Patent ID: 7910372

Claim:
A method for executing quantitation of protein content in a sample of biological material, said method comprising the steps of: (a) identifying by mass spectrometry one or more proteins to be quantified; (b) measuring by LC-MS/MS a number of observed peptides per protein (N obsd ) from an enzymatic digestion of each protein; (c) calculating a number of observable peptides per protein (N obsbl ) from in silico modeling of the enzymatic digestion of each protein; and (d) computing the following equation to obtain an exponentially modified Protein Abundance Index (EMPAI) of each protein EMPAI= 10 Nobsd/Nobsbl −1; (e) calculating protein contents based on protein ⁢ ⁢ contents ⁢ ⁢ ( mol ⁢ ⁢ % ) = EMPAI ∑ ( EMPAI ) × 100 , or protein ⁢ ⁢ contents ⁢ ⁢ ( weight ⁢ ⁢ ⁢ % ) = EMPAI × MW ∑ ( EMPAI × MW ) × 100 , wherein Σ(EMPAI) is the summation of EMPAI values for all identified protein or proteins and MW represents molecular weight of each protein identified.