Typic: A Practical and Robust Tool to Rank Proteotypic Peptides for Targeted Proteomics

The selection of a suitable proteotypic peptide remains a challenge for designing a targeted quantitative proteomics assay. Although the criteria are well-established in the literature, the selection of these peptides is often performed in a subjective and time-consuming manner. Here, we have developed a practical and semiautomated workflow implemented in an open-source program named Typic. Typic is designed to run in a command line and a graphical interface to help selecting a list of proteotypic peptides for targeted quantitation. The tool combines the input data and downloads additional data from public repositories to produce a file per protein as output. Each output file includes relevant information to the selection of proteotypic peptides organized in a table, a colored ranking of peptides according to their potential value as targets for quantitation and auxiliary plots to assist users in the task of proteotypic peptides selection. Taken together, Typic leads to a practical and straightforward data extraction from multiple data sets, allowing the identification of most suitable proteotypic peptides based on established criteria, in an unbiased and standardized manner, ultimately leading to a more robust targeted proteomics assay.在靶向定量蛋白质组学检测的设计过程中，筛选合适的蛋白特征肽（proteotypic peptide）仍是一项颇具挑战的任务。尽管相关筛选标准在学术文献中已有成熟规范，但这类肽段的筛选往往仍依赖主观判断且耗时较长。为此，我们开发了一款名为Typic的开源程序，其内置了实用且半自动化的分析流程。Typic支持命令行与图形界面两种运行模式，可辅助研究人员筛选用于靶向定量的蛋白特征肽列表。该工具可整合用户输入数据，并从公共数据库下载补充信息，最终为每个靶标蛋白生成专属输出文件。每份输出文件均包含与蛋白特征肽筛选相关的信息：以表格形式整理的核心数据、基于定量靶标潜力生成的彩色肽段分级结果，以及用于辅助筛选工作的可视化辅助图表。综上，Typic可实现多数据集的便捷高效数据提取，能够以无偏、标准化的方式基于既定标准筛选出最优蛋白特征肽，最终助力构建更可靠的靶向定量蛋白质组学检测体系。