Corrects retention time distortions between maps by aligning spectra.
potential predecessor tools | ![]() ![]() | potential successor tools |
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):
Name | Type | Default | Restrictions | Description |
---|---|---|---|---|
type | string | interpolated | linear, b_spline, interpolated | Type of model |
linear:symmetric_regression | string | false | true, false | Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'. |
b_spline:num_breakpoints | int | 5 | min: 2 | Number of breakpoints of the cubic spline in the smoothing step. More breakpoints mean less smoothing. Reduce this number if the transformation has an unexpected shape. |
b_spline:break_positions | string | uniform | uniform, quantiles | How to distribute the breakpoints on the retention time scale. 'uniform': intervals of equal size; 'quantiles': equal number of data points per interval. |
interpolated:interpolation_type | string | cspline | linear, cspline, akima | Type of interpolation to apply. |
MapAlignerSpectrum -- Corrects retention time distortions between maps by spectrum alignment. Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976 Usage: MapAlignerSpectrum <options> This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti on or use the --helphelp option. Options (mandatory options marked with '*'): -in <files>* Input files separated by blanks (all must have the same file type) (valid formats: 'mzM L') -out <files> Output files separated by blanks. Either 'out' or 'trafo_out' has to be provided. They can be used together. (valid formats: 'mzML') -trafo_out <files> Transformation output files separated by blanks. Either 'out' or 'trafo_out' has to be provided. They can be used together. (valid formats: 'trafoXML') Common TOPP options: -ini <file> Use the given TOPP INI file -threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1') -write_ini <file> Writes the default configuration file --help Shows options --helphelp Shows all options (including advanced) The following configuration subsections are valid: - algorithm Algorithm parameters section - model Options to control the modeling of retention time transformations from data You can write an example INI file using the '-write_ini' option. Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor. Have a look at the OpenMS documentation for more information.
INI file documentation of this tool:
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |