ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics

Mass spectrometry (MS) is a technique widely employed for the identification and characterization of proteins, personalized medicine, systems biology and biomedical applications. By combining MS with different proteomics approaches such as immunopurification MS, immunopeptidomics, and total protein proteomics, researchers can gain insights into protein-protein interactions, immune responses, cellular processes, and disease mechanisms. The application of MS-based proteomics in these areas continues to advance our understanding of protein function, cellular signaling, and complex biological systems. Data analysis for mass spectrometry is a critical process that includes identifying and quantifying proteins and peptides and exploring biological functions for these proteins in downstream analysis. To address the complexities associated with MS data analysis, we developed ProtPipe to streamline and automate the processing and analysis of high-throughput proteomics and peptidomics datasets. The pipeline facilitates data quality control, sample filtering, and normalization, ensuring robust and reliable downstream analysis. ProtPipe provides downstream analysis including identifying differential abundance proteins and peptides, pathway enrichment analysis, protein-protein interaction analysis, and MHC1-peptide binding affinity. ProtPipe generates annotated tables and diagnostic visualizations from statistical postprocessing and computation of fold-changes across pairwise conditions, predefined in an experimental design. ProtPipe is well-documented open-source software and is available at https://github.com/NIH-CARD/ProtPipe, accompanied by a web interface.

质谱法（mass spectrometry，MS）是一种被广泛应用于蛋白质鉴定与表征、个性化医疗、系统生物学及生物医学研究的技术。将质谱法与免疫纯化质谱（immunopurification MS）、免疫肽组学（immunopeptidomics）、全蛋白质组学等不同蛋白质组学方法相结合，研究人员可深入解析蛋白质-蛋白质相互作用、免疫应答、细胞进程与疾病机制。基于质谱的蛋白质组学在上述领域的应用，持续推动我们对蛋白质功能、细胞信号传导及复杂生物系统的认知。质谱数据分析是一项核心流程，涵盖蛋白质与肽段的鉴定、定量，以及在下游分析中探究这些蛋白质的生物学功能。为解决质谱数据分析面临的复杂性挑战，我们开发了ProtPipe工具，以简化并自动化高通量蛋白质组学与肽组学数据集的处理与分析流程。该工具可实现数据质量控制、样本过滤与归一化，保障下游分析的稳健性与可靠性。ProtPipe提供丰富的下游分析功能，包括差异丰度蛋白质与肽段的鉴定、通路富集分析、蛋白质-蛋白质相互作用分析，以及主要组织相容性复合体I类（MHC1）肽段结合亲和力预测。ProtPipe可根据实验设计中预设的成对实验条件，通过统计后处理与倍数变化计算，生成带注释的数据表格与诊断可视化结果。ProtPipe是一款文档完备的开源软件，可通过https://github.com/NIH-CARD/ProtPipe获取，并配套有网页交互界面。