University of Wisconsin-Madison, Department of Chemistry, Madison, WI, USA.
Methods Mol Biol. 2023;2426:35-66. doi: 10.1007/978-1-0716-1967-4_3.
MetaMorpheus is a free and open-source software program dedicated to the comprehensive analysis of proteomic data. In bottom-up proteomics, protein samples are digested into peptides prior to chromatographic separation and tandem mass spectrometric analysis. The resulting fragmentation spectra are subsequently analyzed with search software programs to obtain peptide identifications and infer the presence of proteins in the samples. MetaMorpheus seeks to maximize the information gleaned from proteomic data through the use of (a) mass calibration, (b) post-translational modification discovery, (c) multiple search algorithms, which aid in the analysis of data from traditional, crosslinking, and glycoproteomic experiments, (d) isotope-based or label-free quantification, (e) multi-protease protein inference, and (f) spectral annotation and data visualization capabilities. This protocol provides detailed descriptions of how use MetaMorpheus and how to customize data analysis workflows using MetaMorpheus tasks to meet the specific needs of the user.
MetaMorpheus 是一款免费的开源软件程序，致力于对蛋白质组学数据进行全面分析。在自上而下的蛋白质组学中，在进行色谱分离和串联质谱分析之前，将蛋白质样品消化成肽。随后，使用搜索软件程序分析得到的碎片光谱，以获得肽鉴定，并推断样品中存在的蛋白质。MetaMorpheus 通过使用 (a) 质量校准、(b) 翻译后修饰发现、(c) 多种搜索算法，帮助分析传统、交联和糖蛋白质组学实验的数据，(d) 基于同位素或无标记定量、(e) 多蛋白酶蛋白质推断，以及 (f) 光谱注释和数据可视化功能，来最大限度地从蛋白质组学数据中获取信息。本方案详细描述了如何使用 MetaMorpheus，以及如何使用 MetaMorpheus 任务定制数据分析工作流程，以满足用户的特定需求。
