An Xcalibur sample list with associated
data files - this is the data we want to deconvolute ProMass can process data either automatically from an Xcalibur sequence list or in a fully interactive mode (i.e., manually) from the Build ZNova Params screen.
Fully Interactive Processing
In it's simplest form, you can use ProMass to process spectra one at a time. You might choose this method for infusion data for example. To do this kind of processing all you need is an Xcalibur data file. You copy spectra to the clipboard and process them individually using the paste from clipboard function in the Build ZNova Params screen.
Automatic Processing
In order to process data automatically using ProMass you need:
An Xcalibur sample list with associated
data files - this is the data we want to deconvolute
An Xcalibur Qual processing method - this
tells Xcalibur how to process chromatographic peaks into summed mass spectra
A ZNova
parameter file - this tells ZNova (the
deconvolution algorithm) how the individual raw mass spectra should be
deconvoluted
If you keep these basic requirements in mind, the steps for running ProMass in an automated mode are actually quite simple. When setting up sequences, processing methods, and parameter files, try to take a template approach. In other words, re-use what you have setup previously, and just make the necessary modifications for processing new data files. This will save you a lot of time and confusion. If you are new to Xcalibur and automated processing, it may take you a while to get the hang of this. Automated Processing with ProMass gives all the details for setting up automated processing.