Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
Sci Data. 2022 Oct 15;9(1):626. doi: 10.1038/s41597-022-01736-1.
The holistic nature of omics studies makes them ideally suited to generate hypotheses on health and disease. Sequencing-based genomics and mass spectrometry (MS)-based proteomics are linked through epigenetic regulation mechanisms. However, epigenomics is currently mainly focused on DNA methylation status using sequencing technologies, while studying histone posttranslational modifications (hPTMs) using MS is lagging, partly because reuse of raw data is impractical. Yet, targeting hPTMs using epidrugs is an established promising research avenue in cancer treatment. Therefore, we here present the most comprehensive MS-based preprocessed hPTM atlas to date, including 21 T-cell acute lymphoblastic leukemia (T-ALL) cell lines. We present the data in an intuitive and browsable single licensed Progenesis QIP project and provide all essential quality metrics, allowing users to assess the quality of the data, edit individual peptides, try novel annotation algorithms and export both peptide and protein data for downstream analyses, exemplified by the PeptidoformViz tool. This data resource sets the stage for generalizing MS-based histone analysis and provides the first reusable histone dataset for epidrug development.
组学研究的整体性使其非常适合生成关于健康和疾病的假设。基于测序的基因组学和基于质谱 (MS) 的蛋白质组学通过表观遗传调控机制联系在一起。然而，表观基因组学目前主要集中在使用测序技术研究 DNA 甲基化状态，而使用 MS 研究组蛋白翻译后修饰 (hPTM) 则相对滞后，部分原因是原始数据的重复使用不切实际。然而，使用表皮药物靶向 hPTMs 是癌症治疗中一种已确立的有前途的研究途径。因此，我们在这里展示了迄今为止最全面的基于 MS 的预处理 hPTM 图谱，其中包括 21 种 T 细胞急性淋巴细胞白血病 (T-ALL) 细胞系。我们以直观且可浏览的单个许可 Progenesis QIP 项目呈现数据，并提供所有必要的质量指标，允许用户评估数据的质量、编辑单个肽段、尝试新的注释算法，并导出肽和蛋白质数据以进行下游分析，例如 PeptidoformViz 工具。该数据集为基于 MS 的组蛋白分析提供了基础，并为表皮药物开发提供了第一个可重复使用的组蛋白数据集。
