I am now developing a python module for ms2 database searching, would like to realize a function that similar to what Xcalibur did, choose multiple mass spectra and get an averaged spectra. But how this realized and what is the process behind. Tried linear interpolation and a method that firstly do peak picking followed by peak alignment, but none of them can produce the results similar to Xcalibur, does anyone have some clue?
For unit mass resolution and clean standards things are simple. You can choose multiple low resolution mass spectra, normalize each of this spectrum to the largest m/z value of the respective spectra and perform an arithmetic mean or median operation.
The problem that most likely arise is background. The influence of the background is higher at the start and end of the peak than at the peak maximum. You need some kind of baseline correction that minimizes this influence in order to produce clean spectra. There is some data available about this issue, eg
Article A Practical Approach for Determination of Mass Spectral Baselines
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