MassChroQ：质谱定量的多功能工具
MassChroQ: A versatile tool for mass spectrometry quantification
摘要：
最近，已经开发了许多软件工具来在LC-MS分析中进行定量。然而，它们中的大多数是特定于定量策略（例如无标记或同位素标记）或质谱系统（例如高或低分辨率）。在这种情况下，我们开发了MassChroQ，这是一种多功能软件，可通过提取离子色谱图的峰面积积分进行LC-MS数据比对和肽定量。MassChroQ适用于标记或不标记的定量，并且不限于高分辨率系统。感兴趣的肽（例如所有鉴定的肽）可以通过提供目标m/z和保留时间值来自动或手动测定。它可以处理包括蛋白质或肽分级分离（如SDS-PAGE，2D-LC）的大型实验。它是完全可配置的。每个处理步骤都是可追溯的，产生的数据是开放的标准格式，其模块化允许轻松集成到蛋白质组学管道中。输出结果可用于统计分析。MassChroQ对从低分辨率和高分辨率质谱仪获得的复杂无标记数据的评估显示技术再现性的CV较低（1.4%），与蛋白质量的相关系数较高（0.98）。MassChroQ在GNU通用公共许可证v3.0下可在http://pappso.inra.fr/bioinfo/masschroq/免费获得。
英文摘要：
Recently, many software tools have been developed to perform quantification in LC-MS analyses. However, most of them are specific to either a quantification strategy (e.g. label-free or isotopic labelling) or a mass-spectrometry system (e.g. high or low resolution). In this context, we have developed MassChroQ, a versatile software that performs LC-MS data alignment and peptide quantification by peak area integration on extracted ion chromatograms. MassChroQ is suitable for quantification with or without labelling and is not limited to high resolution systems. Peptides of interest (for example all the identified peptides) can be determined automatically or manually by providing targeted m/z and retention time values. It can handle large experiments that include protein or peptide fractionation (as SDS-PAGE, 2D-LC). It is fully configurable. Every processing step is traceable, the produced data are in open standard format and its modularity allows easy integration into proteomic pipelines. The output results are ready for use in statistical analyses. Evaluation of MassChroQ on complex label-free data obtained from low and high resolution mass spectrometers showed low CVs for technical reproducibility (1.4%) and high coefficients of correlation to protein quantity (0.98). MassChroQ is freely available under the GNU General Public Licence v3.0 at http://pappso.inra.fr/bioinfo/masschroq/.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
