Implementing the MSFragger Search Engine as a Node in Proteome Discoverer.
Implementing the MSFragger Search Engine as a Node in Proteome Discoverer.
复制标题
将 MSFragger 搜索引擎实现为 Proteome Discoverer 中的节点。
DOI：
10.1021/acs.jproteome.2c00485
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发表时间：
2023
影响因子：
4.4
通讯作者：
Nesvizhskii,AlexeyI
中科院分区：
文献类型：
--
作者：
Chang,Hui-Yin;Haynes,SarahE;Yu,Fengchao;Nesvizhskii,AlexeyI
在这里，我们描述了实现的快速蛋白质组学搜索引擎MSFragger作为一个处理节点，在广泛使用的蛋白质组发现（PD）软件平台。PeptideProphet（通过Philosopher工具包）也被实现为额外的PD节点，以允许验证MSFragger开放（质量容忍）搜索结果。这两个节点，沿着现有的Percolator验证模块，允许用户采用不同的搜索策略，并通过PD方便地检查搜索结果。我们的研究结果表明，与传统的SEQUEST/Percolator PD工作流程相比，MSFragger与Percolator结合识别的PSM，肽和蛋白质的数量有所增加，搜索速度明显加快。MSFragger-PD节点可在https://github.com/nesvilab/PD-Nodes/releases/上获得。
Here, we describe the implementation of the fast proteomics search engine MSFragger as a processing node in the widely used Proteome Discoverer (PD) software platform. PeptideProphet (via the Philosopher tool kit) is also implemented as an additional PD node to allow validation of MSFragger open (mass-tolerant) search results. These two nodes, along with the existing Percolator validation module, allow users to employ different search strategies and conveniently inspect search results through PD. Our results have demonstrated the improved numbers of PSMs, peptides, and proteins identified by MSFragger coupled with Percolator and significantly faster search speed compared to the conventional SEQUEST/Percolator PD workflows. The MSFragger-PD node is available at https://github.com/nesvilab/PD-Nodes/releases/.