SimPLIT: Simplified Sample Preparation for Large-Scale Isobaric Tagging Proteomics

• DOI: 10.1021/acs.jproteome.2c00092
• Publication Date: 2022-07-18T10:13:58Z
• Authors: Fernando J. Sialana; Theodoros I. Roum...; Habib Bouguenina; Laura Chan Wah Hak; Hannah Wang; John Caldwell; Ian Collins; Rajesh Chopra; Jyoti S. Choudhary
• Keywords: Isobaric process; Isobaric labeling; Sample Preparation; Sample (material)

Large scale proteomic profiling of cell lines can reveal molecular signatures attributed to variable genotypes or induced perturbations, enabling proteogenomic associations and elucidation pharmacological mechanisms action. Although isobaric labeling has increased the throughput analysis, commonly used sample preparation workflows often require time-consuming steps costly consumables, limiting their suitability for large studies. Here, we present a simplified cost-effective one-pot reaction workflow in 96-well plate format (SimPLIT) that minimizes processing demonstrates improved reproducibility compared alternative approaches. The is based on sodium deoxycholate lysis buffer single detergent cleanup step after peptide labeling, followed by quick off-line fractionation MS2 analysis. We showcase applicability panel colorectal cancer performing target discovery set glue degraders different lines, 96-sample assay. Using this workflow, report frequently dysregulated proteins cells uncover cell-dependent protein degradation profiles seven cereblon E3 ligase modulators (CRL4