Use File > Open to select the file you want to view. Files are normally expected to end with an xml or mxdata extension, but anything will work as long as the content is OK.
Selecting File > Print will print the current display. Where a multi-panel display is showing, both panels will be printed. The print is scaled up from the current display so the current shape of the application window, and positioning of the divider between the displays will affect the print.
There are two different versions of the main view depending on the nature of the data in the mzData file you have opened. If you open a multi-spectrum file then you will see a split display where the top half of the window shows a chromatogram of a spectral series. You can then click within this chromatogram to view an individual spectrum in the bottom half of the display.
For a single spectrum file (or a file containing multiple spectra but with no more than one spectrum per ms level) you will see only the single spectrum display, with no chromatogram.
The chromatogram panel displays the combined data from a spectral series. You can select from the drop down boxes at the top which ms level you want to use for the chromatogram, and the type of plot you want to see. The options are:
You can zoom into a region of the chromatogram by dragging your mouse outside the axes of the plot. The region selected by the drag becomes the limits of the plot. You can zoom on both the x and y axes.
Once you've zoomed into the plot you can double click anywhere outside the axes to zoom out so you can see the whole plot.
To view the chromatogram underlying any point on the plot simply click within the main body of the chromatogram. The spectrum will then be displayed in the bottom half of the screen.
The spectrum panel can display one or more spectra in an associated series. Only one spectrum at a time is actually displayed.
The spectrum panel is able to display both discrete and continuous spectra, with the type being determined by the spectrum's description in the mzData file.
You can zoom in and out of the spectrum display by dragging your mouse outside the axes of the plot, in the same way as for the chromatogram panel. Double clicking on one of the axes resets the zoom.
In the y-axis of the spectrum display is a small red triangle which can be clicked and dragged to set the intensity cutoff for the display of m/z values on individual peaks within the plot.
If you encounter any problems with the mzviewer program then please tell use about them so we can fix them.
Bugs can be reported directly into our bug tracking system at: http://www.bioinformatics.bbsrc.ac.uk/bugzilla/ or emailed to simon.andrews@bbsrc.ac.uk.
If you are having problems with a particular mzData file we are much more likely to be able to fix the problem if you include a copy of the file. You should be aware though that our bug tracking system is public and that any uploaded files will be publically accessible. We are not able to work with files restricted by a non-disclosure agreement.