Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study

ABSTRACT: Proteome profiling of formalin-fixed paraffin-embedded (FFPE) specimens has gained traction for the analysis of cancer tissue for the discovery of molecular biomarkers. However, reports so far focused on single cancer entities, comprised relatively few cases and did not assess the long-term performance of experimental workflows. In this study, we analyze 1,220 tumors from six cancer entities processed over the course of three years. Key findings include the need for a new normalization method ensuring equal and reproducible sample loading for LC-MS/MS analysis across cohorts, showing that tumors can, on average, be profiled to a depth of >4,000 proteins and discovering that current software fails to process such large ion mobility-based online fractionated data sets. We report the first

SUBMITTER: Dr. Johanna Tueshaus 

PROVIDER: S-SCDT-10_1038-S44318-024-00289-W | biostudies-other |

REPOSITORIES: biostudies-other