(a) extracting a sample comprising one or more proteins selected from the group consisting of γ-carboxylated proteins, γ-carboxylated protein proteoforms, and des-carboxylated proteins from the biological sample with a solvent, wherein the sample is a protein precipitate and extracting the sample with the solvent provides a liquid extract and a residual protein precipitate, wherein the residual protein precipitate is enriched with the one or more proteins relative to the sample;

(b) separating the liquid extract from the residual protein precipitate;

(c) dissolving the residual protein precipitate in an aqueous medium to provide a solution comprising the one or more proteins;

(d) contacting the solution comprising the one or more proteins with a protease, to provide a solution of peptides comprising one or more of γ-carboxylated peptides, γ-carboxylated peptide proteoforms, and des-carboxylated peptides; and

(e) determining the quantity of the one or more of γ-carboxylated peptides, γ-carboxylated peptide proteoforms, and des-carboxylated peptides in the solution of peptides.