Protocol for proteogenomic dissection of intronic splicing enhancer interactome for prediction of individualized cancer prognosis

STAR Protocols

John A. Wrobel¹  Xian Chen¹  Ling Xie²  Li Wang² 

[1] Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;;Department of Biochemistry &

关键词: Cancer;    Genomics;    Molecular/chemical probes;    Proteomics;    Mass spectrometry;   

DOI  :  

来源: DOAJ

【 摘 要 】

Summary: 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).

【 授权许可】

Unknown