Looking for selective protein markers for cytosolic and mitochondrial fraction. It would be big help if someone can suggest a working antibody too for those proteins.
What Petra suggests is that exists several good options, but some depend on the type of cell you are interested.
For general purposes we would recommend you VDAC (outer mitochondrial membrane transporter) for the mitochondrial fraction, and some of the glycolitic enzymes, such as PGAM, for the cytosolic. Also, histones (for example H3) for nuclear fraction.
We also use SOD1 and SOD2, that are the cytosolic and Mitochondrial superoxide dismutase, respectively.
COXII and MEK1/2 are also good options for M and C.
Sometimes we have a good control in our freezer, check for the subcellular localization of the proteins that you usually work with.