Quantitative proteomic analysis of LPS-induced differential immune response associated with TLR4 Polymorphisms by multiplex amino acid coded mass tagging.

Polymorphisms at toll-like receptor 4 (TLR4) gene have been found to be associated with immune disorders. A murine macrophage cell line GG2EE derived from C3H/HeJ mice with a polymorphism site at TLR4 is hyposensitive to lipopolysaccharide (LPS). To study the molecular base of diverse TLR4-mediated immune responses, the proteomic changes in both TLR4-deficient and wild-type cell lines in response to the same LPS challenge were quantitatively compared by using multiplex amino acid coded mass tagging (AACT)/SILAC-assisted MS. This strategy allows encoding of two distinct cell populations with different stable isotope-tagged lysine residues as the "in-spectra" quantitative markers. In MS analysis of tryptic peptides derived from the equally mixed three cell populations, the lysine-containing peptides originated from two LPS-stimulated cell populations can be clearly distinguished by their different mass shifts from the unstimulated and unlabeled counterpart. The LPS-induced differential protein expression in TLR4-deficient and wild-type proteomes were obtained by comparing the intensities of isotopically encoded peptides. Among the more than 900 proteins identified, 35 were found to be deregulated at different levels in these two cell lines stimulated by LPS. This multiplex mass-tagging methodology can be readily extended to other comparative proteomic quantitation of different cell populations.