Centroid_algorithms

Converting a profile mode dataset to centroid mode dataset

Profile vs. Centroid datasets

Originally, MS scans are classically recorded as a continuous trace where each ion is visualised as a Gaussian peak. MS peak widths are related to the mass analyser resolving power. Accurate masses are obtained via centroid algorithms that will detect in every scans all peaks and calculate for each peak, its position (centre or apex) and maximum intensity. Centroid algorithms allow transforming a profile spectrum to a centroid spectrum where only the position and intensity of each peak is recorded. This permit not only to decrease the size of the file by a factor 10 to 100 but also to obtain an accurate and precise measurement of the position of every peak. Centroid datasets are usually processed by the MS software and are the typical MS bar plots.

doCentroid a method in the Finnee object

The doCentroid method allows transforming a profile dataset to a centroid dataset. doCentroid takes, as parameters, the dataset to process and a method to detect the peaks and calculate keys figure of merits (FOM). Multiple methods can be implemented. At present the possible method is

'LocalMax:n'

This algorithm will detect every local maximum, where a local maximum is any data point whose intensity is higher or equal to the intensity of its n closest neighbours on each side. The accurate masses are obtained by fitting the peak maxima and its two neighbours to a polynomial of degree 2. The peak position and intensity are calculated via the parameters of the polynomial.

Example with the CETOFMS urine dataset

For this example, we will use centroid and profile mzML files. Two Finnee objects have been created: myFnnPrf created using the profile mzML file and myFnnCtr created using the centroid mzML file.

1. First, we will compare the BPP from both dataset. We can use myFnnCtr.Datasets{1}.BPP.plot, however this does not allow to compare two set of data. In this case the best way is to extract the BPP data and plot them in the same graph.

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