Analysis of proteotype, cell growth and metabolic changes induced by caspase-9 inhibition in chondrogenic cells

Caspase-9 is the major apical caspase responsible for triggering the intrinsic apoptotic pathway. Our pilot study indicated that specific inhibition of caspase-9 caused microscopically evident alterations in appearance of the primary chondrogenic cultures which cannot be explained by decrease in apoptosis. In order to search for the complex molecular background of the effect, proteomics analysis after caspase-9 inhibition was performed. A selective fluoromethylketone inhibitor was applied to inhibit caspase-9 in the chondrogenic cultures. In this PRIDE project we present three LC-MS datasets: i) diaPASEF data obtained using timsTOF Pro LC-MS system; ii) iTRAQ-2DLC-MS3 dataset; and iii) conventional LC-DIA-MS dataset, both measured on Orbitrap Lumos. In this project we demonstrate superiority of the diaPASEF method offering better proteome coverage.