Protein quantitation in multicellular tissue specimens

A method for measuring the amount of a target protein in a heterogeneous biospecimen having two or more cell types, the method comprising:

• extracting proteins from a heterogeneous biospecimen;
• cleaving the proteins to form peptides;
• analyzing the peptides by mass spectrometry to measure an amount of a proteotypic peptide of a benchmark protein, an amount of a proteotypic peptide of a component-specific protein, and an amount of a proteotypic peptide of a target protein;
• quantifying an amount of the benchmark protein, an amount of the component-specific protein, and an amount of the target protein in the biospecimen based on the amounts of the corresponding proteotypic peptides;
• normalizing the amount of the component-specific protein to the amount of the benchmark protein to identify a component factor of a component cell type that expresses the component-specific protein;
• normalizing the amount of the target protein to the component factor of the component cell type to identify a component factor adjusted amount representing a target value of the target protein in the heterogeneous biospecimen.