OpenMS

IsotopeLabelingMDVs is a class to support and analyze isotopic labeling experiments (i.e. MDVs : Mass Distribution Vectors, also known as Mass Isotopomer Distribution (MID)) More...
#include <OpenMS/ANALYSIS/QUANTITATION/IsotopeLabelingMDVs.h>
Public Types  
enum class  DerivatizationAgent { NOT_SELECTED , TBDMS , SIZE_OF_DERIVATIZATIONAGENT } 
enum class  MassIntensityType { NORM_MAX , NORM_SUM , SIZE_OF_MASSINTENSITYTYPE } 
Public Member Functions  
IsotopeLabelingMDVs ()  
Constructor. More...  
~IsotopeLabelingMDVs () override  
Destructor. More...  
void  isotopicCorrection (const Feature &normalized_feature, Feature &corrected_feature, const Matrix< double > &correction_matrix, const DerivatizationAgent &correction_matrix_agent) 
This function performs an isotopic correction to account for unlabeled abundances coming from the derivatization agent (e.g., tBDMS) using correction matrix method and is calculated as follows: MDV_corrected = CM^1 * MDV_normalized_feature The formula is obtained from "The importance of accurately correcting for the natural abundance of stable isotopes", Midani et al, doi:10.1016/j.ab.2016.12.011. More...  
void  isotopicCorrections (const FeatureMap &measured_fm, FeatureMap &corrected_fm, const Matrix< double > &correction_matrix, const DerivatizationAgent &correction_matrix_agent) 
This function performs an isotopic correction to account for unlabeled abundances coming from the derivatization agent (e.g., tBDMS) using correction matrix method and is calculated as follows: MDV_corrected = CM^1 * MDV_normalized_feature The formula is obtained from "The importance of accurately correcting for the natural abundance of stable isotopes", Midani et al, doi:10.1016/j.ab.2016.12.011. More...  
void  calculateIsotopicPurity (Feature &normalized_feature, const std::vector< double > &experiment_data, const std::string &isotopic_purity_name) 
This function calculates the isotopic purity of the MDV using the following formula: isotopic purity of tracer (atom % 13C) = n / [n + (M + n1)/(M + n)], where n in M+n is represented as the index of the result. The formula is extracted from "Highresolution 13C metabolic flux analysis", Long et al, doi:10.1038/s4159601902040. More...  
void  calculateIsotopicPurities (FeatureMap &measured_fm, const std::vector< std::vector< double >> &experiment_data, const std::vector< std::string > &isotopic_purity_name) 
This function calculates the isotopic purity of the MDVs using the following formula: isotopic purity of tracer (atom % 13C) = n / [n + (M + n1)/(M + n)], where n in M+n is represented as the index of the result. The formula is extracted from "Highresolution 13C metabolic flux analysis", Long et al, doi:10.1038/s4159601902040. More...  
void  calculateMDVAccuracy (Feature &normalized_feature, const std::string &feature_name, const std::string &fragment_isotopomer_theoretical_formula) 
This function calculates the accuracy of the MDV as compared to the theoretical MDV (only for 12C quality control experiments) using average deviation to the mean. The result is mapped to the meta value "average_accuracy" in the updated Feature. More...  
void  calculateMDVAccuracies (FeatureMap &normalized_fm, const std::string &feature_name, const std::map< std::string, std::string > &fragment_isotopomer_theoretical_formulas) 
This function calculates the accuracy of the MDVs as compared to the theoretical MDVs (only for 12C quality control experiments) using average deviation to the mean. More...  
void  calculateMDV (const Feature &measured_feature, Feature &normalized_feature, const MassIntensityType &mass_intensity_type, const std::string &feature_name) 
This function calculates the mass distribution vector (MDV) either normalized to the highest mass intensity (norm_max) or normalized to the sum of all mass intensities (norm_sum) More...  
void  calculateMDVs (const FeatureMap &measured_fm, FeatureMap &normalized_fm, const MassIntensityType &mass_intensity_type, const std::string &feature_name) 
This function calculates the mass distribution vector (MDV) either normalized to the highest mass intensity (norm_max) or normalized to the sum of all mass intensities (norm_sum) 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...  
DefaultParamHandler &  operator= (const DefaultParamHandler &rhs) 
Assignment operator. More...  
virtual bool  operator== (const DefaultParamHandler &rhs) const 
Equality operator. More...  
void  setParameters (const Param ¶m) 
Sets the parameters. More...  
const Param &  getParameters () const 
Nonmutable access to the parameters. More...  
const Param &  getDefaults () const 
Nonmutable access to the default parameters. More...  
const String &  getName () const 
Nonmutable access to the name. More...  
void  setName (const String &name) 
Mutable access to the name. More...  
const std::vector< String > &  getSubsections () const 
Nonmutable access to the registered subsections. More...  
Static Public Attributes  
static const std::string  NamesOfDerivatizationAgent [static_cast< int >(DerivatizationAgent::SIZE_OF_DERIVATIZATIONAGENT)] 
static const std::string  NamesOfMassIntensityType [static_cast< int >(MassIntensityType::SIZE_OF_MASSINTENSITYTYPE)] 
Protected Member Functions  
void  updateMembers_ () override 
Synchronize members with param class. More...  
Protected Member Functions inherited from DefaultParamHandler  
void  defaultsToParam_ () 
Updates the parameters after the defaults have been set in the constructor. More...  
Additional Inherited Members  
Static Public Member Functions inherited from DefaultParamHandler  
static void  writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="") 
Writes all parameters to meta values. 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...  
IsotopeLabelingMDVs is a class to support and analyze isotopic labeling experiments (i.e. MDVs : Mass Distribution Vectors, also known as Mass Isotopomer Distribution (MID))

