| OpenMS 2.5.0

Classes | Public Types | Public Member Functions | Protected Member Functions | List of all members
ReactionMonitoringTransition Class Reference

This class stores a SRM/MRM transition. More...

`#include <OpenMS/ANALYSIS/MRM/ReactionMonitoringTransition.h>`

Inheritance diagram for ReactionMonitoringTransition:

## Classes

struct | ProductMZLess
| Comparator by Product ion MZ. More...

## Public Types

enum | DecoyTransitionType { UNKNOWN, TARGET, DECOY }
typedef TargetedExperimentHelper::Configuration | Configuration
typedef TargetedExperimentHelper::RetentionTime | RetentionTime
typedef TargetedExperimentHelper::TraMLProduct | Product
typedef TargetedExperimentHelper::Prediction | Prediction

## Public Member Functions

ReactionMonitoringTransition & | operator= (const ReactionMonitoringTransition &rhs)
| assignment operator More...
ReactionMonitoringTransition & | operator= (ReactionMonitoringTransition &&rhs)
| move assignment operator More...
Constructors and destructors
| ReactionMonitoringTransition ()
| default constructor More...
| ReactionMonitoringTransition (const ReactionMonitoringTransition &rhs)
| copy constructor More...
| ReactionMonitoringTransition (ReactionMonitoringTransition &&) noexcept
| Move constructor. More...
| ~ReactionMonitoringTransition () override
| destructor More...
Accessors
void | setName (const String &name)
const String & | getName () const
void | setNativeID (const String &name)
const String & | getNativeID () const
void | setPeptideRef (const String &peptide_ref)
const String & | getPeptideRef () const
void | setCompoundRef (const String &compound_ref)
const String & | getCompoundRef () const
void | setPrecursorMZ (double mz)
| sets the precursor mz (Q1 value) More...
double | getPrecursorMZ () const
| get the precursor mz (Q1 value) More...
bool | hasPrecursorCVTerms () const
| Returns true if precursor CV Terms exist (means it is safe to call getPrecursorCVTermList) More...
void | setPrecursorCVTermList (const CVTermList &list)
void | addPrecursorCVTerm (const CVTerm &cv_term)
const CVTermList & | getPrecursorCVTermList () const
| Obtain the list of CV Terms for the precursor. More...
void | setProductMZ (double mz)
double | getProductMZ () const
int | getProductChargeState () const
bool | isProductChargeStateSet () const
void | addProductCVTerm (const CVTerm &cv_term)
const std::vector< Product > & | getIntermediateProducts () const
void | addIntermediateProduct (Product product)
void | setIntermediateProducts (const std::vector< Product > &products)
void | setProduct (Product product)
const Product & | getProduct () const
bool | hasPrediction () const
| Returns true if a Prediction object exists (means it is safe to call getPrediction) More...
void | setPrediction (const Prediction &prediction)
void | addPredictionTerm (const CVTerm &prediction)
const Prediction & | getPrediction () const
| Obtain the Prediction object. More...
DecoyTransitionType | getDecoyTransitionType () const
| Returns the type of transition (target or decoy) More...
void | setDecoyTransitionType (const DecoyTransitionType &d)
| Sets the type of transition (target or decoy) More...
double | getLibraryIntensity () const
| Returns the library intensity (ion count or normalized ion count from a spectral library) More...
void | setLibraryIntensity (double intensity)
| Sets the library intensity (ion count or normalized ion count from a spectral library) More...
Retention time
Retention time set on transition level

Note
  Retention time can be set on analyte level (peptide / compound level) or transition level – usually the retention time set here on transition level is ignored, therefore only use this if you have a good reason.

void | setRetentionTime (RetentionTime rt)
| Sets the retention time on transition level. More...
const RetentionTime & | getRetentionTime () const
| Gets the retention time on transition level. More...
Detecting transitions
Transitions used for detection of analyte Detecting transitions represent the set of transitions of an assay that should be used to enable candidate peak group detection. Ideally they were observed and validated in previous experiments and have an associated library intensity.

