Legend:

required parameter

advanced parameter

+MapAlignerIdentificationCorrects retention time distortions between maps based on common peptide identifications.

version1.10.0 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