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OpenMS
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Corrects retention time distortions between maps by aligning spectra.
potential predecessor tools | → MapAlignerSpectrum → | potential successor tools |
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FileConverter | FeatureFinderCentroided (or another feature finding algorithm) |
This tool provides an algorithm to align the retention time scales of multiple input files, correcting shifts and distortions between them. Retention time adjustment may be necessary to correct for chromatography differences e.g. before data from multiple LC-MS runs can be combined (feature grouping), or when one run should be annotated with peptide identifications obtained in a different run.
All map alignment tools (MapAligner...) collect retention time data from the input files and - by fitting a model to this data - compute transformations that map all runs to a common retention time scale. They can apply the transformations right away and return output files with aligned time scales (parameter out
), and/or return descriptions of the transformations in trafoXML format (parameter trafo_out
). Transformations stored as trafoXML can be applied to arbitrary files with the MapRTTransformer tool.
The map alignment tools differ in how they obtain retention time data for the modeling of transformations, and consequently what types of data they can be applied to. Here, an experimental algorithm based on spectrum alignment is implemented. It is only applicable to peak maps (mzML format). For more details and algorithm-specific parameters (set in the INI file) see "Detailed Description" in the algorithm documentation.
Since OpenMS 1.8, the extraction of data for the alignment has been separate from the modeling of RT transformations based on that data. It is now possible to use different models independently of the chosen algorithm. This algorithm has been tested mostly with the "interpolated" model. The different available models are:
The following parameters control the modeling of RT transformations (they can be set in the "model" section of the INI file):
The command line parameters of this tool are:
INI file documentation of this tool: