Institute for Advanced Biosciences Keio University
MathDAMP Mathematica package for differential analysis of metabolite profiles
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MathDAMP > Examples > MathDAMP source > Data Import/Export

Data Import/Export

Imported datasets are processed into a nested list (further referred to as msdata). The first element is a matrix containing ion signal intensities, rows corresponding to individual chromatograms/electropherograms. The second element is a list of m/z values and the third element is a list of scan timepoints (in minutes). The dimensions of the signal intensity matrix are determined by the length of the lists containing the m/z values and timepoints. The fourth element is a list of rules containing additional information about the dataset. Currently, it is used to store the sample name only.

Sample dataset with 2 m/z values and 6 timepoints in MathDAMP internal representation: {{{0,0,1,3,1,0},{0,0,0,0,0,0}},{100.,150.},{1,2,3,4,5,6},{SampleName→"Dummy Profile"}}

The datasets may be imported in two modes: sequential and selective. The modes determine the way in which the m/z values are generated (along with the matrix of signal intensities). In the sequential mode, the list of m/z values will contain an ordered list of m/z values in which the difference between two neighboring m/z values (step size) will be fixed. The values of the first and the last element in the m/z list are determined by the minimum and maximum m/z value in the imported dataset (rounded according to specified resolution as described in the next paragraph). In the selective mode, the list of m/z values will contain only those m/z values, which are present in the imported dataset (and rounded according to the selected resolution as described in the next paragraph). Selective mode import is recommended for datasets acquired by selected ion monitoring (SIM) for instance. Selective mode works for scan data also, using sequential mode leads to faster data import. Additionally, using selective mode for scan data may lead to an omission of some chromatograms (leading to a non-sequential m/z scale) if no signal intensities are present within a particular m/z interval (as determined by resolution).

The raw data is binned along the m/z axis during import. The binning interval is determined by the option Resolution. All signal intensities falling within the binning interval at a particular timepoint are averaged. For example, if resolution is set to 1, the signal intensities at a particular timepoint falling within an interval <mz-0.5,mz+0.5) will be averaged (mz represents a whole number in this case). For resolution 0.5, the binning interval would be <mz-0.25,mz+0.25) (with mz representing a whole number multiple of 0.5), etc...

Scan binning

Agilent ChemStation MS format

Analyst QS CSV format

mzXML format

CDF format

BDT format