Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
STAR Protoc. 2021 Feb 11;2(1):100338. doi: 10.1016/j.xpro.2021.100338. eCollection 2021 Mar 19.
Inter- or intra-patient tumor heterogeneity hinders the discovery of biomarkers for predicting individualized prognosis. Here, we present a protocol for an alternative splicing activity-based proteogenomic approach for identification of candidate prognostic markers in cancer cell lines and human breast cancer specimens. The pull-down of protein complexes with intronic splicing enhancer (ISE) probes is followed by tandem mass spectrometry (MS/MS) peptide sequencing. The proteogenomic analysis of data from these ISE-MS/MS assays identifies new prognostic markers that can be utilized to stratify patients with poor prognosis. For complete details on the use and execution of this protocol, please refer to Wang et al. (2018).
肿瘤内或肿瘤间异质性阻碍了预测个体化预后的生物标志物的发现。在这里，我们提出了一种剪接活性的基于蛋白质基因组学的方法，用于鉴定癌症细胞系和人类乳腺癌标本中的候选预后标志物。用内含子剪接增强子 (ISE) 探针进行蛋白质复合物的下拉，然后进行串联质谱 (MS/MS) 肽测序。对这些 ISE-MS/MS 测定数据的蛋白质基因组学分析确定了新的预后标志物，可用于对预后不良的患者进行分层。有关该方案的使用和执行的完整详细信息，请参阅 Wang 等人 (2018 年)。