strong 

strong 
Constructor.

override 
Destructor.
void calculateIsotopicPurities  (  FeatureMap &  measured_fm, 
const std::vector< std::vector< double >> &  experiment_data,  
const std::vector< std::string > &  isotopic_purity_name  
) 
This function calculates the isotopic purity of the MDVs using the following formula: isotopic purity of tracer (atom % 13C) = n / [n + (M + n1)/(M + n)], where n in M+n is represented as the index of the result. The formula is extracted from "Highresolution 13C metabolic flux analysis", Long et al, doi:10.1038/s4159601902040.
[in,out]  measured_fm  FeatureMap with normalized values for each component and the number of heavy labeled e.g., carbons. Out is a FeatureMap with the calculated isotopic purity for the component group. 
[in]  experiment_data  Vector of vectors of Experiment data in percent. 
[in]  isotopic_purity_name  Vector of names of the isotopic purity tracer to be saved as a meta value. 
void calculateIsotopicPurity  (  Feature &  normalized_feature, 
const std::vector< double > &  experiment_data,  
const std::string &  isotopic_purity_name  
) 
This function calculates the isotopic purity of the MDV using the following formula: isotopic purity of tracer (atom % 13C) = n / [n + (M + n1)/(M + n)], where n in M+n is represented as the index of the result. The formula is extracted from "Highresolution 13C metabolic flux analysis", Long et al, doi:10.1038/s4159601902040.
[in,out]  normalized_feature  Feature with normalized values for each component and the number of heavy labeled e.g., carbons. Out is a Feature with the calculated isotopic purity for the component group. 
[in]  experiment_data  Vector of experiment data in percent. 
[in]  isotopic_purity_name  Name of the isotopic purity tracer to be saved as a meta value. 
void calculateMDV  (  const Feature &  measured_feature, 
Feature &  normalized_feature,  
const MassIntensityType &  mass_intensity_type,  
const std::string &  feature_name  
) 
This function calculates the mass distribution vector (MDV) either normalized to the highest mass intensity (norm_max) or normalized to the sum of all mass intensities (norm_sum)
[in]  measured_feature  Feature with measured intensity for each component. 
[out]  normalized_feature  Feature with normalized values for each component. 
[in]  mass_intensity_type  Mass intensity type (either norm_max or norm_sum). 
[in]  feature_name  Feature name to determine which features are needed to apply calculations on. 
void calculateMDVAccuracies  (  FeatureMap &  normalized_fm, 
const std::string &  feature_name,  
const std::map< std::string, std::string > &  fragment_isotopomer_theoretical_formulas  
) 
This function calculates the accuracy of the MDVs as compared to the theoretical MDVs (only for 12C quality control experiments) using average deviation to the mean.
[in]  normalized_fm  FeatureMap with normalized values for each component and the chemical formula of the component group. Out is a FeatureMap with the component group accuracy and accuracy for the error for each component. 
[in]  feature_name  Feature name to determine which features are needed to apply calculations on. 
[in]  fragment_isotopomer_theoretical_formulas  A map of ProteinName/peptideRef to Empirical formula from which the theoretical values will be generated. 
void calculateMDVAccuracy  (  Feature &  normalized_feature, 
const std::string &  feature_name,  
const std::string &  fragment_isotopomer_theoretical_formula  
) 
This function calculates the accuracy of the MDV as compared to the theoretical MDV (only for 12C quality control experiments) using average deviation to the mean. The result is mapped to the meta value "average_accuracy" in the updated Feature.
