Proteomic analysis of FKBP8 knockdown in HEK293T cells

To investigate the effects of FKBP8 depletion in HEK293T cells, cells were transfected with siRNA targeting FKBP8 or with a non-targeting control siRNA for 48 hours. After transfection, cells were collected; 10% of the material was used for whole-cell proteome analysis, and the remaining 90% was used for mitochondrial isolation. Both whole-cell and mitochondrial pellets were snap-frozen in liquid nitrogen and subjected to LC-MS/MS proteomic analysis.