.Skyline中可安装外部工具的框架。
Bioinformatics. 2014 Sep 1;30(17):2521-3. doi: 10.1093/bioinformatics/btu148. Epub 2014 May 9.
4
Panorama: a targeted proteomics knowledge base.全景图:一个靶向蛋白质组学知识库。
J Proteome Res. 2014 Sep 5;13(9):4205-10. doi: 10.1021/pr5006636. Epub 2014 Aug 18.
5
Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline.全景公共库:Skyline 处理的定量数据集公共存储库。
Mol Cell Proteomics. 2018 Jun;17(6):1239-1244. doi: 10.1074/mcp.RA117.000543. Epub 2018 Feb 27.
6
Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics.小分子等高线图:定量代谢组学的统一软件包
J Proteome Res. 2020 Apr 3;19(4):1447-1458. doi: 10.1021/acs.jproteome.9b00640. Epub 2020 Mar 26.
7
Recent developments in proteome informatics for mass spectrometry analysis.用于质谱分析的蛋白质组信息学的最新进展。
Comb Chem High Throughput Screen. 2009 Feb;12(2):194-202. doi: 10.2174/138620709787315508.
8
Targeted Proteomics as a Tool for Quantifying Urine-Based Biomarkers.靶向蛋白质组学作为一种定量尿液生物标志物的工具。
Methods Mol Biol. 2020;2051:277-295. doi: 10.1007/978-1-4939-9744-2_12.
9
Bioinformatics challenges in mass spectrometry-driven proteomics.质谱驱动蛋白质组学中的生物信息学挑战。
Methods Mol Biol. 2011;753:359-71. doi: 10.1007/978-1-61779-148-2_24.
10
MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments.MSstats:一个用于基于定量质谱的蛋白质组学实验统计分析的R软件包。
Bioinformatics. 2014 Sep 1;30(17):2524-6. doi: 10.1093/bioinformatics/btu305. Epub 2014 May 2.

引用本文的文献

1
Transient ligand contacts of the intrinsically disordered N-terminus of neuropeptide Y receptor regulate arrestin-3 recruitment.神经肽Y受体内在无序N端的瞬时配体接触调节抑制蛋白3的募集。
Nat Commun. 2025 Sep 19;16(1):8326. doi: 10.1038/s41467-025-64051-4.
2
Coastal methane emissions driven by aerotolerant methanogens using seaweed and seagrass metabolites.耐氧产甲烷菌利用海藻和海草代谢产物驱动的沿海甲烷排放。
Nat Geosci. 2025;18(9):854-861. doi: 10.1038/s41561-025-01768-3. Epub 2025 Aug 7.
3
Molecular Organ Lysate Imprinting: For Precision Recognition and Analysis of Organ-Derived Proteins.

本文引用的文献

1
An Automated Pipeline to Monitor System Performance in Liquid Chromatography-Tandem Mass Spectrometry Proteomic Experiments.一种用于监测液相色谱-串联质谱蛋白质组学实验中系统性能的自动化流程。
J Proteome Res. 2016 Dec 2;15(12):4763-4769. doi: 10.1021/acs.jproteome.6b00744. Epub 2016 Oct 4.
2
Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes.通过定量靶向质谱测量的简化磷酸化信号特征可表征细胞状态并实现药物诱导表型的大规模比较。
Mol Cell Proteomics. 2016 May;15(5):1622-41. doi: 10.1074/mcp.M116.058354. Epub 2016 Feb 24.
3
分子器官裂解物印迹法:用于器官衍生蛋白质的精准识别与分析
Rapid Commun Mass Spectrom. 2025 Dec 15;39(23):e10125. doi: 10.1002/rcm.10125.
4
Upstream open reading frame translation enhances immunogenic peptide presentation in mitotically arrested cancer cells.上游开放阅读框翻译增强有丝分裂停滞癌细胞中的免疫原性肽呈递。
Nat Commun. 2025 Aug 27;16(1):8008. doi: 10.1038/s41467-025-63405-2.
5
Lipid profiling reveals unsaturated lipid reduction in women with Alzheimer's disease.脂质分析显示,阿尔茨海默病女性患者的不饱和脂质减少。
Alzheimers Dement. 2025 Aug;21(8):e70512. doi: 10.1002/alz.70512.
6
Insights into a water-mediated catalytic triad architecture in CE20 carbohydrate esterases.对CE20碳水化合物酯酶中水介导催化三联体结构的深入了解。
Nat Commun. 2025 Jul 31;16(1):7034. doi: 10.1038/s41467-025-62387-5.
7
Fusion of SARS-CoV-2 neutralizing LCB1 peptide with Bacillus amyloliquefaciens RNase improves antiviral efficacy.将严重急性呼吸综合征冠状病毒2(SARS-CoV-2)中和性LCB1肽与解淀粉芽孢杆菌核糖核酸酶融合可提高抗病毒疗效。
Sci Rep. 2025 Jul 31;15(1):28039. doi: 10.1038/s41598-025-12444-2.
8
Novel (1S,3R)-RSL3-Encapsulated Polyunsaturated Fatty Acid Rich Liposomes Sensitise Multiple Myeloma Cells to Ferroptosis-Mediated Cell Death.新型(1S,3R)-RSL3包裹的富含多不饱和脂肪酸的脂质体使多发性骨髓瘤细胞对铁死亡介导的细胞死亡敏感。
Int J Mol Sci. 2025 Jul 9;26(14):6579. doi: 10.3390/ijms26146579.
9
Sex and Age but Not Body Mass Index (BMI) Predict Serum Retinol Binding Protein 4 (RBP4) and Transthyretin (TTR) Concentrations.性别和年龄而非体重指数(BMI)可预测血清视黄醇结合蛋白4(RBP4)和甲状腺素转运蛋白(TTR)的浓度。
FASEB J. 2025 Jul 31;39(14):e70842. doi: 10.1096/fj.202501772R.
10
NNMT inhibition in cancer-associated fibroblasts restores antitumour immunity.抑制癌症相关成纤维细胞中的NNMT可恢复抗肿瘤免疫力。
Nature. 2025 Jul 23. doi: 10.1038/s41586-025-09303-5.
Ranking Fragment Ions Based on Outlier Detection for Improved Label-Free Quantification in Data-Independent Acquisition LC-MS/MS.
基于异常值检测对数据非依赖采集液相色谱-串联质谱中碎片离子进行排序以改进无标记定量分析
J Proteome Res. 2015 Nov 6;14(11):4581-93. doi: 10.1021/acs.jproteome.5b00394. Epub 2015 Oct 14.
4
The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity.太平洋西北国家实验室的细菌和古菌蛋白质组生物多样性文库。
Sci Data. 2015 Aug 18;2:150041. doi: 10.1038/sdata.2015.41. eCollection 2015.
5
The Use of Variable Q1 Isolation Windows Improves Selectivity in LC-SWATH-MS Acquisition.使用可变Q1隔离窗口可提高液相色谱-同步全扫描质谱采集的选择性。
J Proteome Res. 2015 Oct 2;14(10):4359-71. doi: 10.1021/acs.jproteome.5b00543. Epub 2015 Sep 3.
6
Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data.以肽段为中心的蛋白质组分析:串联质谱数据分析的替代策略
Mol Cell Proteomics. 2015 Sep;14(9):2301-7. doi: 10.1074/mcp.O114.047035. Epub 2015 Jul 27.
7
Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments.利用数据非依赖采集(DIA)为靶向蛋白质组学实验对高响应肽段进行建模。
Mol Cell Proteomics. 2015 Sep;14(9):2331-40. doi: 10.1074/mcp.M115.051300. Epub 2015 Jun 22.
8
Enhancing bottom-up and top-down proteomic measurements with ion mobility separations.通过离子淌度分离增强自下而上和自上而下的蛋白质组学测量。
Proteomics. 2015 Aug;15(16):2766-76. doi: 10.1002/pmic.201500048. Epub 2015 Jul 3.
9
Multiplexed peptide analysis using data-independent acquisition and Skyline.使用数据非依赖采集和Skyline进行多重肽分析。
Nat Protoc. 2015 Jun;10(6):887-903. doi: 10.1038/nprot.2015.055. Epub 2015 May 21.
10
Comprehensive profiling of amino acid response uncovers unique methionine-deprived response dependent on intact creatine biosynthesis.氨基酸反应的全面分析揭示了依赖完整肌酸生物合成的独特蛋氨酸缺乏反应。
PLoS Genet. 2015 Apr 7;11(4):e1005158. doi: 10.1371/journal.pgen.1005158. eCollection 2015 Apr.