# Centroid Extraction from Mass Spectra

A general overview of the centroid extraction→deconvolution→analyte identification workflow is illustrated at fig_centroidation-to-analyte-identification-workflow .

The low mass deconvolution algorithm can be tightly configured using a large set of parameter settings that are detailed below and that are accessible via the application preferences window shown in fig_application_preferences_wnd_low_mass_deconvolver_page and detailed below.

The centroidation of a mass spectrum is also called peak picking. This process is aimed at converting a profile-mode spectrum, that has its peaks properly shaped in Gaussian-like form, into a set of &mz; values that recapitulate the initial peaks.

The configuration of the centroid extraction process is performed in the application preferences window, under the Centroidation section, as shown in fig_application-preferences-wnd-centroidation-page . There are two aspects in that configuration: the signal-to-noise estimator needs to be configured for the peak picker to be able to actually pick peaks. The peak picker needs also to be configured.

One aspect that is very important in peak picking is the determination of what is considered to be noise and what is considered to be actual signal. The signal-to-noise estimation is an optional task that is only carried out when the Signal to noise ratio is set to a value greater than 0. The signal-to-noise estimator needs a number of parameters to be set up (in the Configuration of the signal to noise estimator group box widget). One important configuration bit is related to the determination of what intensity value is considered to be the maximum intensity value over the whole mass spectrum. There are multiple ways to define that maximum intensity value, as described in .

- Manual setting: this is the simplest method to define that maximum intensity value, by having the user setting it up.

- Standard deviation factor: the software first makes a statistical analysis of the intensity values throughout the mass spectrum and any data point that has an intensity over the standard deviation compounded by this factor is discarded.

- Max percentile: any data point that has an intensity over the intensity of the data point representing the top 5 percent of the intensity value space of the mass spectrum is discarded.

Other configuration bits are the Rolling window size (m/z) which specifies the &mz; range considered when computing the local signal-to-noise ratio. The rolling window is moved data point by data point over the whole mass spectrum. Each mass spectrum data point has thus a corresponding signal-to-noise ratio value.The Intensity histogram bins configuration bit is the number of bins in the histogram of the intensities in the mass spectrum. This parameter defines the granularity with which the signal-to-noise ratio is computed for each mass spectrum data point. The Mininum required elements configuration bit is the number of data points that are required to be found inside the rolling window.

## Configuration of the centroidation of mass spectra

The peak picker needs the following bits of configuration. The Min. intensity configures the signal intensity below which the centroids are not extracted. This is useful for highly noisy traces or when one knows that the signal of interest is above a determinat value. The Signal to noise ratio value determines the ratio below which the peak centroid is not extracted. Setting this value to 0.0 will disable the signal to noise process step. Finally, one last bit of configuration for the centroid extraction is the Allowed missing peaks value that defines the number of &mz; values that can be found to be absent from the rolling window mentioned above. This parameter provides some leeway when dealing with sparse mass spectra.

The menu to start the centroid extraction is described in fig_extract-centroids-menu-over-spectrum . The figure show the mass spectrum for which centroidation is asked. When the centroidation is actually performed, the centroids are plotted in the form of a bar graph, colored in blue (see fig_successful-extraction-centroids-over-spectrum .

## Menu to be used to extract centroids from a trace

Centroid extraction from a profile mode mass spectrum.

When the centroid extraction process is terminated, the centroids are plotted as a bar graph. These centroid data points can be exported to a file or a clipboard exactly the same way as for the normal trace graphs (see fig_successful-extraction-centroids-over-spectrum ).

## The successfully extracted centroids are displayed in the form of a bar plot

The centroids are plotted as a bar graph that can be exported to the clipboard or to a file exactly like for any trace mass spectrum.

Upon successful extraction of centroids, these are output to the console window.