LiP-MS on HEK293 lysate treated with rapamycin

Limited proteolysis coupled to mass spectrometry (LiP-MS) is a structural proteomics technique that can be used to identify the targets of small molecules. This is achieved by incubating lysate with the drug of interest, which induces structural changes such as occupation of the binding site or changes and protein-protein interactions. This is followed by a limited proteolysis step in which the unspecific protease proteinase K is added to the treated lysate. The protease preferentially cleaves accessible and flexible regions of the proteins, thus generating peptides that reflect the changes in surface accessibility caused by the treatment with the small molecule. Here we treated HEK293 cell lysate with rapamycin and identify the known main target FKBP1A. This data is intended to be used as a model dataset for LiP-MS data evaluation and was created as part of the IMI EUbOPEN project.

有限蛋白水解联用质谱技术（Limited proteolysis coupled to mass spectrometry, LiP-MS）是一种结构蛋白质组学技术，可用于识别小分子的靶标蛋白。其实现方式为将细胞裂解液与目标药物共同孵育，该药物可诱导蛋白质结构发生改变，例如结合位点被占据，或蛋白质间相互作用发生变化。随后进行有限蛋白水解步骤：向经药物处理的裂解液中加入非特异性蛋白酶蛋白酶K（proteinase K）。该蛋白酶会优先切割蛋白质表面可及且柔性的区域，由此产生的肽段可反映小分子药物处理后蛋白质表面可及性的变化。本研究使用雷帕霉素（rapamycin）处理HEK293细胞裂解液，并成功鉴定出已知的主要靶标FK506结合蛋白1A（FKBP1A）。本数据集旨在作为LiP-MS数据评估的示范数据集，其构建工作隶属于创新药物倡议（Innovative Medicines Initiative, IMI）旗下的EUbOPEN项目。