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OpenMS
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Corrects retention time distortions between maps, using a pose clustering approach.
| potential predecessor tools | → MapAlignerPoseClustering → | potential successor tools |
|---|---|---|
| FeatureFinderCentroided (or another feature finding algorithm) | FeatureLinkerUnlabeled or FeatureLinkerUnlabeledQT |
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. The alignment algorithm implemented here is the pose clustering algorithm as described in doi:10.1093/bioinformatics/btm209. It is used to find an affine transformation, which is further refined by a feature grouping step. This algorithm can be applied to features (featureXML) and peaks (mzML), but it has mostly been developed and tested on features. For more details and algorithm-specific parameters (set in the INI file) see "Detailed Description" in the algorithm documentation.
This algorithm uses an affine transformation model.
To speed up the alignment, consider reducing 'max_number_of_peaks_considered'. If your alignment is not good enough, consider increasing this number (the alignment will take longer though).
The command line parameters of this tool are:
stty: 'standard input': Inappropriate ioctl for device
MapAlignerPoseClustering -- Corrects retention time distortions between maps using a pose clustering approach.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_MapAlignerPoseClustering.html
Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
+ Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.
Usage:
MapAlignerPoseClustering <options>
This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed description or use the --helphelp option
Options (mandatory options marked with '*'):
-in <files>* Input files to align (all must have the same file type) (valid formats: 'featureXML', 'mzML')
-out <files> Output files (same file type as 'in'). This option or 'trafo_out' has to be provided; they can be used together. (valid formats: 'featureXML', 'mzML')
-trafo_out <files> Transformation output files. This option or 'out' has to be provided; they can be used together. (valid formats: 'trafoXML')
Options to define a reference file (use either 'file' or 'index', not both):
-reference:file <file> File to use as reference (same file format as input files required) (valid formats: 'featureXML', 'mzML')
-reference:index <number> Use one of the input files as reference ('1' for the first file, etc.).
If '0', no explicit reference is set - the algorithm will select a reference. (default: '0') (min: '0')
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
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.
For more information, please consult the online documentation for this tool:
- http://www.openms.de/doxygen/nightly/html/TOPP_MapAlignerPoseClustering.html
INI file documentation of this tool:
1.9.1