MRMaid: The SRM Assay Design Tool for Arabidopsis and Other Species.
MRMaid: The SRM Assay Design Tool for Arabidopsis and Other Species.
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DOI：
10.3389/fpls.2012.00164
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发表时间：
2012
影响因子：
5.6
通讯作者：
Bessant C
中科院分区：
文献类型：
--
作者：
Fan J;Mohareb F;Jones AM;Bessant C
选择反应监测（SRM），有时也称为多反应监测（MRM），正在成为植物科学界定量蛋白质组学的首选工具。成功的SRM实验的关键是预先鉴定感兴趣蛋白质的不同肽，并确定可以编程到LC-MS/MS中以监测这些肽的所谓转换。给定肽的跃迁包括完整肽m/z和可在特征保留时间（RT）处监测的高强度产物离子。为了帮助SRM实验的设计，已经产生了一些在线工具和数据库，以帮助研究人员选择他们感兴趣的蛋白质的转换，但这些工具中的许多工具仅限于最流行的模型生物，如人类，酵母和小鼠，或需要实验采集本地光谱库。在本文中，我们提出了MRMaid 1，一个基于网络的SRM检测设计工具，其转换是通过挖掘EBI的PRIDE数据库中的数百万个已识别的肽谱产生的。通过使用来自这个大型公共存储库的数据，MRMaid能够覆盖广泛的物种，这些物种可以随着PRIDE覆盖范围的增加而增加。本文对25种拟南芥蛋白质的MRMaid转换进行了实验评估，发现能够定量其中的23种蛋白质。发现这种性能与使用本地获得的轨道阱数据设计转换的更耗时的方法相当，表明MRMaid是靶向拟南芥蛋白质组学的有价值的工具。
Selected reaction monitoring (SRM), sometimes called multiple reaction monitoring (MRM), is becoming the tool of choice for targeted quantitative proteomics in the plant science community. Key to a successful SRM experiment is prior identification of the distinct peptides for the proteins of interest and the determination of the so-called transitions that can be programmed into an LC-MS/MS to monitor those peptides. The transition for a given peptide comprises the intact peptide m/z and a high intensity product ion that can be monitored at a characteristic retention time (RT). To aid the design of SRM experiments, several online tools and databases have been produced to help researchers select transitions for their proteins of interest, but many of these tools are limited to the most popular model organisms such as human, yeast, and mouse or require the experimental acquisition of local spectral libraries. In this paper we present MRMaid1, a web-based SRM assay design tool whose transitions are generated by mining the millions of identified peptide spectra held in the EBI’s PRIDE database. By using data from this large public repository, MRMaid is able to cover a wide range of species that can increase as the coverage of PRIDE grows. In this paper MRMaid transitions for 25 Arabidopsis thaliana proteins are evaluated experimentally, and found capable of quantifying 23 of these proteins. This performance was found to be comparable with the more time consuming approach of designing transitions using locally acquired orbitrap data, indicating that MRMaid is a valuable tool for targeted Arabidopsis proteomics.
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影响因子：
3
作者：
Cote, Richard G;Jones, Philip;Martens, Lennart;Kerrien, Samuel;Reisinger, Florian;Lin, Quan;Leinonen, Rasko;Apweiler, Rolf;Hermjakob, Henning
通讯作者：
Hermjakob, Henning
影响因子：
9.9
作者：
Lange, Vinzenz;Picotti, Paola;Domon, Bruno;Aebersold, Ruedi
通讯作者：
Aebersold, Ruedi
影响因子：
3.4
作者：
Vizcaino, Juan Antonio;Cote, Richard;Martens, Lennart
通讯作者：
Martens, Lennart
影响因子：
11.6
作者：
Greer, Emma;Martin, Azahara C.;Shaw, Peter
通讯作者：
Shaw, Peter
影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium