apLCMS--adaptive processing of high-resolution LC/MS data.

MOTIVATION: Liquid chromatography-mass spectrometry (LC/MS) profiling is a promising approach for the quantification of metabolites from complex biological samples. Significant challenges exist in the analysis of LC/MS data, including noise reduction, feature identification/ quantification, feature alignment and computation efficiency. RESULT: Here we present a set of algorithms for the processing of high-resolution LC/MS data. The major technical improvements include the adaptive tolerance level searching rather than hard cutoff or binning, the use of non-parametric methods to fine-tune intensity grouping, the use of run filter to better preserve weak signals and the model-based estimation of peak intensities for absolute quantification. The algorithms are implemented in an R package apLCMS, which can efficiently process large LC/ MS datasets. AVAILABILITY: The R package apLCMS is available at www.sph.emory.edu/apLCMS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.