2025年4月22日，Mathias MSAID GmbHWilhelm课题组在《自然—方法学》杂志发表论文，报道了用CHIMERYS统一自下而上的蛋白质组学数据分析。

研究小组介绍了CHIMERYS，这是一种以光谱为中心的搜索算法，旨在统一蛋白质组学数据分析的嵌合光谱的反卷积。使用肽保留时间，片段离子强度和应用正则化线性回归的准确预测，它解释尽可能多的片段离子强度与尽可能少的肽。与严格的错误发现率控制一起，CHIMERYS在数据依赖，数据独立或平行反应监测实验中准确地识别和定量每个串联质谱的多个肽。

研究人员表示，蛋白质组学工作流程产生非常复杂的多肽混合物，通过液相色谱-串联质谱分析，产生多种光谱，其中大多数是嵌合的，包含来自多个多肽的片段离子。由于数据获取策略（如数据依赖、数据独立或平行反应监测）的差异，采用不同分析概念的单独软件包以进行肽鉴定和定量为主题，即使底层信息基本相同。

附：英文原文

Title: Unifying the analysis of bottom-up proteomics data with CHIMERYS

Author: Frejno, Martin, Berger, Michelle T., Tshaus, Johanna, Hogrebe, Alexander, Seefried, Florian, Graber, Michael, Samaras, Patroklos, Ben Fredj, Samia, Sukumar, Vishal, Eljagh, Layla, Bronshtein, Igor, Mamisashvili, Lizi, Schneider, Markus, Gessulat, Siegfried, Schmidt, Tobias, Kuster, Bernhard, Zolg, Daniel P., Wilhelm, Mathias

Issue&Volume: 2025-04-22

Abstract: Proteomic workflows generate vastly complex peptide mixtures that are analyzed by liquid chromatography–tandem mass spectrometry, creating thousands of spectra, most of which are chimeric and contain fragment ions from more than one peptide. Because of differences in data acquisition strategies such as data-dependent, data-independent or parallel reaction monitoring, separate software packages employing different analysis concepts are used for peptide identification and quantification, even though the underlying information is principally the same. Here, we introduce CHIMERYS, a spectrum-centric search algorithm designed for the deconvolution of chimeric spectra that unifies proteomic data analysis. Using accurate predictions of peptide retention time, fragment ion intensities and applying regularized linear regression, it explains as much fragment ion intensity as possible with as few peptides as possible. Together with rigorous false discovery rate control, CHIMERYS accurately identifies and quantifies multiple peptides per tandem mass spectrum in data-dependent, data-independent or parallel reaction monitoring experiments.

DOI: 10.1038/s41592-025-02663-w

Source: https://www.nature.com/articles/s41592-025-02663-w