Data Analysis Framework

Data Analysis Framework (DAF) is an infrastructure program providing data processing services based on integrated tools. DAF is open source and the source code in java is available

You can use the data processing services provided by DAF by clicking on the orange "+ Join DAF" button.

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2D Time Alignment

Warp2D is a new time alignment method that takes advantage of both dimensions of LC-MS data to resolve ambiguities in peak matching while remaining computationally efficient. Warp2D use extracted peak lists of chromatograms with a two-dimensional correlation function to provide a reliable alignment scoring function that is insensitive to spurious peaks and background noise. One-dimensional alignment methods are often based on the total-ion-current elution profile and are unable to distinguish peaks of different masses.

Our approach uses one-dimensional alignment in time, but with a scoring function derived from the overlap of peaks in two dimensions, thereby combining the specificity of two-dimensional methods with the computational performance of one-dimensional methods. The peaks are approximated as two-dimensional Gaussians of varying width, depending on the mass and chromatographic resolutions. This approximation allows peak overlap (the measure of alignment quality) to be calculated analytically, without computationally intensive numerical integration in two dimensions. To measure the alignment quality improvement Warp2D provide a score between 1 (all peaks overlap perfectly) and 0 (no peak overlap) based on standardized geometric mean of overlapping peak volumes. This score can be calculated before and after alignment and the difference reflects the alignment enhancement.

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We provide user friendly, online data processing services based on Warp2D approach using the Dutch Life Science Grid to enable processing of amount of data for high number of users. This service enables you to upload peak lists containing information on the retention time, mass and quantity on LC-MS peaks. The processing results in aligned peaks lists with changed retention time and in a file containing the retention time transformation function in series of subsequent linear interpolations.

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