OpenMS  3.0.0
IDMapper

Assigns protein/peptide identifications to features or consensus features.

potential predecessor tools $ \longrightarrow $ IDMapper $ \longrightarrow $ 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:

IDMapper -- Assigns protein/peptide identifications to features or consensus features.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_IDMapper.html
Version: 3.0.0-pre-nightly-2022-07-20 Jul 21 2022, 00:07:28, Revision: ea0316e
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:
  IDMapper <options>

Options (mandatory options marked with '*'):
  -id <file>*                        Protein/peptide identifications file (valid formats: 'mzid', 'idXML')
  -in <file>*                        Feature map/consensus map file (valid formats: 'featureXML', 'consensusX
                                     ML', 'mzq')
  -out <file>*                       Output file (the format depends on the input file format). (valid format
                                     s: 'featureXML', 'consensusXML', 'mzq')
                                     
  -rt_tolerance <value>              RT tolerance (in seconds) for the matching of peptide identifications 
                                     and (consensus) features.
                                     Tolerance is understood as 'plus or minus x', so the matching range inc
                                     reases by twice the given value. (default: '5.0' min: '0.0')
  -mz_tolerance <value>              M/z tolerance (in ppm or Da) for the matching of peptide identifications
                                     and (consensus) features.
                                     Tolerance is understood as 'plus or minus x', so the matching range inc
                                     reases by twice the given value. (default: '20.0' min: '0.0')
  -mz_measure <choice>               Unit of 'mz_tolerance'. (default: 'ppm' valid: 'ppm', 'Da')
  -mz_reference <choice>             Source of m/z values for peptide identifications. If 'precursor', the 
                                     precursor-m/z from the idXML is used. If 'peptide',
                                     masses are computed from the sequences of peptide hits; in this case, a
                                     n identification matches if any of its hits matches.
                                     ('peptide' should be used together with 'feature:use_centroid_mz' to av
                                     oid false-positive matches.) (default: 'peptide' valid: 'precursor',
                                     'peptide')
                                     

Additional options for featureXML input:
  -feature:use_centroid_rt <choice>  Use the RT coordinates of the feature centroids for matching, instead 
                                     of the RT ranges of the features/mass traces. (default: 'false' valid:
                                     'true', 'false')
  -feature:use_centroid_mz <choice>  Use the m/z coordinates of the feature centroids for matching, instead 
                                     of the m/z ranges of the features/mass traces.
                                     (If you choose 'peptide' as 'mz_reference', you should usually set this
                                     flag to avoid false-positive matches.) (default: 'true' valid: 'true',
                                     'false')

                                     

Additional options for consensusXML input:
  -consensus:use_subelements         Match using RT and m/z of sub-features instead of consensus RT and m/z. 
                                     A consensus feature matches if any of its sub-features matches.

Additional options for mzML input:
  -spectra:in <file>                 MS run used to annotated unidentified spectra to features or consensus 
                                     features. (valid formats: 'mzML')

                                     
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)

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+IDMapperAssigns protein/peptide identifications to features or consensus features.
version3.0.0-pre-nightly-2022-07-20 Version of the tool that generated this parameters file.
++1Instance '1' section for 'IDMapper'
id Protein/peptide identifications fileinput file*.mzid,*.idXML
in Feature map/consensus map fileinput file*.featureXML,*.consensusXML,*.mzq
out Output file (the format depends on the input file format).output file*.featureXML,*.consensusXML,*.mzq
rt_tolerance5.0 RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features.
Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value.
0.0:∞
mz_tolerance20.0 m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features.
Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value.
0.0:∞
mz_measureppm Unit of 'mz_tolerance'.ppm,Da
mz_referencepeptide Source of m/z values for peptide identifications. If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',
masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.
('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)
precursor,peptide
ignore_chargefalse For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature.true,false
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
forcefalse Overrides tool-specific checkstrue,false
testfalse Enables the test mode (needed for internal use only)true,false
+++featureAdditional options for featureXML input
use_centroid_rtfalse Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces.true,false
use_centroid_mztrue Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces.
(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)
true,false
+++consensusAdditional options for consensusXML input
use_subelementsfalse Match using RT and m/z of sub-features instead of consensus RT and m/z. A consensus feature matches if any of its sub-features matches.true,false
annotate_ids_with_subelementsfalse Store the map index of the sub-feature in the peptide ID.true,false
+++spectraAdditional options for mzML input
in MS run used to annotated unidentified spectra to features or consensus features.input file*.mzML

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; 2. 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.