Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
Proteomics. 2023 Feb;23(3-4):e2100369. doi: 10.1002/pmic.202100369. Epub 2022 Sep 20.
Mass spectrometry (MS)-based proteomic analysis of posttranslational modifications (PTMs) usually requires the pre-enrichment of modified proteins or peptides. However, recent ultra-deep whole proteome profiling generates millions of spectra in a single experiment, leaving many unassigned spectra, some of which may be derived from PTM peptides.
Here we present JUMPptm, an integrative computational pipeline, to extract PTMs from unenriched whole proteome. JUMPptm combines the advantages of JUMP, MSFragger and Comet search engines, and includes de novo tags, customized database search and peptide filtering, which iteratively analyzes each PTM by a multi-stage strategy to improve sensitivity and specificity.
We applied JUMPptm to the deep brain proteome of Alzheimer's disease (AD), and identified 34,954 unique peptides with phosphorylation, methylation, acetylation, ubiquitination, and others. The phosphorylated peptides were validated by enriched phosphoproteome from the same sample. TMT-based quantification revealed 482 PTM peptides dysregulated at different stages during AD progression. For example, the acetylation of numerous mitochondrial proteins is significantly decreased in AD. A total of 60 PTM sites are found in the pan-PTM map of the Tau protein.
The JUMPptm program is an effective tool for pan-PTM analysis and the resulting AD pan-PTM profile serves as a valuable resource for AD research.
基于质谱（MS）的翻译后修饰（PTM）蛋白质组学分析通常需要对修饰蛋白或肽进行预富集。然而，最近的超深度全蛋白质组谱分析在单个实验中产生了数百万个谱图，留下了许多未分配的谱图，其中一些可能来自 PTM 肽。
我们在这里提出了 JUMPptm，这是一个综合计算管道，用于从未富集的全蛋白质组中提取 PTM。JUMPptm 结合了 JUMP、MSFragger 和 Comet 搜索引擎的优点，包括从头标签、定制数据库搜索和肽过滤，它通过多阶段策略迭代分析每个 PTM，以提高灵敏度和特异性。
我们将 JUMPptm 应用于阿尔茨海默病（AD）的大脑深部蛋白质组学研究中，鉴定了 34954 种具有磷酸化、甲基化、乙酰化、泛素化和其他修饰的独特肽。从同一样本的富集磷酸肽组学中验证了磷酸化肽。TMT 定量分析显示，在 AD 进展的不同阶段有 482 个 PTM 肽失调。例如，AD 中许多线粒体蛋白的乙酰化明显降低。在 Tau 蛋白的泛 PTM 图谱中总共发现了 60 个 PTM 位点。
JUMPptm 程序是泛 PTM 分析的有效工具，由此产生的 AD 泛 PTM 图谱为 AD 研究提供了有价值的资源。
