OpenMS
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IDMapper

Assigns protein/peptide identifications to features or consensus features.

potential predecessor tools → IDMapper → potential successor tools
MascotAdapter (or other ID engines) ConsensusID
IDFilter MapAlignerIdentification

The mapping is based on retention times and mass-to-charge values. Roughly, a peptide identification is assigned to a (consensus) feature if its position lies within the boundaries of the feature or close enough to the feature centroid. Peptide identifications that don't match anywhere are still recorded in the resulting map, as "unassigned peptides". Protein identifications are annotated to the whole map, i.e. not to any particular (consensus) feature.

In all cases, tolerance in RT and m/z dimension is applied according to the parameters rt_tolerance and mz_tolerance. Tolerance is understood as "plus or minus x", so the matching range is actually increased by twice the tolerance value.

If several features or consensus features overlap the position of a peptide identification (taking the allowed tolerances into account), the identification is annotated to all of them.

Annotation of feature maps (featureXML input):
If all features have at least one convex hull, peptide positions are matched against the bounding boxes of the convex hulls (of individual mass traces, if available) by default. If not, the positions of the feature centroids are used. The respective coordinates of the centroids are also used for matching (in place of the corresponding ranges from the bounding boxes) if feature:use_centroid_rt or feature:use_centroid_mz are true.

Annotation of consensus maps (consensusXML input):
Peptide positions are always matched against centroid positions. By default, the consensus centroids are used. However, if consensus:use_subelements is set, the centroids of sub-features are considered instead. In this case, a peptide identification is mapped to a consensus feature if any of its sub-features matches.

Note
Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

INI file documentation of this tool:

On the peptide side, two sources for m/z values are possible (see parameter mz_reference): 1. m/z of the precursor of the MS2 spectrum that gave rise to the peptide identification;

  1. theoretical masses computed from the amino acid sequences of peptide hits. (When using theoretical masses, make sure that peptide modifications were identified correctly. OpenMS currently "forgets" mass shifts that it can't assign to modifications - if that happens, masses computed from peptide sequences will be off.)
Deprecated
The parameter handling of this tool has been reworked. For greater consistency with other tools, the parameters rt_delta and mz_delta have been renamed to rt_tolerance and mz_tolerance. The possible values of the mz_reference parameter have also been renamed. The default value of mz_tolerance has been increased from 1 ppm to a more realistic 20 ppm.
Most importantly, the use_centroids parameter from previous versions has been split into two parameters, feature:use_centroid_rt and feature:use_centroid_mz. In OpenMS 1.6, peptide identifications would be matched only against monoisotopic mass traces of features if mz_reference was PeptideMass; otherwise, all mass traces would be used. This implicit behaviour has been abandoned, you can now explicitly control it with the feature:use_centroid_mz parameter. feature:use_centroid_mz does not take into account m/z deviations in the monoisotopic mass trace, but this can be compensated by increasing mz_tolerance. The new implementation should work correctly even if the monoisotopic mass trace itself was not detected.