For an overview, see Schubert OT et al., Building high-quality assay libraries for targeted analysis of SWATH MS data., Nat Protoc. 2015 Mar;10(3):426-41. doi: 10.1038/nprot.2015.015. Epub 2015 Feb 12. PMID: 25675208

bool | isDetectingTransition () const
void | setDetectingTransition (bool val)
Identifying transitions
Transitions used for differentiation between different analyte isomers (peptidoforms). Identifying transitions represent the set of transitions of an assay that should be used for the independent identification of a candidate peak group (often in relation to another analyte isomer or peptidoform). These transitions could for example be site-determining transitions in a phospho-proteomic DIA experiment. These transitions will be scored independently of the detecting transitions.
bool | isIdentifyingTransition () const
void | setIdentifyingTransition (bool val)
Quantifying transitions
Transitions used for quantification Quantifying transitions represent the set of transitions of an assay that should be used for the quantification of the peptide. This includes exclusion of e.g. interfered transitions (example: light/heavy peptide pairs isolated in the same swath window), that should not be used for quantification of the peptide.
bool | isQuantifyingTransition () const
void | setQuantifyingTransition (bool val)
Predicates
bool | operator== (const ReactionMonitoringTransition &rhs) const
| equality operator More...
bool | operator!= (const ReactionMonitoringTransition &rhs) const
| inequality operator More...
Public Member Functions inherited from CVTermList
| CVTermList ()=default
| Defaults constructor. More...
| CVTermList (const CVTermList &)=default
| Copy constructor. More...
| CVTermList (CVTermList &&) noexcept
| Move constructor. More...
virtual | ~CVTermList ()
| Destructor. More...
CVTermList & | operator= (const CVTermList &rhs) &=default
| Assignment operator. More...
CVTermList & | operator= (CVTermList &&) &=default
| Move assignment operator. More...
void | setCVTerms (const std::vector< CVTerm > &terms)
| sets the CV terms More...
void | replaceCVTerm (const CVTerm &cv_term)
| replaces the specified CV term More...
void | replaceCVTerms (const std::vector< CVTerm > &cv_terms, const String &accession)
| replaces the specified CV terms using the given accession number More...
void | replaceCVTerms (const Map< String, std::vector< CVTerm > > &cv_term_map)
| replaces all cv terms with a map (can be obtained via getCVTerms) More...
void | consumeCVTerms (const Map< String, std::vector< CVTerm > > &cv_term_map)
| merges the given map into the member map, no duplicate checking More...
const Map< String, std::vector< CVTerm > > & | getCVTerms () const
| returns the accession string of the term More...
void | addCVTerm (const CVTerm &term)
| adds a CV term More...
bool | operator== (const CVTermList &cv_term_list) const
| equality operator More...
bool | operator!= (const CVTermList &cv_term_list) const
| inequality operator More...
bool | hasCVTerm (const String &accession) const
| checks whether the term has a value More...
bool | empty () const
| return true if no terms are available More...
Public Member Functions inherited from MetaInfoInterface
| MetaInfoInterface ()
| Constructor. More...
| MetaInfoInterface (const MetaInfoInterface &rhs)
| Copy constructor. More...
| MetaInfoInterface (MetaInfoInterface &&) noexcept
| Move constructor. More...
| ~MetaInfoInterface ()
| Destructor. More...
MetaInfoInterface & | operator= (const MetaInfoInterface &rhs)
| Assignment operator. More...
MetaInfoInterface & | operator= (MetaInfoInterface &&) noexcept
| Move assignment operator. More...
bool | operator== (const MetaInfoInterface &rhs) const
| Equality operator. More...
bool | operator!= (const MetaInfoInterface &rhs) const
| Equality operator. More...
const DataValue & | getMetaValue (const String &name, const DataValue &default_value=DataValue::EMPTY) const
| Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not found. More...
const DataValue & | getMetaValue (UInt index, const DataValue &default_value=DataValue::EMPTY) const
| Returns the value corresponding to an index, or a default value (default: DataValue::EMPTY) if not found. More...
bool | metaValueExists (const String &name) const
| Returns whether an entry with the given name exists. More...
bool | metaValueExists (UInt index) const
| Returns whether an entry with the given index exists. More...
void | setMetaValue (const String &name, const DataValue &value)
| Sets the DataValue corresponding to a name. More...
void | setMetaValue (UInt index, const DataValue &value)
| Sets the DataValue corresponding to an index. More...
void | removeMetaValue (const String &name)
| Removes the DataValue corresponding to `name` if it exists. More...
void | removeMetaValue (UInt index)
| Removes the DataValue corresponding to `index` if it exists. More...
void | getKeys (std::vector< String > &keys) const
| Fills the given vector with a list of all keys for which a value is set. More...
void | getKeys (std::vector< UInt > &keys) const
| Fills the given vector with a list of all keys for which a value is set. More...
bool | isMetaEmpty () const
| Returns if the MetaInfo is empty. More...
void | clearMetaInfo ()
| Removes all meta values. More...

