The Biotechnology Centre of Oslo, University of Oslo, Oslo, Norway.
J Proteome Res. 2011 Feb 4;10(2):913-20. doi: 10.1021/pr1009977. Epub 2010 Nov 29.
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.
等压肽标记在蛋白质组相对定量比较中起着重要作用。等压标记技术利用 MS/MS 谱进行相对定量，这既可以基于低质量区域报告离子的相对强度（iTRAQ 和 TMT），也可以基于等压肽末端标记（IPTL）整个谱中的定量特征的相对强度。由于最近开发的 IPTL 方法生成的 MS/MS 片段谱中发现了更多的定量信息，因此需要新的软件来提取定量信息。IsobariQ 就是为此目的而专门开发的；但是，也包括对报告离子技术 iTRAQ 和 TMT 的支持。此外，为了解决蛋白质组学数据集方差异质性这一最近强调的问题，IsobariQ 采用了统计软件包 R 和其中提供的方差稳定化归一化（VSN）算法。最后，使用 6 重 TMT 和 IPTL 的实验数据集验证了 IsobariQ 的功能。值得注意的是，蛋白酶切割产生的蛋白质底物可以被识别，如凋亡中 Caspase 靶标所示。
