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Frequently Asked Questions
If you have any questions, please email [email protected], and I'll do my best to add it here.
Low resolution spectra with broad peaks can be challenging because there are inherent uncertainties in the charge state assignments. In other words, several charge states might fit similarly well. There are several things to play with to improve the deconvolution. Start with the low resolution native preset. Then try adjusting the "Suppress Artifacts" and "Smooth Nearby Points" quick controls. Be sure to try adjusting the Peak FWHM and shape. These three will hopefully solve the problem. You can also try adjusting the mass range, charge range, and manual assignments if necessary.
Except when the peak width is set to zero, UniDec assumes that there could be peaks centered at each data point and solves for the intensities of each possible charge. These are called delta functions, which are basically the distribution of peak centroids. For each point, it adds the set peak shape in by convolving the delta functions with the input peak shape and peak width. It basically creates a peak at that position based on what you tell it a peak should look like. When the algorithm is done, it can either spit out the delta functions (which are going to be sharper than the peaks in the raw data) or the reconvolved data (which should have peaks the same width as the raw data). The default is for reconvolved/profile mode because this most faithfully represents the raw data. However, the raw/centroid mode can be used to sharpen peaks to make extraction easier. If you do use the raw/centroid mode, make sure to report it in the methods section of your paper, so that people are clear on how you have processed the data.
Yes, smoothing nearby points will broaden the peaks somewhat. You can compensate by decreasing the peak width. There is a trade-off here between having a clean deconvolution (more smoothing) or having more accurate masses (no smoothing). The most accurate setting is with no point smoothing and the peak FWHM set to 0, but this can lead to artifacts.
UniDec already does this to some extent. Every text file is associated with a <file_name>_unidecfiles folder in the same directory. This folder has a number of files that you can explore. To find it quickly, select Advanced > Open Saved File Directory. This should open a folder where the output data is stored. If you open <file_name>_peaks.dat, it will have a list of peaks and intensities.
For more parameters, select Analysis > Export Peak Parameters and Data. This will create a file that ends in _peakparams.dat. The columns in this file correspond to: Mass; A poor guess of mass standard deviation; Average Charge State; Standard Deviation of Charge States; Peak Height; Peak Area; Mass Centroid; Mass FWHM; Mass Error as calculated from standard deviation between charge states.