A baseline shift occurs in a spectrum as the result of residual
charge buildup in the ion channels during spectrum acquisition,
and therefore, tends to appear below components present at high
concentration, raising them up above the m/z axis. Since the magnitude
of this shift tends to vary from spectrum to spectrum, it is
standard practice to subtract it in such a way that the bases of
all peaks sit along the horizontal axis. In our studies we opt to
model the baseline as a series of cubic splines passing through
the lowest minima within windows a fixed number of bin centres
apart in a manner similar to the msbackadj function from the Matlab
bioinformatics toolbox. Another approach (found for example
in the MassLynx software suite), is to model the baseline as a high
order-polynomial. In our experience, baselines tend to be less pronounced
and less variable in ESI data than in MALDI data