The peakml viewer

A user interface application called PeakML Viewer enables quick visualisation, inspection and manipulation of the contents of a PeakML file (e.g. manual selection and/or export of peaks of interest).

After loading a PeakML file, the ``entry'' view gives an overview of all the entries with the retention time, mass and intensity. The ordering from the original file is kept intact, making the results from sorting tools like mzmatch.ipeak.sort.RelatedPeaks accessible. An entry is highlighted in bold when it has been matched to a compound from a database with mzmatch.ipeak.util.Identify (determined by verifying whether the entry contains the system-defined annotation identification). By clicking on an entry, the associated traces will be displayed in the "graph" view and the identifications in the "identification" view (including the ppm-deviation and the putatively assigned molecular structure when available). There is an additional tab derivatives, which shows all the clustered related peaks with their identification as determined by mzmatch.ipeak.sort.RelatedPeaks (stored in the system defined annotations relation.id and relation.ship). The "filter" view allows the user to perform simple operations on the data (sorting and filtering), for zooming in on the entries of interest. The "trend" view gives an overview of the intensity levels for each entry (which in the case of a peakset can for example consist of multiple mass chromatograms). All the peaks belonging to the same set are grouped together in this plot and the mean, minimum and maximum values are displayed. The "sets" view shows all the measurements used and how they are organized in sets. With the check boxes all the peaks from a set or peaks individually can be switched on or off (i.e. not displayed). The "annotations" view gives an overview of all the annotations that are available for the current entry.