Corrects retention time distortions between maps, using information from peptides identified in different maps.
potential predecessor tools | ![]() ![]() | potential successor tools |
XTandemAdapter (or another search engine adapter) | IDMerger | |
IDFileConverter | FeatureLinkerUnlabeled or FeatureLinkerUnlabeledQT | |
IDMapper |
Reference:
Weisser et al.: An automated pipeline for high-throughput label-free quantitative proteomics (J. Proteome Res., 2013, PMID: 23391308).
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 thus applicable to files containing peptide IDs (idXML, annotated featureXML/consensusXML). It finds peptide sequences that different input files have in common and uses them as points of correspondence between the inputs. 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. For some applications this behaviour is desired, while for others its not, but you can always remove all modifications from the input files if you want to ignore modifications.
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 "b_spline" 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 | b_spline | 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. |
MapAlignerIdentification -- Corrects retention time distortions between maps based on common peptide identifi cations. Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976 Usage: MapAlignerIdentification <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 format s: 'featureXML', 'consensusXML', 'idXML') -out <files> Output files separated by blanks. Either 'out' or 'trafo_out' has to be provided . They can be used together. (valid formats: 'featureXML', 'consensusXML', 'idXM L') -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') Options to define a reference file (use either 'file' or 'index', not both; if neither is given 'index' is used).: -reference:file <file> File to use as reference (same file format as input files required) (valid forma ts: 'featureXML', 'consensusXML', 'idXML') -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 - 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 |