State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
Sci Data. 2022 Jun 9;9(1):283. doi: 10.1038/s41597-022-01407-1.
Data-independent acquisition (DIA)-mass spectrometry (MS)-based proteome strategies are increasingly used for detecting and validating protein biomarkers and therapeutic targets. Here, based on an in-depth proteome analysis of seven pancreatic cancer cell lines, we built a pancreas-specific mass spectrum library containing 10633 protein groups and 184551 peptides. The proteome difference among the seven pancreatic cancer cells was significant, especially for the divergent expression of proteins related to epithelial-mesenchymal transition (EMT). The spectra library was applied to explore the proteome difference of PANC-1 and BxPC-3 cells upon gemcitabine (GEM) treatment, and potential GEM targets were identified. The cytotoxicity test and GEM target analysis found that HPAC, CFPAC-1, and BxPC-3 were sensitive to GEM treatment, whereas PANC-1 and AsPC-1 were resistant. Finally, we found EMT was significant for CFPAC-1, AsPC-1, and PANC-1 cells, whereas BxPC-3 and HPAC cells showed more typical epithelial features. This library provides a valuable resource for in-depth proteomic analysis on pancreatic cancer cell lines, meeting the urgent demands for cell line-dependent protein differences and targeted drug analysis.
基于数据非依赖性采集（DIA）-质谱（MS）的蛋白质组学策略越来越多地用于检测和验证蛋白质生物标志物和治疗靶点。在这里，我们基于对 7 种胰腺癌细胞系的深入蛋白质组学分析，构建了一个包含 10633 个蛋白质组和 184551 个肽段的胰腺特异性质谱文库。这 7 种胰腺癌细胞之间的蛋白质组差异显著，尤其是与上皮-间充质转化（EMT）相关的蛋白质表达差异明显。该图谱库被用于探索吉西他滨（GEM）处理后 PANC-1 和 BxPC-3 细胞的蛋白质组差异，并鉴定潜在的 GEM 靶点。细胞毒性试验和 GEM 靶点分析发现，HPAC、CFPAC-1 和 BxPC-3 对 GEM 治疗敏感，而 PANC-1 和 AsPC-1 则耐药。最后，我们发现 EMT 对 CFPAC-1、AsPC-1 和 PANC-1 细胞很重要，而 BxPC-3 和 HPAC 细胞则表现出更典型的上皮特征。该文库为胰腺癌细胞系的深入蛋白质组学分析提供了有价值的资源，满足了对细胞系依赖性蛋白质差异和靶向药物分析的迫切需求。
