Abstract：
Ion mobility mass spectrometry has become popular in proteomics lately, in particular because the Bruker timsTOF instruments have found significant adoption in proteomics facilities. The Bruker\'s implementation of the ion mobility dimension generates massive amounts of mass spectrometric data that require carefully designed software both to extract meaningful information and to perform processing tasks at reasonable speed. In a historical move, the Bruker company decided to harness the skills of the scientific software development community by releasing to the public the timsTOF data file format specification. As a proteomics facility that has been developing Free Open Source Software (FOSS) solutions since decades, we took advantage of this opportunity to implement the very first FOSS proteomics complete solution to natively read the timsTOF data, low-level process them, and explore them in an integrated quantitative proteomics software environment. We dubbed our software i2MassChroQ because it implements a (peptide)identification-(protein)inference-mass-chromatogram-quantification processing workflow. The software benchmarking results reported in this paper show that i2MassChroQ performed better than competing software on two critical characteristics: (1) feature extraction capability and (2) protein quantitative dynamic range. Altogether, i2MassChroQ yielded better quantified protein numbers, both in a technical replicate MS runs setting and in a differential protein abundance analysis setting.
摘要：
离子迁移质谱最近在蛋白质组学中变得越来越流行,特别是因为BrukertimsTOF仪器已在蛋白质组学设施中发现了重要的应用。Bruker的离子迁移率维度的实现产生了大量的质谱数据，这些数据需要精心设计的软件来提取有意义的信息并以合理的速度执行处理任务。在历史性的举动中，布鲁克公司决定通过向公众发布timsTOF数据文件格式规范来利用科学软件开发社区的技能。作为一个蛋白质组学机构，几十年来一直在开发免费开源软件（FOSS）解决方案，我们利用这个机会实施了第一个FOSS蛋白质组学完整解决方案来本地读取timsTOF数据，低级处理它们，并在集成的定量蛋白质组学软件环境中探索它们。我们将我们的软件称为i2MassChroQ，因为它实现了（肽）鉴定-（蛋白质）推断-质量-色谱-定量处理工作流程。本文报告的软件基准测试结果表明，i2MassChroQ在两个关键特征上比竞争软件表现更好:(1)特征提取能力和(2)蛋白质定量动态范围。总之,i2MassChroQ产生了更好的定量蛋白质数量，在技术复制MS运行设置和差异蛋白质丰度分析设置中。
