Seymour Robert W, van der Post Sjoerd, Mooradian Arshag D, Held Jason M
Department of Medicine, Washington University School of Medicine in St. Louis, Campus Box 8076, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States.
Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden.
J Proteome Res. 2021 Jul 2;20(7):3621-3628. doi: 10.1021/acs.jproteome.1c00203. Epub 2021 May 30.
Large-scale proteomic profiling of protein post-translational modifications has provided important insights into the regulation of cell signaling and disease. These modification-specific proteomics workflows nearly universally enrich modified peptides prior to mass spectrometry analysis, but protein-centric proteomic software tools have many limitations evaluating and interpreting these peptide-centric data sets. We, therefore, developed ProteoSushi, a software tool tailored to analysis of each modified site in peptide-centric proteomic data sets that is compatible with any post-translational modification or chemical label. ProteoSushi uses a unique approach to assign identified peptides to shared proteins and genes, minimizing redundancy by prioritizing shared assignments based on UniProt annotation score and optional user-supplied protein/gene lists. ProteoSushi simplifies quantitation by summing or averaging intensities for each modified site, merging overlapping peptide charge states, missed cleavages, spectral matches, and variable modifications into a single value. ProteoSushi also annotates each PTM site with the most up-to-date biological information available from UniProt, such as functional roles or known modifications, the protein domain in which the site resides, the protein's subcellular location and function, and more. ProteoSushi has a graphical user interface for ease of use. ProteoSushi's flexibility and combination of analysis features streamlines peptide-centric data processing and knowledge mining of large modification-specific proteomics data sets.
蛋白质翻译后修饰的大规模蛋白质组学分析为细胞信号传导和疾病调控提供了重要见解。这些修饰特异性蛋白质组学工作流程几乎普遍在质谱分析之前富集修饰肽段，但以蛋白质为中心的蛋白质组学软件工具在评估和解释这些以肽段为中心的数据集时存在许多局限性。因此，我们开发了ProteoSushi，这是一种专门用于分析以肽段为中心的蛋白质组学数据集中每个修饰位点的软件工具，它与任何翻译后修饰或化学标签兼容。ProteoSushi采用独特方法将鉴定出的肽段分配给共享蛋白质和基因，通过基于UniProt注释分数和用户提供的可选蛋白质/基因列表优先进行共享分配来最小化冗余。ProteoSushi通过对每个修饰位点的强度求和或求平均值来简化定量分析，将重叠的肽段电荷状态、错切、谱图匹配和可变修饰合并为一个单一值。ProteoSushi还使用UniProt提供的最新生物学信息注释每个PTM位点，如功能作用或已知修饰、该位点所在的蛋白质结构域、蛋白质的亚细胞定位和功能等。ProteoSushi具有图形用户界面，便于使用。ProteoSushi的灵活性和分析功能的组合简化了以肽段为中心的数据处理以及对大型修饰特异性蛋白质组学数据集的知识挖掘。
