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OpenMS
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Corrects retention time distortions between maps by aligning spectra.
| potential predecessor tools | → MapAlignerSpectrum → | 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, lowess, 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'. |
| linear:x_weight | string | x | 1/x, 1/x2, ln(x), x | Weight x values |
| linear:y_weight | string | y | 1/y, 1/y2, ln(y), y | Weight y values |
| linear:x_datum_min | float | 1.0e-15 | Minimum x value | |
| linear:x_datum_max | float | 1.0e15 | Maximum x value | |
| linear:y_datum_min | float | 1.0e-15 | Minimum y value | |
| linear:y_datum_max | float | 1.0e15 | Maximum y value | |
| b_spline:wavelength | float | 0.0 | min: 0.0 | Determines the amount of smoothing by setting the number of nodes for the B-spline. The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points. |
| b_spline:num_nodes | int | 5 | min: 0 | Number of nodes for B-spline fitting. Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing. |
| b_spline:extrapolate | string | linear | linear, b_spline, constant, global_linear | Method to use for extrapolation beyond the original data range. 'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range). |
| b_spline:boundary_condition | int | 2 | min: 0 max: 2 | Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero) |
| lowess:span | float | 0.666666666666667 | min: 0.0 max: 1.0 | Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing). Choosing this parameter in the range .2 to .8 usually results in a good fit. |
| lowess:num_iterations | int | 3 | min: 0 | Number of robustifying iterations for lowess fitting. |
| lowess:delta | float | -1.0 | Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input, e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this. | |
| lowess:interpolation_type | string | cspline | linear, cspline, akima | Method to use for interpolation between datapoints computed by lowess. 'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation |
| lowess:extrapolation_type | string | four-point-linear | two-point-linear, four-point-linear, global-linear | Method to use for extrapolation outside the data range. 'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation. |
| interpolated:interpolation_type | string | cspline | linear, cspline, akima | Type of interpolation to apply. |
| interpolated:extrapolation_type | string | two-point-linear | two-point-linear, four-point-linear, global-linear | Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model. Note that global-linear may not be continuous at the border. |
MapAlignerSpectrum -- Corrects retention time distortions between maps by spectrum alignment.
Full documentation: http://www.openms.de/doxygen/release/3.0.0/html/TOPP_MapAlignerSpectrum.html
Version: 3.0.0 Jul 14 2023, 11:57:33, Revision: be787e9
To cite OpenMS:
+ Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for
mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.
Usage:
MapAlignerSpectrum <options>
This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript
ion 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: '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: 'mzML')
-trafo_out <files> Transformation output files. This option or '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.
For more information, please consult the online documentation for this tool:
- http://www.openms.de/doxygen/release/3.0.0/html/TOPP_MapAlignerSpectrum.html
INI file documentation of this tool:
1.9.1