Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA.
J Proteome Res. 2011 Mar 4;10(3):1228-37. doi: 10.1021/pr1010058. Epub 2011 Jan 25.
Stable isotope labeling (SIL) methods coupled with nanoscale liquid chromatography and high resolution tandem mass spectrometry are increasingly useful for elucidation of the proteome-wide differences between multiple biological samples. Development of more effective programs for the sensitive identification of peptide pairs and accurate measurement of the relative peptide/protein abundance are essential for quantitative proteomic analysis. We developed and evaluated the performance of a new program, termed UNiquant, for analyzing quantitative proteomics data using stable isotope labeling. UNiquant was compared with two other programs, MaxQuant and Mascot Distiller, using SILAC-labeled complex proteome mixtures having either known or unknown heavy/light ratios. For the SILAC-labeled Jeko-1 cell proteome digests with known heavy/light ratios (H/L = 1:1, 1:5, and 1:10), UNiquant quantified a similar number of peptide pairs as MaxQuant for the H/L = 1:1 and 1:5 mixtures. In addition, UNiquant quantified significantly more peptides than MaxQuant and Mascot Distiller in the H/L = 1:10 mixtures. UNiquant accurately measured relative peptide/protein abundance without the need for postmeasurement normalization of peptide ratios, which is required by the other programs.
稳定同位素标记（SIL）方法与纳米液相色谱和高分辨串联质谱联用，对于阐明多个生物样本之间的蛋白质组学差异越来越有用。开发更有效的肽对灵敏识别程序和准确测量相对肽/蛋白质丰度的程序，对于定量蛋白质组学分析至关重要。我们开发并评估了一种新程序 UNiquant 的性能，该程序用于使用稳定同位素标记分析定量蛋白质组学数据。使用 SILAC 标记的具有已知或未知重/轻比的复杂蛋白质混合物，将 UNiquant 与另外两个程序 MaxQuant 和 Mascot Distiller 进行了比较。对于具有已知重/轻比（H/L = 1:1、1:5 和 1:10）的 SILAC 标记的 Jeko-1 细胞蛋白质组消化物，UNiquant 对 H/L = 1:1 和 1:5 混合物定量的肽对数量与 MaxQuant 相似。此外，在 H/L = 1:10 混合物中，UNiquant 定量的肽比 MaxQuant 和 Mascot Distiller 多得多。UNiquant 无需对肽比进行测量后归一化（其他程序需要），即可准确测量相对肽/蛋白质丰度。
