A method of validating data produced from a multiplexing process on an analytical instrument is disclosed. In one embodiment, the method includes using a pseudorandom sequence to encode a multiplexed segment of data; applying Hadamard transform to generate a demultiplexed segment of the data; aligning the pseudorandom sequence to the multiplexed data; and calculating a score for at least one positive value in the demultiplexed segment to find a valid demultiplexed value.