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OpenMS
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Corrects retention time distortions between maps, using information from peptides identified in different maps.
| potential predecessor tools | → MapAlignerTreeGuided → | potential successor tools |
|---|---|---|
| IDMapper (or any other source of FDR-filtered featureXMLs) | FeatureLinkerUnlabeledKD 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 based on peptide identifications and applicable to annotated featureXML files. It finds peptide sequences that each pair of input files have in common, uses them as points of correspondence between the inputs and to evaluate the distances between the maps for hierarchical clustering. Tree based, the alignment of each cluster pair is performed with the method align() of the OpenMS::MapAlignmentAlgorithmIdentification. For more details and algorithm-specific parameters (set in the INI file) see "Detailed Description" in the algorithm documentation.
Note that alignment is based on the sequence including modifications, thus an exact match is required. I.e., a peptide with oxidised methionine will not be matched to its unmodified version. This behavior is generally desired since (some) modifications can cause retention time shifts.
Also note that convex hulls are removed for alignment and are therefore missing in the output files.
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 with the "b_spline" model. The different available models are:
The command line parameters of this tool are:
stty: 'standard input': Inappropriate ioctl for device
MapAlignerTreeGuided -- Tree guided correction of retention time distortions between maps.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_MapAlignerTreeGuided.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:
MapAlignerTreeGuided <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')
-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')
-trafo_out <files> Transformation output files. This option or 'out' has to be provided; they can be used together. (valid formats: 'trafoXML')
-copy_data String Copy data (faster, more memory required) or reload data (slower, less memory required) when aligning many files. (default: 'true') (valid: 'true', 'false')
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_MapAlignerTreeGuided.html
INI file documentation of this tool:
1.9.1