Improving signal-to-noise ratios of liquid chromatography–tandem mass spectrometry peaks using noise frequency spectrum modification between two consecutive matched-filtering procedures

This paper reports a simple chemometric technique to alter the noise spectrum of liquid chromatography–tandem mass spectrometry (LC–MS-MS) chromatogram between two consecutive matched filter procedures to improve the peak signal-to-noise (S/N) ratio enhancement. This technique is to multiply one match-filtered LC–MS-MS chromatogram with another artificial chromatogram added with thermal noises prior to the second matched filter. Because matched filter cannot eliminate low-frequency components inherent in the flicker noises of spike-like sharp peaks randomly riding on LC–MS-MS chromatograms, efficient peak S/N ratio improvement cannot be accomplished using one-step or consecutive matched filter procedures to process LC–MS-MS chromatograms. In contrast, when the match–filtered LC–MS-MS chromatogram is conditioned with the multiplication alteration prior to the second matched filter, much better efficient ratio improvement is achieved. The noise frequency spectrum of match-filtered chromatogram, which originally contains only low-frequency components, is altered to span a boarder range with multiplication operation. When the frequency range of this modified noise spectrum shifts toward higher frequency regime, the second matched filter, working as a low-pass filter, is able to provide better filtering efficiency to obtain higher peak S/N ratios. Real LC–MS-MS chromatograms containing random spike-like peaks, of which peak S/N ratio improvement is less than four times with two consecutive matched filters typically, are remedied to accomplish much better ratio enhancement approximately 16-folds when the noise frequency spectrum is modified between two matched filters.