## Protected Member Functions

void | updateMembers_ ()
Protected Member Functions inherited from MetaInfoInterface
void | createIfNotExists_ ()
| Creates the MetaInfo object if it does not exist. More...

## Protected Attributes

Attributes
String | name_
| id, required attribute More...
String | peptide_ref_
| Reference to a specific peptide. More...
String | compound_ref_
| Reference to a specific compound. More...
double | library_intensity_
| Intensity of the product (q3) ion (stored in CV Term 1001226 inside the <Transition> tag) More...
DecoyTransitionType | decoy_type_
| specific properties of a transition (e.g. specific CV terms) More...
Subelements
double | precursor_mz_
| A transition has exactly one precursor and it must supply the CV Term 1000827 (isolation window target m/z) More...
CVTermList * | precursor_cv_terms_
| (Other) CV Terms of the Precursor (Q1) of the transition or target More...
Product | product_
| Product (Q3) of the transition. More...
std::vector< Product > | intermediate_products_
| Intermediate product ion information of the transition when using MS3 or above (optional) More...
RetentionTime | rts
| Information about predicted or calibrated retention time (optional) More...
Prediction * | prediction_
| Information about a prediction for a suitable transition using some software (optional) More...
std::bitset< 3 > | transition_flags_
Protected Attributes inherited from CVTermList
Map< String, std::vector< CVTerm > > | cv_terms_
Protected Attributes inherited from MetaInfoInterface
MetaInfo * | meta_
| Pointer to the MetaInfo object (0 by default) More...

## Additional Inherited Members

Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry & | metaRegistry ()
| Returns a reference to the MetaInfoRegistry. More...

## Detailed Description

This class stores a SRM/MRM transition.

This class is capable of representing a <Transition> tag in a TraML document completely and contains all associated information.

The default values for precursor m/z is 0.0 which indicates that it is uninitialized.

## Member Typedef Documentation

## ◆ Configuration

typedef TargetedExperimentHelper::Configuration Configuration

## ◆ Prediction

typedef TargetedExperimentHelper::Prediction Prediction

## ◆ Product

typedef TargetedExperimentHelper::TraMLProduct Product

## ◆ RetentionTime

typedef TargetedExperimentHelper::RetentionTime RetentionTime

## Member Enumeration Documentation

## ◆ DecoyTransitionType

enum DecoyTransitionType

Enumerator
UNKNOWN | Unknown type.
TARGET | Target transition.
DECOY | Decoy transition.

## Constructor & Destructor Documentation

## ◆ ReactionMonitoringTransition() [1/3]

ReactionMonitoringTransition | ( |  | ) |

default constructor

## ◆ ReactionMonitoringTransition() [2/3]

ReactionMonitoringTransition | ( | const ReactionMonitoringTransition & | rhs | ) |

copy constructor

## ◆ ReactionMonitoringTransition() [3/3]

ReactionMonitoringTransition | ( | ReactionMonitoringTransition && |  | ) |

noexcept

Move constructor.

## ◆ ~ReactionMonitoringTransition()

~ReactionMonitoringTransition | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ addIntermediateProduct()

void addIntermediateProduct | ( | Product | product | ) |

## ◆ addPrecursorCVTerm()

void addPrecursorCVTerm | ( | const CVTerm & | cv_term | ) |

## ◆ addPredictionTerm()

void addPredictionTerm | ( | const CVTerm & | prediction | ) |

## ◆ addProductCVTerm()

void addProductCVTerm | ( | const CVTerm & | cv_term | ) |

## ◆ getCompoundRef()

const String& getCompoundRef | ( |  | ) | const

Referenced by ChromatogramExtractor::prepareSpectra_().

## ◆ getDecoyTransitionType()

DecoyTransitionType getDecoyTransitionType | ( |  | ) | const

Returns the type of transition (target or decoy)

## ◆ getIntermediateProducts()

const std::vector<Product>& getIntermediateProducts | ( |  | ) | const

## ◆ getLibraryIntensity()

double getLibraryIntensity | ( |  | ) | const

Returns the library intensity (ion count or normalized ion count from a spectral library)

## ◆ getName()

const String& getName | ( |  | ) | const

## ◆ getNativeID()

const String& getNativeID | ( |  | ) | const

Referenced by ChromatogramExtractor::prepareSpectra_().

## ◆ getPeptideRef()

const String& getPeptideRef | ( |  | ) | const

Referenced by ChromatogramExtractor::prepareSpectra_().

## ◆ getPrecursorCVTermList()

const CVTermList& getPrecursorCVTermList | ( |  | ) | const

Obtain the list of CV Terms for the precursor.

Note
  You first need to check whether they exist using hasPrecursorCVTerms()

## ◆ getPrecursorMZ()

double getPrecursorMZ | ( |  | ) | const

get the precursor mz (Q1 value)

Referenced by ChromatogramExtractor::prepareSpectra_().

## ◆ getPrediction()

const Prediction& getPrediction | ( |  | ) | const

Obtain the Prediction object.

Note
  You first need to check whether the object is accessible using hasPrediction()

## ◆ getProduct()

const Product& getProduct | ( |  | ) | const

## ◆ getProductChargeState()

int getProductChargeState | ( |  | ) | const

## ◆ getProductMZ()

double getProductMZ | ( |  | ) | const

Referenced by ReactionMonitoringTransition::ProductMZLess::operator()(), and ChromatogramExtractor::prepareSpectra_().

## ◆ getRetentionTime()

const RetentionTime& getRetentionTime | ( |  | ) | const

Gets the retention time on transition level.

Stores a retention time on the level of an individual transition

Note
  This is very likely not what you want, to set the retention time of an analyte use TargetedExperimentHelper::PeptideCompound::getRetentionTime()

## ◆ hasPrecursorCVTerms()

bool hasPrecursorCVTerms | ( |  | ) | const

Returns true if precursor CV Terms exist (means it is safe to call getPrecursorCVTermList)

## ◆ hasPrediction()

bool hasPrediction | ( |  | ) | const

Returns true if a Prediction object exists (means it is safe to call getPrediction)

## ◆ isDetectingTransition()

bool isDetectingTransition | ( |  | ) | const

## ◆ isIdentifyingTransition()

bool isIdentifyingTransition | ( |  | ) | const

## ◆ isProductChargeStateSet()

bool isProductChargeStateSet | ( |  | ) | const

## ◆ isQuantifyingTransition()

bool isQuantifyingTransition | ( |  | ) | const

## ◆ operator!=()

bool operator!= | ( | const ReactionMonitoringTransition & | rhs | ) | const

inequality operator

## ◆ operator=() [1/2]

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

assignment operator

## ◆ operator=() [2/2]

ReactionMonitoringTransition& operator= | ( | ReactionMonitoringTransition && | rhs | ) |

move assignment operator

## ◆ operator==()

bool operator== | ( | const ReactionMonitoringTransition & | rhs | ) | const

equality operator

## ◆ setCompoundRef()

void setCompoundRef | ( | const String & | compound_ref | ) |

## ◆ setDecoyTransitionType()

void setDecoyTransitionType | ( | const DecoyTransitionType & | d | ) |

Sets the type of transition (target or decoy)

## ◆ setDetectingTransition()

void setDetectingTransition | ( | bool | val | ) |

## ◆ setIdentifyingTransition()

void setIdentifyingTransition | ( | bool | val | ) |

## ◆ setIntermediateProducts()

void setIntermediateProducts | ( | const std::vector< Product > & | products | ) |

## ◆ setLibraryIntensity()

void setLibraryIntensity | ( | double | intensity | ) |

Sets the library intensity (ion count or normalized ion count from a spectral library)

## ◆ setName()

void setName | ( | const String & | name | ) |

## ◆ setNativeID()

void setNativeID | ( | const String & | name | ) |

## ◆ setPeptideRef()

void setPeptideRef | ( | const String & | peptide_ref | ) |

## ◆ setPrecursorCVTermList()

void setPrecursorCVTermList | ( | const CVTermList & | list | ) |

## ◆ setPrecursorMZ()

void setPrecursorMZ | ( | double | mz | ) |

sets the precursor mz (Q1 value)

## ◆ setPrediction()

void setPrediction | ( | const Prediction & | prediction | ) |

## ◆ setProduct()

void setProduct | ( | Product | product | ) |

## ◆ setProductMZ()

void setProductMZ | ( | double | mz | ) |

## ◆ setQuantifyingTransition()

void setQuantifyingTransition | ( | bool | val | ) |

## ◆ setRetentionTime()

void setRetentionTime | ( | RetentionTime | rt | ) |

Sets the retention time on transition level.

Stores a retention time on the level of an individual transition

Note
  This is very likely not what you want, to set the retention time of an analyte use TargetedExperimentHelper::PeptideCompound::getRetentionTime()

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

protected

## Member Data Documentation

## ◆ compound_ref_

String compound_ref_

protected

Reference to a specific compound.

## ◆ decoy_type_

DecoyTransitionType decoy_type_

protected

specific properties of a transition (e.g. specific CV terms)

## ◆ intermediate_products_

std::vector<Product> intermediate_products_

protected

Intermediate product ion information of the transition when using MS3 or above (optional)

## ◆ library_intensity_

double library_intensity_

protected

Intensity of the product (q3) ion (stored in CV Term 1001226 inside the <Transition> tag)

## ◆ name_

String name_

protected

id, required attribute

## ◆ peptide_ref_

String peptide_ref_

protected

Reference to a specific peptide.

## ◆ precursor_cv_terms_

CVTermList* precursor_cv_terms_

protected

(Other) CV Terms of the Precursor (Q1) of the transition or target

## ◆ precursor_mz_

double precursor_mz_

protected

A transition has exactly one precursor and it must supply the CV Term 1000827 (isolation window target m/z)

## ◆ prediction_

Prediction* prediction_

protected

Information about a prediction for a suitable transition using some software (optional)

## ◆ product_

Product product_

protected

Product (Q3) of the transition.

## ◆ rts

RetentionTime rts

protected

Information about predicted or calibrated retention time (optional)

## ◆ transition_flags_

std::bitset<3> transition_flags_

protected

A set of flags to store information about the transition at hand (currently: detecting, identifying and quantifying)