A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS
A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS
复制标题
DOI：
10.1093/bioinformatics/btl276
复制
发表时间：
2006-08-01
期刊：
影响因子：
5.8
通讯作者：
McIntosh, Martin
中科院分区：
文献类型：
--
作者：
Bellew, Matthew;Coram, Marc;McIntosh, Martin
动机：比较两个或两个以上的复杂的蛋白质混合物，使用液相色谱质谱（LC-MS）需要多个分析步骤，以定位和定量天然肽在一个单一的实验，并在多个experiments.Results对齐和规范化的结果：我们描述msInspect，一个开源的应用程序，包括算法和可视化工具，用于分析多个LC-MS实验测量。该平台集成了用于在单个LC-MS测量中检测天然肽特征的新算法，并将多个实验测量组合到肽阵列中，然后可以使用传统上应用于基因组阵列分析的分析工具进行挖掘。该平台支持通过无标记和同位素标记方法进行定量。软件实现的设计使得许多关键组件可以很容易地替换，使其成为集成不断发展的研究社区开发的其他新颖算法的工作台。可用性：msInspect软件根据Apache 2.0许可证免费发布。该软件以及包含生成本文中的表格和图所需的所有肽特征文件和脚本的Zip文件可在http://proteomics.fhcrc.org/上获得
Motivation: Comparing two or more complex protein mixtures using liquid chromatography mass spectrometry (LC-MS) requires multiple analysis steps to locate and quantitate natural peptides within a single experiment and to align and normalize findings across multiple experiments.Results: We describe msInspect, an open-source application comprising algorithms and visualization tools for the analysis of multiple LC-MS experimental measurements. The platform integrates novel algorithms for detecting signatures of natural peptides within a single LC-MS measurement and combines multiple experimental measurements into a peptide array, which may then be mined using analysis tools traditionally applied to genomic array analysis. The platform supports quantitation by both label-free and isotopic labeling approaches. The software implementation has been designed so that many key components may be easily replaced, making it useful as a workbench for integrating other novel algorithms developed by a growing research community.Availability: The msInspect software is distributed freely under an Apache 2.0 license. The software as well as a Zip file with all peptide feature files and scripts needed to generate the tables and figures in this article are available at http://proteomics.fhcrc.org/