Applied Bioinformatics, Department for Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany; Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany.
Applied Bioinformatics, Department for Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany; Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany.
Cell Syst. 2020 Feb 26;10(2):213-218.e6. doi: 10.1016/j.cels.2020.01.003. Epub 2020 Feb 19.
Top-down mass spectrometry (TD-MS)-based proteomics analyzes intact proteoforms and thus preserves information about individual protein species. The MS signal of these high-mass analytes is complex and challenges the accurate determination of proteoform masses. Fast and accurate feature deconvolution (i.e., the determination of intact proteoform masses) is, therefore, an essential step for TD data analysis. Here, we present FLASHDeconv, an algorithm achieving higher deconvolution quality, with an execution speed two orders of magnitude faster than existing approaches. FLASHDeconv transforms peak positions (m/z) within spectra into log m/z space. This simple transformation turns the deconvolution problem into a search for constant patterns, thereby greatly accelerating the process. In both simple and complex samples, FLASHDeconv reports more genuine feature masses and substantially fewer artifacts than other existing methods. FLASHDeconv is freely available for download here: https://www.openms.org/flashdeconv/. A record of this paper's Transparent Peer Review process is included in the Supplemental Information.
基于自上而下的质谱（TD-MS）的蛋白质组学分析完整的蛋白形式，因此保留了关于个体蛋白质种类的信息。这些高质量分析物的 MS 信号复杂，这对准确确定蛋白形式的质量提出了挑战。因此，快速准确的特征解卷积（即确定完整的蛋白形式质量）是 TD 数据分析的一个基本步骤。在这里，我们提出了 FLASHDeconv，这是一种算法，能够实现更高的解卷积质量，其执行速度比现有方法快两个数量级。FLASHDeconv 将谱中的峰位置（m/z）转换为 log m/z 空间。这种简单的转换将解卷积问题转化为寻找恒定模式，从而大大加速了这一过程。在简单和复杂的样本中，FLASHDeconv 报告的真实特征质量比其他现有方法多得多，而伪像则少得多。FLASHDeconv 可在此处免费下载：https://www.openms.org/flashdeconv/。本文透明同行评审过程的记录包含在补充信息中。
