Tips and Tricks
To rename a variable in MetaUniDec, click File > Variables > Rename Variable 1 (or 2). This will rename the axes on your plots and the variable label. It should also automatically export the variable and save it to the HDF5 file in the metadata. You can also manually export variables from the main panel or import them from the HDF5. For example, you could have multiple sets of metadata with each data set (for example protein and ligand concentrations) and then import each into either variable 1 or 2.
Use ctrl+W or Tools > Automatic Peak Width to have UniDec set the peak width for you.
To manually set the peak width, use Tools > Peak Width Tool. Use the mouse to zoom in on a single peak. Select the peak shape function you want, and hit the "Fit Peak Shape" button. If you like the fit, hit "Ok" and the main window will update with this parameter.
Under Analysis, select Label Average Charge State to get the average charge state for each peak. To get the charge state distribution width, select Analysis > Export Peak Parameters and Data. It will output a _peakparam.dat file to the _unidecfiles folder but also print the charge state distribution standard deviation to the terminal. It should also write _chargedata.dat and _chargedata_areas.dat, which are the peak heights and areas respectively for the various charge states of each peak (each peak is one line). You will need to reconstruct the charge states each column corresponds to, but these are simply a list from the lowest allowed charge state to the highest.
If you have broad peaks and are getting artifacts in the deconvolution from +/- 1 charge state mistaken assignments, try increasing your peak width. If that works, you can artificially multiply your peak width without disrupting the analysis by using the Peak Shape Inflate parameter in the Advanced > Additional Parameters menu. If you set this parameter to 2, it will double your peak width for deconvolution and reset it after.
Why this works: With larger peak widths you are telling UniDec that a single species should have a bigger footprint in the spectrum. Thus, UniDec can assign more of the intensity from fewer species, which reduces artifacts.