Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg 4232, Austria.
VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium.
J Proteome Res. 2024 Aug 2;23(8):3200-3207. doi: 10.1021/acs.jproteome.3c00785. Epub 2024 Mar 16.
Rescoring of peptide-spectrum matches (PSMs) has emerged as a standard procedure for the analysis of tandem mass spectrometry data. This emphasizes the need for software maintenance and continuous improvement for such algorithms. We introduce MSRescore 3.0, a versatile, modular, and user-friendly platform designed to increase peptide identifications. Researchers can install MSRescore across various platforms with minimal effort and benefit from a graphical user interface, a modular Python API, and extensive documentation. To showcase this new version, we connected MSRescore 3.0 with MS Amanda 3.0, a new release of the well-established search engine, addressing previous limitations on automatic rescoring. Among new features, MS Amanda now contains additional output columns that can be used for rescoring. The full potential of rescoring is best revealed when applied on challenging data sets. We therefore evaluated the performance of these two tools on publicly available single-cell data sets, where the number of PSMs was substantially increased, thereby demonstrating that MSRescore offers a powerful solution to boost peptide identifications. MSRescore's modular design and user-friendly interface make data-driven rescoring easily accessible, even for inexperienced users. We therefore expect the MSRescore to be a valuable tool for the wider proteomics community. MSRescore is available at https://github.com/compomics/ms2rescore.
重新评分肽-谱匹配（PSM）已经成为串联质谱数据分析的标准程序。这强调了此类算法的软件维护和持续改进的必要性。我们引入了 MSRescore 3.0，这是一个通用的、模块化的、用户友好的平台，旨在增加肽的鉴定。研究人员可以在不费吹灰之力的情况下在各种平台上安装 MSRescore，并从图形用户界面、模块化 Python API 和广泛的文档中受益。为了展示这个新版本，我们将 MSRescore 3.0 与 MS Amanda 3.0 连接起来，这是一个经过充分验证的搜索引擎的新版本，解决了以前在自动重新评分方面的限制。除了新特性外，MS Amanda 现在还包含了可用于重新评分的额外输出列。当应用于具有挑战性的数据集时，重新评分的全部潜力得到了最好的体现。因此，我们在公开可用的单细胞数据集上评估了这两个工具的性能，其中 PSM 的数量大大增加，这表明 MSRescore 提供了一个强大的解决方案，可以提高肽的鉴定。MSRescore 的模块化设计和用户友好的界面使得基于数据的重新评分变得容易，即使对于没有经验的用户也是如此。因此，我们期望 MSRescore 成为更广泛的蛋白质组学社区的一个有价值的工具。MSRescore 可在 https://github.com/compomics/ms2rescore 上获得。
