A Universal Denoising and Peak Picking Algorithm for LC-MS Based on Matched Filtration in the Chromatographic Time Domain

Victor P. Andreev, Tomas Rejtar, Hsuan Shen Chen, Eugene V. Moskovets, Alexander R. Ivanov, Barry L. Karger

Research output: Contribution to journalArticle

107 Scopus citations

Abstract

A new denoising and peak picking algorithm (MEND, matched filtration with experimental noise determination) for analysis of LC-MS data is described. The algorithm minimizes both random and chemical noise in order to determine MS peaks corresponding to sample components. Noise characteristics in the data set are experimentally determined and used for efficient denoising. MEND is shown to enable low-intensity peaks to be detected, thus providing additional useful information for sample analysis. The process of denoising, performed in the chromatographic time domain, does not distort peak shapes in the m/z domain, allowing accurate determination of MS peak centroids, including low-intensity peaks. MEND has been applied to denoising of LC-MALDI-TOF-MS and LC-ESI-TOF-MS data for tryptic digests of protein mixtures. MEND is shown to suppress chemical and random noise and baseline fluctuations, as well as filter out false peaks originating from the matrix (MALDI) or mobile phase (ESI). In addition, MEND is shown to be effective for protein expression analysis by allowing selection of a large number of differentially expressed ICAT pairs, due to increased signal-to-noise ratio and mass accuracy.

Original languageEnglish (US)
Pages (from-to)6314-6326
Number of pages13
JournalAnalytical Chemistry
Volume75
Issue number22
DOIs
StatePublished - Nov 15 2003

ASJC Scopus subject areas

  • Analytical Chemistry

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    Andreev, V. P., Rejtar, T., Chen, H. S., Moskovets, E. V., Ivanov, A. R., & Karger, B. L. (2003). A Universal Denoising and Peak Picking Algorithm for LC-MS Based on Matched Filtration in the Chromatographic Time Domain. Analytical Chemistry, 75(22), 6314-6326. https://doi.org/10.1021/ac0301806