This invention aims at high-thoughput high-sensitivity analysis of biological samples using an automated platform that encompasses LC fractionation and multiplexed IMS-TOF instrument. High sensitivity is achieved by correlating the analyte abundances from a particular fraction with the order of an encoding sequence, so as to provide the optimum use of ion trap charge capacity prior to IMS separation. Identification of the interesting features detected in the multiplexed IMS-TOF experiments with different LC fractions will be accomplished using multiplexed IMS-MS/MS approach.