MS instruments typically allow storing spectra in profile mode (several data points per m/z peak) or in the more condensed centroid mode (one data point per m/z peak). The process of converting a profile mass spectrum into a centroided one is called peak centroiding or peak picking.

Note: The term peak picking is ambiguous as it is also used for features detection (i.e. 3D peak finding).

First, we load some profile data:

Let’s zoom in on an isotopic pattern in profile mode and plot it.


Because of the limited resolution of MS instruments m/z measurements are not of unlimited precision. Consequently, peak shapes spreads in the m/z dimension and resemble a gaussian distribution. Using the PeakPickerHiRes algorithm, we can convert data from profile to centroided mode. Usually, not much information is lost by storing only centroided data. Thus, many algorithms and tools assume that centroided data is provided.


After centroiding, a single m/z value for every isotopic peak is retained. By plotting the centroided data as stem plot we discover that (in addition to the isotopic peaks) some low intensity peaks (intensity at approx. 4k) were present in the profile data.