IsobariQ: Software for Isobaric Quantitative Proteomics using IPTL, iTRAQ, and TMT
IsobariQ: Software for Isobaric Quantitative Proteomics using IPTL, iTRAQ, and TMT
复制标题
DOI：
10.1021/pr1009977
复制
发表时间：
2011-02-01
影响因子：
4.4
通讯作者：
Thiede, Bernd
中科院分区：
文献类型：
--
作者：
Arntzen, Magnus O.;Koehler, Christian J.;Thiede, Bernd
等压肽标记在蛋白质组的相对定量比较中起着重要作用。等压标记技术利用MS/MS光谱进行相对定量，这既可以基于报告离子在低质量区域(iTRAQ和TMT)的相对强度，也可以基于由于等压肽末端标记(IPTL)而在整个光谱中的量化特征的相对强度。由于最近开发的IPTL方法产生的MS/MS碎片光谱中发现的定量信息增加，需要新的软件来提取定量信息。IsobariQ是专门为此目的开发的；但是，还包括对报告离子技术iTRAQ和TMT的支持。此外，为了解决最近强调的蛋白质组学数据集方差异质性问题，IsobariQ使用了统计软件包R和其中提供的方差稳定化归一化(VSN)算法。最后，使用6-plex TMT和IPTL的实验数据集对IsobariQ的功能进行了验证。值得注意的是，通过酶的切割产生的蛋白质底物可以被识别为caspase在细胞凋亡中的靶标。
Isobaric peptide labeling plays an important role in relative quantitative comparisons of proteomes. Isobaric labeling techniques utilize MS/MS spectra for relative quantification, which can be either based on the relative intensities of reporter ions in the low mass region (iTRAQ and TMT) or on the relative intensities of quantification signatures throughout the spectrum due to isobaric peptide termini labeling (IPTL). Due to the increased quantitative information found in MS/MS fragment spectra generated by the recently developed IPTL approach, new software was required to extract the quantitative information. IsobariQ was specifically developed for this purpose; however, support for the reporter ion techniques iTRAQ and TMT is also included. In addition, to address recently emphasized issues about heterogeneity of variance in proteomics data sets, IsobariQ employs the statistical software package R and variance stabilizing normalization (VSN) algorithms available therein. Finally, the functionality of IsobariQ is validated with data sets of experiments using 6-plex TMT and IPTL. Notably, protein substrates resulting from cleavage by proteases can be identified as shown for caspase targets in apoptosis.