Biomedical Engineering Reference
In-Depth Information
3D Image of a LC-MS scan using the plot surf
command from the RGL R-package
Figure 4.4
fi les. (For the Thermo Xcalibur fi les it is necessary either to have the
Thermo Xcalibur software installed on the same machine or to have
downloaded and installed the free ThermoMSFilereader software [27].)
One of the great advantages of mzMine is its interactivity. Importing
and processing the data is achieved using standard graphical fi le dialogs.
For instance, the TIC visualiser produces a high-quality spectrum plot
shown in Figure 4.5. The plot is fully zoomable and interactive, and
double clicking a peak leads to its mass spectrum and associated data.
Peak detection is enabled using the chromatogram builder that has several
different peak detection methods. Figure 4.5 demonstrates the use of the
peak-list Wavelet method where the threshold for peak detection in the mass
dimension and other options can be interactively adjusted. The ultimate aim
is to create a set of parameters able to distinguish between true peaks
and irrelevant/noisy features. Other options for peak detection in the
mass dimension are Centroid (for previously centroided data), and Exact
Mass Detector (which defi nes the peak centre at half maximum height),
Local Maximum (simple local maxima) and Recursive Threshold (for
noisy data).
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