[in,out]  normalized_feature  Feature with normalized values for each component and the chemical formula of the component group. Out is a Feature with the component group accuracy and accuracy for the error for each component. 
[in]  feature_name  Feature name to determine which features are needed to apply calculations on. 
[in]  fragment_isotopomer_theoretical_formula  Empirical formula from which the theoretical values will be generated. 
void calculateMDVs  (  const FeatureMap &  measured_fm, 
FeatureMap &  normalized_fm,  
const MassIntensityType &  mass_intensity_type,  
const std::string &  feature_name  
) 
This function calculates the mass distribution vector (MDV) either normalized to the highest mass intensity (norm_max) or normalized to the sum of all mass intensities (norm_sum)
[in]  measured_fm  FeatureMap with measured intensity for each component. 
[out]  normalized_fm  FeatureMap with normalized values for each component. 
[in]  mass_intensity_type  Mass intensity type (either norm_max or norm_sum). 
[in]  feature_name  Feature name to determine which features are needed to apply calculations on. 
void isotopicCorrection  (  const Feature &  normalized_feature, 
Feature &  corrected_feature,  
const Matrix< double > &  correction_matrix,  
const DerivatizationAgent &  correction_matrix_agent  
) 
This function performs an isotopic correction to account for unlabeled abundances coming from the derivatization agent (e.g., tBDMS) using correction matrix method and is calculated as follows: MDV_corrected = CM^1 * MDV_normalized_feature The formula is obtained from "The importance of accurately correcting for the natural abundance of stable isotopes", Midani et al, doi:10.1016/j.ab.2016.12.011.
normalized_feature  Feature with normalized values for each component and unlabeled chemical formula for each component group.  
[out]  corrected_feature  Feature with corrected values for each component. 
correction_matrix  Square matrix holding correction factors derived either experimentally or theoretically which describe how spectral peaks of naturally abundant 13C contribute to spectral peaks that overlap (or convolve) the spectral peaks of the corrected MDV of the derivatization agent.  
correction_matrix_agent  name of the derivatization agent, the internally stored correction matrix if the name of the agent is supplied, only "TBDMS" is supported for now. 
void isotopicCorrections  (  const FeatureMap &  measured_fm, 
FeatureMap &  corrected_fm,  
const Matrix< double > &  correction_matrix,  
const DerivatizationAgent &  correction_matrix_agent  
) 
This function performs an isotopic correction to account for unlabeled abundances coming from the derivatization agent (e.g., tBDMS) using correction matrix method and is calculated as follows: MDV_corrected = CM^1 * MDV_normalized_feature The formula is obtained from "The importance of accurately correcting for the natural abundance of stable isotopes", Midani et al, doi:10.1016/j.ab.2016.12.011.
measured_fm  FeatureMap with normalized values for each component and unlabeled chemical formula for each component group.  
[out]  corrected_fm  FeatureMap with corrected values for each component. 
correction_matrix  Square matrix holding correction factors derived either experimentally or theoretically which describe how spectral peaks of naturally abundant 13C contribute to spectral peaks that overlap (or convolve) the spectral peaks of the corrected MDV of the derivatization agent.  
correction_matrix_agent  name of the derivatization agent, the internally stored correction matrix if the name of the agent is supplied, only "TBDMS" is supported for now. 

overrideprotectedvirtual 
Synchronize members with param class.
Reimplemented from DefaultParamHandler.

static 

static 