Glutamine (Gln) is converted to excitatory (glutamate, aspartate) and inhibitory (γ-amino butyric acid) amino acid neurotransmitters in brain, and is a source of energy during glucose deprivation. Current research utilized an Analytical Quality by Design approach to optimize levels and combinations of critical gas pressure (sheath, auxiliary, sweep) and temperature (ion transfer tube, vaporizer) parameters for high-sensitivity mass spectrometric quantification of brain tissue glutamine. A Design of Experiments (DOE) matrix for evaluation of relationships between these multiple independent variables and a singular response variable, e.g. glutamine chromatogram area, was developed by statistical response surface methodology using central composite design. A second-order polynomial equation was generated to identify and predict singular versus combinatory effects of synergistic and antagonistic factors on chromatograph area. Predicted versus found outcomes overlapped, with enhanced area associated with the latter. DOE methodology was subsequently used to evaluate liquid chromatographic variable effects, e.g. flow rate, column temperature, and mobile phase composition on the response variable. Results demonstrate that combinatory AQbD-guided mass spectrometric/liquid chromatographic optimization significantly enhanced analytical sensitivity for Gln, thus enabling down-sized brain tissue sample volume procurement for quantification of this critical amino acid.