OpenMS
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MapRTTransformer

Applies retention time transformations to maps.

potential predecessor tools → MapRTTransformer → potential successor tools
MapAlignerIdentification
(or another alignment algorithm)
FeatureLinkerUnlabeled or
FeatureLinkerUnlabeledQT

This tool can apply retention time transformations to different types of data (mzML, featureXML, consensusXML, and idXML files). The transformations might have been generated by a previous invocation of one of the MapAligner tools (linked below). However, the trafoXML file format is not very complicated, so it is relatively easy to write (or generate) your own files. Each input file will give rise to one output file.

See also
MapAlignerIdentification MapAlignerPoseClustering MapAlignerSpectrum

With this tool it is also possible to invert transformations, or to fit a different model than originally specified to the retention time data in the transformation files. To fit a new model, choose a value other than "none" for the model type (see below).

Original retention time values can be kept as meta data. With the option store_original_rt, meta values with the name "original_RT" and the original retention time will be created for every major data element (spectrum, chromatogram, feature, consensus feature, peptide identification), unless they already exist - "original_RT" values from a previous invocation will not be overwritten.

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. The different available models are:

  • linear: Linear model.
  • b_spline: Smoothing spline (non-linear).
  • interpolated: Different types of interpolation.

The following parameters control the modeling of RT transformations (they can be set in the "model" section of the INI file):

Note
As output options, either out or trafo_out has to be provided. They can be used together.
Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

INI file documentation of this tool: