| OpenMS 2.5.0

Classes | Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
IDMapper Class Reference

Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications. More...

`#include <OpenMS/ANALYSIS/ID/IDMapper.h>`

Inheritance diagram for IDMapper:

## Classes

struct | SpectraIdentificationState
| Result of a partitioning by identification state with mapPrecursorsToIdentifications(). More...

## Public Types

enum | Measure { MEASURE_PPM = 0, MEASURE_DA }

## Public Member Functions

| IDMapper ()
| Default constructor. More...
| IDMapper (const IDMapper &cp)
| Copy C'Tor. More...
IDMapper & | operator= (const IDMapper &rhs)
| Assignment. More...
void | annotate (PeakMap &map, const std::vector< PeptideIdentification > &peptide_ids, const std::vector< ProteinIdentification > &protein_ids, const bool clear_ids=false, const bool map_ms1=false)
| Mapping method for peak maps. More...
void | annotate (PeakMap &map, FeatureMap fmap, const bool clear_ids=false, const bool map_ms1=false)
| Mapping method for peak maps. More...
void | annotate (FeatureMap &map, const std::vector< PeptideIdentification > &ids, const std::vector< ProteinIdentification > &protein_ids, bool use_centroid_rt=false, bool use_centroid_mz=false, const PeakMap &spectra=PeakMap())
| Mapping method for feature maps. More...
void | annotate (ConsensusMap &map, const std::vector< PeptideIdentification > &ids, const std::vector< ProteinIdentification > &protein_ids, bool measure_from_subelements=false, bool annotate_ids_with_subelements=false, const PeakMap &spectra=PeakMap())
| Mapping method for consensus maps. More...
Public Member Functions inherited from DefaultParamHandler
| DefaultParamHandler (const String &name)
| Constructor with name that is displayed in error messages. More...
| DefaultParamHandler (const DefaultParamHandler &rhs)
| Copy constructor. More...
virtual | ~DefaultParamHandler ()
| Destructor. More...
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs)
| Assignment operator. More...
virtual bool | operator== (const DefaultParamHandler &rhs) const
| Equality operator. More...
void | setParameters (const Param &param)
| Sets the parameters. More...
const Param & | getParameters () const
| Non-mutable access to the parameters. More...
const Param & | getDefaults () const
| Non-mutable access to the default parameters. More...
const String & | getName () const
| Non-mutable access to the name. More...
void | setName (const String &name)
| Mutable access to the name. More...
const std::vector< String > & | getSubsections () const
| Non-mutable access to the registered subsections. More...

## Static Public Member Functions

static SpectraIdentificationState | mapPrecursorsToIdentifications (const PeakMap &spectra, const std::vector< PeptideIdentification > &ids, double mz_tol=0.001, double rt_tol=0.001)
| Mapping of peptide identifications to spectra This helper function partitions all spectra into those that had: More...

## Protected Member Functions

void | updateMembers_ () override
| This method is used to update extra member variables at the end of the setParameters() method. More...
double | getAbsoluteMZTolerance_ (const double mz) const
bool | isMatch_ (const double rt_distance, const double mz_theoretical, const double mz_observed) const
| check if distance constraint is fulfilled (using `rt_tolerance_`, `mz_tolerance_` and `measure_`) More...
void | checkHits_ (const std::vector< PeptideIdentification > &ids) const
| helper function that checks if all peptide hits are annotated with RT and MZ meta values More...
void | getIDDetails_ (const PeptideIdentification &id, double &rt_pep, DoubleList &mz_values, IntList &charges, bool use_avg_mass=false) const
void | increaseBoundingBox_ (DBoundingBox< 2 > &box)
| increase a bounding box by the given RT and m/z tolerances More...
bool | checkMassType_ (const std::vector< DataProcessing > &processing) const
Protected Member Functions inherited from DefaultParamHandler
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...

## Protected Attributes

double | rt_tolerance_
| Allowed RT deviation. More...
double | mz_tolerance_
| Allowed m/z deviation. More...
Measure | measure_
| Measure used for m/z. More...
bool | ignore_charge_
| Ignore charge states during matching? More...
Protected Attributes inherited from DefaultParamHandler
Param | param_
| Container for current parameters. More...
Param | defaults_
| Container for default parameters. This member should be filled in the constructor of derived classes! More...
std::vector< String > | subsections_
| Container for registered subsections. This member should be filled in the constructor of derived classes! More...
String | error_name_
| Name that is displayed in error messages during the parameter checking. More...
bool | check_defaults_
| If this member is set to false no checking if parameters in done;. More...
bool | warn_empty_defaults_
| If this member is set to false no warning is emitted when defaults are empty;. More...

## Detailed Description

Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications.

ProteinIdentifications are assigned to the whole map.

The retention time and mass-to-charge ratio of the PeptideIdentification as the respective "MZ" and "RT" members.

m/z-matching on peptide side can be done either with the precursor m/z value of the peptide identification or with the theoretical masses of the peptide hits (see "mz_reference" parameter).

See the documentation of the individual `annotate` methods for more in-depth information.

Parameters of this class are:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
rt_tolerance | float | 5.0 | min: 0.0 | RT tolerance (in seconds) for the matching
mz_tolerance | float | 20.0 | min: 0.0 | m/z tolerance (in ppm or Da) for the matching
mz_measure | string | ppm | ppm, Da | unit of 'mz_tolerance' (ppm or Da)
mz_reference | string | precursor | precursor, peptide | source of m/z values for peptide identifications
ignore_charge | string | false | true, false | For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature.

Note:

- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.

## Class Documentation

## ◆ OpenMS::IDMapper::SpectraIdentificationState

struct OpenMS::IDMapper::SpectraIdentificationState

Result of a partitioning by identification state with mapPrecursorsToIdentifications().

Class Members
vector< Size > | identified |
vector< Size > | no_precursors |
vector< Size > | unidentified |

## Member Enumeration Documentation

## ◆ Measure

enum Measure

Enumerator
MEASURE_PPM |
MEASURE_DA |

## Constructor & Destructor Documentation

## ◆ IDMapper() [1/2]

IDMapper | ( |  | ) |

Default constructor.

## ◆ IDMapper() [2/2]

IDMapper | ( | const IDMapper & | cp | ) |

Copy C'Tor.

## Member Function Documentation

## ◆ annotate() [1/4]

void annotate | ( | PeakMap & | map,
|  | const std::vector< PeptideIdentification > & | peptide_ids,
|  | const std::vector< ProteinIdentification > & | protein_ids,
|  | const bool | clear_ids = `false`,
|  | const bool | map_ms1 = `false`
| ) |  |

Mapping method for peak maps.

The identifications stored in a PeptideIdentification instance can be added to the corresponding spectrum. Note that a PeptideIdentication is added to ALL spectra which are within the allowed RT and MZ boundaries.

Parameters

  map | MSExperiment to receive the identifications
  peptide_ids | PeptideIdentification for the MSExperiment
  protein_ids | ProteinIdentification for the MSExperiment
  clear_ids | Reset peptide and protein identifications of each scan before annotating
  map_ms1 | Attach Ids to MS1 spectra using RT mapping only (without precursor, without m/z)

Exceptions

  Exception::MissingInformation | is thrown if entries of `peptide_ids` do not contain 'MZ' and 'RT' information.

Referenced by TOPPViewBase::annotateMS1FromMassFingerprinting_(), and TOPPViewBase::annotateWithID().

## ◆ annotate() [2/4]

void annotate | ( | PeakMap & | map,
|  | FeatureMap | fmap,
|  | const bool | clear_ids = `false`,
|  | const bool | map_ms1 = `false`
| ) |  |

Mapping method for peak maps.

Add peptide identifications stored in a feature map to their corresponding spectrum.

This function converts the feature map to a vector of peptide identifications (all peptide IDs from each feature are taken) and calls the respective annotate() function. RT and m/z are taken from the peptides, or (if missing) from the feature itself.

Parameters

  map | MSExperiment to receive the identifications
  fmap | FeatureMap with PeptideIdentifications for the MSExperiment
  clear_ids | Reset peptide and protein identifications of each scan before annotating
  map_ms1 | attach Ids to MS1 spectra using RT mapping only (without precursor, without m/z)

## ◆ annotate() [3/4]

void annotate | ( | FeatureMap & | map,
|  | const std::vector< PeptideIdentification > & | ids,
|  | const std::vector< ProteinIdentification > & | protein_ids,
|  | bool | use_centroid_rt = `false`,
|  | bool | use_centroid_mz = `false`,
|  | const PeakMap & | spectra = `PeakMap()`
| ) |  |

Mapping method for feature maps.

If all features have at least one convex hull, peptide positions are matched against the bounding boxes of the convex hulls 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 `use_centroid_rt` or `use_centroid_mz` are true.

In any case, tolerance in RT and m/z dimension is applied according to the global 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 (incl. tolerance) overlap the position of a peptide identification, the identification is annotated to all of them.

Parameters

  map | FeatureMap to receive the identifications
  ids | PeptideIdentification for the ConsensusFeatures
  protein_ids | ProteinIdentification for the ConsensusMap
  use_centroid_rt | Whether to use the RT value of feature centroids even if convex hulls are present
  use_centroid_mz | Whether to use the m/z value of feature centroids even if convex hulls are present
  spectra | Whether precursors not contained in the identifications are annotated with an empty PeptideIdentification object containing the scan index.

Exceptions

  Exception::MissingInformation | is thrown if entries of `ids` do not contain 'MZ' and 'RT' information.

## ◆ annotate() [4/4]

void annotate | ( | ConsensusMap & | map,
|  | const std::vector< PeptideIdentification > & | ids,
|  | const std::vector< ProteinIdentification > & | protein_ids,
|  | bool | measure_from_subelements = `false`,
|  | bool | annotate_ids_with_subelements = `false`,
|  | const PeakMap & | spectra = `PeakMap()`
| ) |  |

Mapping method for consensus maps.

If several consensus features lie inside the allowed deviation, the peptide identifications are mapped to all the consensus features.

Parameters

  map | ConsensusMap to receive the identifications
  ids | PeptideIdentification for the ConsensusFeatures
  protein_ids | ProteinIdentification for the ConsensusMap
  measure_from_subelements | Do distance estimate from FeatureHandles instead of Centroid
  annotate_ids_with_subelements | Store map index of FeatureHandle in peptide identification?
  spectra | Whether precursors not contained in the identifications are annotated with an empty PeptideIdentification object containing the scan index.

Exceptions

  Exception::MissingInformation | is thrown if the MetaInfoInterface of `ids` does not contain 'MZ' and 'RT'

## ◆ checkHits_()

void checkHits_ | ( | const std::vector< PeptideIdentification > & | ids | ) | const

protected

helper function that checks if all peptide hits are annotated with RT and MZ meta values

## ◆ checkMassType_()

bool checkMassType_ | ( | const std::vector< DataProcessing > & | processing | ) | const

protected

try to determine the type of m/z value reported for features, return whether average peptide masses should be used for matching

## ◆ getAbsoluteMZTolerance_()

double getAbsoluteMZTolerance_ | ( | const double | mz | ) | const

protected

compute absolute Da tolerance, for a given m/z, when `measure` is MEASURE_DA, the value is unchanged, for MEASURE_PPM it is computed according to currently allowed ppm tolerance

## ◆ getIDDetails_()

void getIDDetails_ | ( | const PeptideIdentification & | id,
|  | double & | rt_pep,
|  | DoubleList & | mz_values,
|  | IntList & | charges,
|  | bool | use_avg_mass = `false`
| ) |  | const

protected

get RT, m/z and charge value(s) of a PeptideIdentification

- multiple m/z values are returned if "mz_reference" is set to "peptide" (one for each PeptideHit)
- one m/z value is returned if "mz_reference" is set to "precursor"

## ◆ increaseBoundingBox_()

void increaseBoundingBox_ | ( | DBoundingBox< 2 > & | box | ) |

protected

increase a bounding box by the given RT and m/z tolerances

## ◆ isMatch_()

bool isMatch_ | ( | const double | rt_distance,
|  | const double | mz_theoretical,
|  | const double | mz_observed
| ) |  | const

protected

check if distance constraint is fulfilled (using `rt_tolerance_`, `mz_tolerance_` and `measure_`)

## ◆ mapPrecursorsToIdentifications()

static SpectraIdentificationState mapPrecursorsToIdentifications | ( | const PeakMap & | spectra,
|  | const std::vector< PeptideIdentification > & | ids,
|  | double | mz_tol = `0.001`,
|  | double | rt_tol = `0.001`
| ) |  |

inline static

Mapping of peptide identifications to spectra This helper function partitions all spectra into those that had:

- no precursor (e.g. MS1 spectra),
- at least one identified precursor,
- or only unidentified precursor.
  Parameters

    spectra | The mass spectra
    ids | The peptide identifications Tolerance used to map to precursor m/z Tolerance used to map to spectrum retention time

  Note: mz/tol and rt_tol should, in principle, be zero (or close to zero under numeric inaccuracies).

Returns
  A struct of vectors holding spectra indices of the partitioning.

References PeptideIdentification::getHits(), PeptideIdentification::getMZ(), SpectrumSettings::getPrecursors(), PeptideIdentification::getRT(), MSSpectrum::getRT(), IDMapper::SpectraIdentificationState::identified, IDMapper::SpectraIdentificationState::no_precursors, MSExperiment::size(), and IDMapper::SpectraIdentificationState::unidentified.

## ◆ operator=()

IDMapper& operator= | ( | const IDMapper & | rhs | ) |

Assignment.

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override protected virtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

## Member Data Documentation

## ◆ ignore_charge_

bool ignore_charge_

protected

Ignore charge states during matching?

## ◆ measure_

Measure measure_

protected

Measure used for m/z.

## ◆ mz_tolerance_

double mz_tolerance_

protected

Allowed m/z deviation.

## ◆ rt_tolerance_

double rt_tolerance_

protected

Allowed RT deviation.