J Proteome Res. 2020 Jan 3;19(1):204-211. doi: 10.1021/acs.jproteome.9b00496. Epub 2019 Nov 8.
Relative label-free quantification (LFQ) of shotgun proteomics data using precursor (MS1) signal intensities is one of the most commonly used applications to comprehensively and globally quantify proteins across biological samples and conditions. Due to the popularity of this technique, several software packages, such as the popular software suite MaxQuant, have been developed to extract, analyze, and compare spectral features and to report quantitative information of peptides, proteins, and even post-translationally modified sites. However, there is still a lack of accessible tools for the interpretation and downstream statistical analysis of these complex data sets, in particular for researchers and biologists with no or only limited experience in proteomics, bioinformatics, and statistics. We have therefore created LFQ-Analyst, which is an easy-to-use, interactive web application developed to perform differential expression analysis with "one click" and to visualize label-free quantitative proteomic data sets preprocessed with MaxQuant. LFQ-Analyst provides a wealth of user-analytic features and offers numerous publication-quality result graphics to facilitate statistical and exploratory analysis of label-free quantitative data sets. LFQ-Analyst, including an in-depth user manual, is freely available at https://bioinformatics.erc.monash.edu/apps/LFQ-Analyst .
基于 MS1 信号强度的相对无标记定量（LFQ）是一种广泛应用于全面、全局定量生物样本和条件下蛋白质的方法。由于该技术的普及，已经开发了几个软件包，如流行的 MaxQuant 软件套件，用于提取、分析和比较光谱特征，并报告肽、蛋白质甚至翻译后修饰位点的定量信息。然而，对于没有或只有有限蛋白质组学、生物信息学和统计学经验的研究人员和生物学家来说，仍然缺乏对这些复杂数据集进行解释和下游统计分析的工具。因此，我们创建了 LFQ-Analyst，这是一个易于使用的交互式 Web 应用程序，旨在通过“一键”执行差异表达分析，并可视化使用 MaxQuant 预处理的无标记定量蛋白质组数据集。LFQ-Analyst 提供了丰富的用户分析功能，并提供了许多出版质量的结果图形，以方便无标记定量数据集的统计和探索性分析。LFQ-Analyst 包括详细的用户手册，可在 https://bioinformatics.erc.monash.edu/apps/LFQ-Analyst 免费获得。
