Lesne Jean, Bousquet Marie-Pierre, Marcoux Julien, Locard-Paulet Marie
Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France.
Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
Bioinform Biol Insights. 2019 Aug 16;13:1177932219868223. doi: 10.1177/1177932219868223. eCollection 2019.
The rise of intact protein analysis by mass spectrometry (MS) was accompanied by an increasing need for flexible tools allowing data visualization and analysis. These include inspection of the deconvoluted molecular weights of the proteoforms eluted alongside liquid chromatography (LC) through their representation in three-dimensional (3D) liquid chromatography coupled to mass spectrometry (LC-MS) maps (plots of deconvoluted molecular weights, retention times, and intensity of the MS signal). With this aim, we developed a free and open-source web application named VisioProt-MS (https://masstools.ipbs.fr/mstools/visioprot-ms/). VisioProt-MS is highly compatible with many algorithms and software developed by the community to integrate and deconvolute top-down and intact protein MS data. Its dynamic and user-friendly features greatly facilitate analysis through several graphical representations dedicated to MS and tandem mass spectrometry (MS/MS) analysis of proteoforms in complex samples. Here, we will illustrate the importance of LC-MS map visualization to optimize top-down acquisition/search parameters and analyze intact protein MS data. We will go through the main features of VisioProt-MS using the human proteasomal 20S core particle as a user-case.
通过质谱（MS）进行完整蛋白质分析的兴起，伴随着对允许数据可视化和分析的灵活工具的需求日益增加。这些工具包括通过在三维（3D）液相色谱-质谱联用（LC-MS）图谱（解卷积分子量、保留时间和MS信号强度的图谱）中表示，来检查与液相色谱（LC）一起洗脱的蛋白质变体的解卷积分子量。为此，我们开发了一个名为VisioProt-MS（https://masstools.ipbs.fr/mstools/visioprot-ms/）的免费开源网络应用程序。VisioProt-MS与社区开发的许多用于整合和解卷积自上而下和完整蛋白质MS数据的算法和软件高度兼容。其动态且用户友好的功能通过几种专门用于复杂样品中蛋白质变体的MS和串联质谱（MS/MS）分析的图形表示，极大地促进了分析。在这里，我们将说明LC-MS图谱可视化对于优化自上而下采集/搜索参数和分析完整蛋白质MS数据的重要性。我们将以人类蛋白酶体20S核心颗粒为例，介绍VisioProt-MS的主要功能。
