A novel algorithm of the wavelet packets transform, which is more suitable than the multiresolution signal decomposition (MRSD) algorithm to process the practical signals in analytical instrumental analysis, was proposed. There is no limitation of data length for the algorithm like the MRSD algorithm and, sometimes, no need to perform the inverse transform in practical uses by the algorithm. Two methods for de-noising were proposed based on the algorithm, and application of the methods to de-noising of noisy chromatograms was investigated. The results showed that the efficiency of the proposed methods is higher than that of the conventional thresholding methods.