ZNova parameters are used to instruct ZNova how to deconvolute your spectra and where to put the results. Here we will provide some basic information about how to build and save parameter files. For more detailed information about what each parameter does, refer to the context sensitive help in the Build ZNova Params dialog.
Click on the Build ZNova Params button on the ProMass home page.
You should see the ZNova parameters screen, which is a tabbed dialog where you can enter parameters. If you move your mouse over the tool bar buttons at the top you should see help text that identifies the function of each button. If you move your mouse over any of the parameters areas, information about that parameter will appear in the status area at the bottom of Build ZNova Params window. From the tool bar at the top, click on the Default Parameters button. The default molecule types provide a good set of parameters for you to start working with. As shown in the dialog below, select a molecule type for the type of analysis you are performing, then click on OK.
The default molecule types have
the following output mass ranges, and other significant
features:
peptide: 500-5000
Da
oligonucleotide: 500-20000 Da, negative ion (adduct mass
= -1.008)
small protein:
500-20000 Da
large
protein: 20000-80000 Da, baseline factor =
0.7
IgG: 100000-180000 Da, peak width
= 40
You can edit the
output deconvolution mass range or other settings after restoring a set of
default parameters.
Make sure the following are set:
If you are deconvoluting a positive
ion data file, from the Advanced
Deconvolution options tab make sure the
Adduct Ion
Mass is set to 1.0079 (the mass of a proton),
or -1.0079 for a negative ion.
From either the Basic or Advanced Deconvolution tab,
select the input deconvolution
range, first m/z and last m/z. Leave the
fields blank to allow ZNova to automatically determine the input range from the
scan limits.
Select the output deconvolution range,
minimum mass and maximum mass. Make sure these settings cover a range where you
expect to see deconvoluted masses.
Click on the Save As button on the tool bar to save your parameter file as name that you specify. Click on the Done button to exit the Build ZNova Params
program.
Information about each option in the Build ZNova Params dialog is available here: