Peptide cutter is a site that gives protease cleavage prediction option with a list of proteases

http://web.expasy.org/peptide_cutter/

but for mitochondria (unless caspases enter mitochondria) there is not much option in peptide cutter site. Instead PARL-rhomboid proteases are implicated in mitochondria. You might want to have a look at

http://www.annualreviews.org/doi/pdf/10.1146/annurev.genet.42.110807.091628

You might also want to biochemically localize your protein of interest at sub-mitochondrial locations as described in my paper

https://www.researchgate.net/publication/283306685_Smac_Mimetic_with_TNF-_Targets_Pim-1_Isoforms_and_Reactive_Oxygen_Species_Production_to_Abrogate_Transformation_from_Blebbishields

Article Smac Mimetic with TNF- Targets Pim-1 Isoforms and Reactive O...