Max-Planck-Institute of Biochemistry, Martinsried, Germany.
Proteomics. 2010 Jan;10(2):315-26. doi: 10.1002/pmic.200900174.
The main goal of many proteomics experiments is an accurate and rapid quantification and identification of regulated proteins in complex biological samples. The bottleneck in quantitative proteomics remains the availability of efficient software to evaluate and quantify the tremendous amount of mass spectral data acquired during a proteomics project. A new software suite, ICPLQuant, has been developed to accurately quantify isotope-coded protein label (ICPL)-labeled peptides on the MS level during LC-MALDI and peptide mass fingerprint experiments. The tool is able to generate a list of differentially regulated peptide precursors for subsequent MS/MS experiments, minimizing time-consuming acquisition and interpretation of MS/MS data. ICPLQuant is based on two independent units. Unit 1 performs ICPL multiplex detection and quantification and proposes peptides to be identified by MS/MS. Unit 2 combines MASCOT MS/MS protein identification with the quantitative data and produces a protein/peptide list with all the relevant information accessible for further data mining. The accuracy of quantification, selection of peptides for MS/MS-identification and the automated output of a protein list of regulated proteins are demonstrated by the comparative analysis of four different mixtures of three proteins (Ovalbumin, Horseradish Peroxidase and Rabbit Albumin) spiked into the complex protein background of the DGPF Proteome Marker.
许多蛋白质组学实验的主要目标是准确快速地定量和鉴定复杂生物样品中受调控的蛋白质。定量蛋白质组学的瓶颈仍然是缺乏有效的软件来评估和量化蛋白质组学项目中获得的大量质谱数据。开发了一套新的软件套件 ICPLQuant，用于在 LC-MALDI 和肽质量指纹实验中在 MS 水平上准确地定量同位素编码的蛋白质标签 (ICPL) 标记的肽。该工具能够生成一份差异调节肽前体列表，供随后的 MS/MS 实验使用，从而最大限度地减少了耗时的 MS/MS 数据采集和解释。ICPLQuant 基于两个独立的单元。单元 1 执行 ICPL 多重检测和定量，并提出通过 MS/MS 鉴定的肽。单元 2 将 Mascot MS/MS 蛋白质鉴定与定量数据相结合，生成一个包含所有相关信息的蛋白质/肽列表，可用于进一步的数据挖掘。通过将四种不同的三种蛋白质（卵清蛋白、辣根过氧化物酶和兔白蛋白）混合物分别掺入 DGPF 蛋白质组标记物的复杂蛋白质背景中进行比较分析，证明了定量的准确性、用于 MS/MS-鉴定的肽的选择以及受调控蛋白质的蛋白质列表的自动输出。
