OpenMS
Loading...
Searching...
No Matches
FeatureFinderIsotopeWavelet

The feature detection application for quantitation.

pot. predecessor tools → FeatureFinderIsotopeWavelet → pot. successor tools
NoiseFilterSGolay MapAlignerPoseClustering
(or another alignment tool)
NoiseFilterGaussian FeatureLinkerUnlabeled
(or another feature grouping tool)

This module identifies "features" in a LC/MS map. By feature, we understand a peptide in a MS sample that reveals a characteristic isotope distribution. The algorithm computes positions in rt and m/z dimension and a charge estimate of each peptide.

The algorithm identifies pronounced regions of the data around so-called seeds. In the next step, we iteratively fit a model of the isotope profile and the retention time to these data points. Data points with a low probability under this model are removed from the feature region. The intensity of the feature is then given by the sum of the data points included in its regions.

How to find suitable parameters and details of the different algorithms implemented are described in the TOPP tutorial.

Note
that the wavelet transform is very slow on high-resolution spectra (i.e. FT, Orbitrap). We recommend to use a noise or intensity filter to remove spurious points first and to speed-up the feature detection process.

Specialized tools are available for some experimental techniques: IsobaricAnalyzer.

The command line parameters of this tool are:

INI file documentation of this tool:

For the parameters of the algorithm section see the algorithms documentation:
isotope_wavelet