US 9360487 B2 abstract the current disclosure provides specific peptides and derived ionization characteristics of the peptides from the estrogen receptor progesterone receptor and or antigen ki67 proteins that are particularly advantageous for quantifying the er pr and or ki67 proteins directly in biological samples that have been fixed in formalin by the method of selected reaction monitoring multiple reaction monitoring mass spectrometry such biological samples are chemically preserved and fixed wherein the biological sample is selected from tissues and cells treated with formaldehyde containing agents fixatives including formalin fixed tissue cells formalin fixed paraffin embedded tissue cells ffpe tissue blocks and cells from those blocks and tissue culture cells that have been formalin fixed and or paraffin embedded a protein sample is prepared from a biological sample using the liquid tissue u2122 reagents and protocol and the er pr and or ki67 proteins are quantitated in the liquid tissue u2122 sample by the method of srm mrm mass spectrometry by quantitating in the protein sample at least one or more of the peptides described for one or more of the er pr and or ki67 proteins these peptides can be quantitated if they reside in a modified or in an unmodified form an example.