Additional elements of APML. XML schema graph notation is the same as described in Figure 1 above. A) Both FeatureType in peak_list and AlignedFeatureType in alignment elements have CoordinateType, which contains coordinates for each feature, defined by required attributes of m/z, rt (retention time), charge and mass. It also has optional retention time, m/z and scan range child elements. B) We also defined the optional PpidCollectionType element for each feature, to store putative feature identification, via MS/MS tandem mass spectrometry experiments and/or other existing database references. C) ClusterProfile Type element is to store grouped features, by referencing the features defined in either peak_list or alignment, since some post-alignment processing tools might need to cluster LC-MS processed features by some criteria. For example, features whose intensities display a correlation with a sample concentration dilution series can be grouped and stored in this optional element.
Brusniak et al. BMC Bioinformatics 2008 9:542 doi:10.1186/1471-2105-9-542