A multiplexed targeted proteomic assay using a mTRAQ-MRM/MS-based approach was developed and assessed to systematically quantify the relative expressions of five candidate plasma apolipoproteins that have been previously shown to be dysregulated in neuropsychiatric disorders and cognitive dysfunction:apolipoprotein H(APOH),apolipoprotein J(APOJ),apolipoprotein A4(APOA4),apolipoprotein E(APOE),and apolipoprotein D(APOD).The peptides and transitions of each APO were carefully selected according to the tandem MS signals acquired on a TripleTOFTM 5600,followed by optimization of the declustering potential and collision energy voltages for transitions on a QTRAP 5500.Our results showed that the collision energies of mTRAQ-labeled peptides were approximately 15%–20%higher than corresponding non-labeled peptides.Through optimized transitions and parameters,we analyzed the relative abundances of the five APOs in human plasma with and without depletion of high abundant proteins.The results indicated that the MRM signals of four target APOs were significantly increased after depletion,while the MRM signal of one APO,APOD,was decreased.Furthermore,the relative abundances of the five target APOs in healthy human plasma were stable,and the ranking of these proteins according to their MS responses changed slightly.Therefore,we deduced that the rank order of the MS signals for these target proteins can be developed as a diagnostic signature for diseased plasma. A multiplexed targeted proteomic assay using a mTRAQ-MRM / MS-based approach was developed and assessed to systematically quantify the relative expressions of five candidate plasma apolipoproteins that have been previously shown to be dysregulated in neuropsychiatric disorders and cognitive dysfunction: apolipoprotein H (APOH) , apolipoprotein J (APOJ), apolipoprotein A4 (APOA4), apolipoprotein E (APOE), and apolipoprotein D (APOD) .The peptides and transitions of each APO were carefully selected according to the tandem MS signals acquired on a TripleTOFTM 5600, followed by optimization of the declustering potential and collision energy voltages for transitions on a QTRAP 5500.Our results showed that the collisional energies of mTRAQ-labeled peptides were approximately 15% -20% higher than corresponding non-labeled peptides. Through optimized transitions and parameters, we analyzed the relative abundances of the five APOs in human plasma with and without depletion of high abundant proteins. The results in dicated that the MRM signals of four target APOs were significantly increased after after depletion, while the MRM signal of one APO, APOD, was decreased. Future plus, the relative abundances of the five target APOs in healthy human plasma were stable, and the ranking of these proteins according to their MS responses changed slightly.Therefore, we deduced that the rank order of the MS signals for these target proteins can be developed as a diagnostic signature for diseased plasma.