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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 @p out), and/or return descriptions of the transformations in trafoXML format (parameter @p trafo_out). Transformations stored as trafoXML can be applied to arbitrary files with the @ref TOPP_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 @ref OpenMS::MapAlignmentAlgorithmSpectrumAlignment "algorithm documentation".

@see @ref TOPP_MapAlignerIdentification @ref TOPP_MapAlignerPoseClustering @ref TOPP_MapRTTransformer

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:

- @ref OpenMS::TransformationModelLinear "linear": Linear model.

- @ref OpenMS::TransformationModelBSpline "b_spline": Smoothing spline (non-linear).

- @ref OpenMS::TransformationModelInterpolated "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):

@htmlinclude OpenMS_MapAlignerSpectrumModel.parameters @n

<B>The command line parameters of this tool are:</B> @n

@verbinclude TOPP_MapAlignerSpectrum.cli

// We do not want this class to show up in the docu:

/// @cond TOPPCLASSES

class TOPPMapAlignerSpectrum

: public TOPPMapAlignerBase

{

public:

TOPPMapAlignerSpectrum()

: TOPPMapAlignerBase("MapAlignerSpectrum", "Corrects retention time distortions between maps by spectrum alignment.")

{

}

protected:

void registerOptionsAndFlags_()

{

String formats = "mzML";

TOPPMapAlignerBase::registerOptionsAndFlags_(formats);

// no support for a reference file yet

registerSubsection_("algorithm", "Algorithm parameters section");

registerSubsection_("model", "Options to control the modeling of retention time transformations from data");

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}

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Param getSubsectionDefaults_(const String& section) const

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{

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if (section == "algorithm")

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{

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MapAlignmentAlgorithmSpectrumAlignment algo;

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return algo.getParameters();

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}

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if (section == "model")

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{

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return getModelDefaults("interpolated");

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}

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return Param(); // shouldn't happen

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}

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ExitCodes main_(int, const char**)

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{

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MapAlignmentAlgorithmSpectrumAlignment algorithm;

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return TOPPMapAlignerBase::commonMain_(&algorithm);

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}

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};

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int main(int argc, const char** argv)

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{

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TOPPMapAlignerSpectrum tool;

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return tool.main(argc, argv);

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}

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/// @endcond

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