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MapAlignerIdentification

Corrects retention time distortions between maps, using information from peptides identified in different maps.

potential predecessor tools $ \longrightarrow $ MapAlignerIdentification $ \longrightarrow $ 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.

See Also
MapAlignerPoseClustering MapAlignerSpectrum MapRTTransformer

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):
NameTypeDefaultRestrictionsDescription
type stringb_spline linear, b_spline, interpolatedType of model
linear:symmetric_regression stringfalse true, falsePerform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'.
b_spline:num_breakpoints int5 min: 2Number 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 stringuniform uniform, quantilesHow 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 stringcspline linear, cspline, akimaType of interpolation to apply.

The command line parameters of this tool are:

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:

Legend:
required parameter
advanced parameter
+MapAlignerIdentificationCorrects retention time distortions between maps based on common peptide identifications.
version1.11.1 Version of the tool that generated this parameters file.
++1Instance '1' section for 'MapAlignerIdentification'
in[] Input files separated by blanks (all must have the same file type)input file*.featureXML,*.consensusXML,*.idXML
out[] Output files separated by blanks. Either 'out' or 'trafo_out' has to be provided. They can be used together.output file*.featureXML,*.consensusXML,*.idXML
trafo_out[] Transformation output files separated by blanks. Either 'out' or 'trafo_out' has to be provided. They can be used together.output file*.trafoXML
log Name of log file (created only when specified)
debug0 Sets the debug level
threads1 Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse Disables progress logging to command linetrue,false
testfalse Enables the test mode (needed for internal use only)true,false
+++referenceOptions to define a reference file (use either 'file' or 'index', not both; if neither is given 'index' is used).
file File to use as reference (same file format as input files required)input file*.featureXML,*.consensusXML,*.idXML
index0 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.
0:∞
+++algorithmAlgorithm parameters section
peptide_score_threshold0 Score threshold for peptide hits to be used in the alignment.
Select a value that allows only 'high confidence' matches.
min_run_occur2 Minimum number of runs (incl. reference, if any) a peptide must occur in to be used for the alignment.
Unless you have very few runs or identifications, increase this value to focus on more informative peptides.
2:∞
max_rt_shift0.5 Maximum realistic RT difference for a peptide (median per run vs. reference). Peptides with higher shifts (outliers) are not used to compute the alignment.
If 0, no limit (disable filter); if > 1, the final value in seconds; if <= 1, taken as a fraction of the range of the reference RT scale.
0:∞
use_unassigned_peptidestrue Should unassigned peptide identifications be used when computing an alignment of feature maps? If 'false', only peptide IDs assigned to features will be used.true,false
use_feature_rtfalse When aligning feature maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to. If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used.
Precludes 'use_unassigned_peptides'.
true,false
+++modelOptions to control the modeling of retention time transformations from data
typeb_spline Type of modellinear,b_spline,interpolated
++++linearParameters for 'linear' model
symmetric_regressionfalse Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'.true,false
++++b_splineParameters for 'b_spline' model
num_breakpoints5 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.2:∞
break_positionsuniform How to distribute the breakpoints on the retention time scale. 'uniform': intervals of equal size; 'quantiles': equal number of data points per interval.uniform,quantiles
++++interpolatedParameters for 'interpolated' model
interpolation_typecspline Type of interpolation to apply.linear,cspline,akima

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5