SimPLIT: Simplified sample preparation for large-scale isobaric tagging proteomics

Large scale proteomic profiling of cell lines can reveal molecular signatures attributed to variable genotypes or induced perturbations. Although isobaric labelling has greatly increased the throughput of proteomic analysis, the commonly used sample preparation workflows often require time-consuming steps and costly consumables, limiting their suitability for large scale studies. Here, we present a simplified and cost effective one-pot reaction workflow in a 96-well plate format (SimPLIT), based on a sodium deoxycholate lysis buffer, that minimizes processing steps and demonstrates improved reproducibility compared to alternative approaches. We showcase the applicability of the workflow in a panel of colorectal cancer cell lines and by performing target discovery for a set of molecular glue degraders in different cell lines, in a 96-sample assay. Using this workflow, we identify frequently dysregulated proteins in colorectal cancer cells and uncover cell-dependent protein degradation profiles of cereblon E3 ligase modulators. Overall, SimPLIT is a robust method that can be easily implemented in any proteomics laboratory for medium-to-large scale TMT-based studies for deep profiling of cell lines.