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Processing Spectra from the Clipboard

On occasion, you may want to manually process spectra.  ProMass Xcali allows for this function by allowing you to import spectra from the clipboard.  This is the way you would process infusion data (data with no chromatographic peaks) or for the purposes of tuning your ZNova parameters.  You can process a spectrum from the windows clipboard using the Build ZNova Params screen or with the ZNova command line interface.

To process a clipboard spectrum from within the Build ZNova Params screen:  launch the ProMass Xcali home page, click the Build Params button, set up your parameters, copy your spectrum from Xcalibur Qual Browser, paste your Xcalibur spectrum to the clipboard, and hit the clipboard button.  To copy an Xcalibur spectrum to the clipboard: launch Qual Browser and activate the spectrum that you want to process. Right mouse click the spectrum to get the Export menu and select Clipboard (Exact Mass). Return to the Build ZNova Params screen and hit the clipboard button.  The spectrum will be processed with the current set of displayed parameters.  When done, ProMass Xcali will launch an internet explorer window to display the results.  Please note: Copying profile spectra to the clipboard can be a very slow process.  This is an Xcalibur "feature".  The ZNova console window may indicate "waiting for clipboard data..." for a minute or so while QualBrowser transfers the spectrum to the clipboard.

 To process a spectrum on the clipboard using the command line interface, open a command prompt (or DOS prompt) window. You can do this from the Windows Start menu by entering cmd in the Run... dialogue. Go to your ProMassXcali\ZNova installation directory. For example, in the command prompt window, enter:

cd c:\program files\promassxcali\znova

Now you can run xznova using the -C command line argument (note command line options are case-sensitive). First, copy an Xcalibur spectrum to the clipboard as discussed above within QualBrowser. Return to the command prompt window and enter:

xznova -C

The spectrum will be processed using the default znova.params found in the install directory. If you want to specify other parameters you can use other command line arguments, or specify a parameter file with the -P option.

Here are a few other examples:

xznova -C -F 5000 -L 40000

Process the current clipboard spectrum using the default znova.params file, but change the first and last deconvoluted mass range to 5000-40000 Da.

xznova -C -P "c:\xcalibur\data\oligo.params" -p 2

Process the current clipboard spectrum using a different parameter file and change the input peak width to 2 m/z units.  Note the required use of double quotes around the filename involving a path, and that command line options are case-sensitive.

For more information about the command line arguments, check out the ZNova Parameter Reference.