| OpenMS 2.5.0

Classes | Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
TheoreticalSpectrumGeneratorXLMS Class Reference
Chemistry

Generates theoretical spectra for cross-linked peptides. More...

`#include <OpenMS/CHEMISTRY/TheoreticalSpectrumGeneratorXLMS.h>`

Inheritance diagram for TheoreticalSpectrumGeneratorXLMS:

## Classes

struct | LossIndex

## Public Member Functions

TheoreticalSpectrumGeneratorXLMS & | operator= (const TheoreticalSpectrumGeneratorXLMS &tsg)
| assignment operator More...
virtual void | getLinearIonSpectrum (PeakSpectrum &spectrum, AASequence &peptide, Size link_pos, bool frag_alpha, int charge=1, Size link_pos_2=0) const
| Generates fragment ions not containing the cross-linker for one peptide. More...
virtual void | getXLinkIonSpectrum (PeakSpectrum &spectrum, AASequence &peptide, Size link_pos, double precursor_mass, bool frag_alpha, int mincharge, int maxcharge, Size link_pos_2=0) const
| Generates fragment ions containing the cross-linker for one peptide. More...
virtual void | getXLinkIonSpectrum (PeakSpectrum &spectrum, OPXLDataStructs::ProteinProteinCrossLink &crosslink, bool frag_alpha, int mincharge, int maxcharge) const
| Generates fragment ions containing the cross-linker for a pair of peptides. More...
void | updateMembers_ () override
| overwrite More...
Constructors and Destructors
| TheoreticalSpectrumGeneratorXLMS ()
| default constructor More...
| TheoreticalSpectrumGeneratorXLMS (const TheoreticalSpectrumGeneratorXLMS &source)
| copy constructor More...
| ~TheoreticalSpectrumGeneratorXLMS () override
| destructor 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...

## Protected Member Functions

virtual void | addLinearPeaks_ (PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, AASequence &peptide, Size link_pos, bool frag_alpha, Residue::ResidueType res_type, std::vector< LossIndex > &forward_losses, std::vector< LossIndex > &backward_losses, int charge=1, Size link_pos_2=0) const
| Adds cross-link-less ions of a specific ion type and charge to a spectrum and adds ion name and charge annotations to the DataArrays. More...
virtual void | addPeak_ (PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, double pos, double intensity, Residue::ResidueType res_type, Size ion_index, int charge, String ion_type) const
| Adds a single peak to a spectrum and its charge and ion name to the given DataArrays. More...
virtual void | addPrecursorPeaks_ (PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, double precursor_mass, int charge) const
| Adds precursor masses including neutral losses for the given charge and adds charge and ion name to the given DataArrays. More...
virtual void | addLinearIonLosses_ (PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, double mono_weight, Residue::ResidueType res_type, Size frag_index, double intensity, int charge, String ion_type, LossIndex &losses) const
| Adds losses for a linear ion. More...
virtual void | addXLinkIonLosses_ (PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, double mono_weight, double intensity, int charge, String ion_name, LossIndex &losses) const
| Adds losses for a cross-linked ion. More...
virtual void | addKLinkedIonPeaks_ (PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, AASequence &peptide, Size link_pos, double precursor_mass, bool frag_alpha, int charge) const
| Adds one-residue-linked ion peaks, that are specific to XLMS. More...
virtual void | addXLinkIonPeaks_ (PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, AASequence &peptide, Size link_pos, double precursor_mass, bool frag_alpha, Residue::ResidueType res_type, std::vector< LossIndex > &forward_losses, std::vector< LossIndex > &backward_losses, int charge, Size link_pos_2=0) const
| Adds cross-linked ions of a specific ion type and charge to a spectrum and adds ion name and charge annotations to the DataArrays. More...
virtual void | addXLinkIonPeaks_ (PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, OPXLDataStructs::ProteinProteinCrossLink &crosslink, bool frag_alpha, Residue::ResidueType res_type, std::vector< LossIndex > &forward_losses, std::vector< LossIndex > &backward_losses, LossIndex &losses_peptide2, int charge) const
| Adds cross-linked ions of a specific ion type and charge to a spectrum and adds ion name and charge annotations to the DataArrays. More...
std::vector< LossIndex > | getForwardLosses_ (AASequence &peptide) const
| Calculates sets of possible neutral losses for each position in the given peptide. More...
std::vector< LossIndex > | getBackwardLosses_ (AASequence &peptide) const
| Calculates sets of possible neutral losses for each position in the given peptide. More...
Protected Member Functions inherited from DefaultParamHandler
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...

## Protected Attributes

bool | add_b_ions_
bool | add_y_ions_
bool | add_a_ions_
bool | add_c_ions_
bool | add_x_ions_
bool | add_z_ions_
bool | add_first_prefix_ion_
bool | add_losses_
bool | add_metainfo_
bool | add_charges_
bool | add_isotopes_
bool | add_precursor_peaks_
bool | add_abundant_immonium_ions_
double | a_intensity_
double | b_intensity_
double | c_intensity_
double | x_intensity_
double | y_intensity_
double | z_intensity_
Int | max_isotope_
double | rel_loss_intensity_
double | pre_int_
double | pre_int_H2O_
double | pre_int_NH3_
bool | add_k_linked_ions_
std::map< String, LossIndex > | loss_db_
double | loss_H2O_ = 0
double | loss_NH3_ = 0
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

Generates theoretical spectra for cross-linked peptides.

The spectra this class generates are instances of the PeakSpectrum class. This class generates the same peak types as SimpleTSGXLMS and the interface is very similar, but it is more complex and slower. If the parameters add_metainfo and add_charges are set to true, it will generate a StringDataArray for String annotations of ion types and an IntegerDataArray for peak charges and add them to the DataArrays of the produced PeakSpectrum. The spectra from this class are mainly used for annotation of matched experimental spectra.

## Class Documentation

## ◆ OpenMS::TheoreticalSpectrumGeneratorXLMS::LossIndex

struct OpenMS::TheoreticalSpectrumGeneratorXLMS::LossIndex

Class Members
bool | has_H2O_loss |
bool | has_NH3_loss |

## Constructor & Destructor Documentation

## ◆ TheoreticalSpectrumGeneratorXLMS() [1/2]

TheoreticalSpectrumGeneratorXLMS | ( |  | ) |

default constructor

## ◆ TheoreticalSpectrumGeneratorXLMS() [2/2]

TheoreticalSpectrumGeneratorXLMS | ( | const TheoreticalSpectrumGeneratorXLMS & | source | ) |

copy constructor

## ◆ ~TheoreticalSpectrumGeneratorXLMS()

~TheoreticalSpectrumGeneratorXLMS | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ addKLinkedIonPeaks_()

virtual void addKLinkedIonPeaks_ | ( | PeakSpectrum & | spectrum,
|  | DataArrays::IntegerDataArray & | charges,
|  | DataArrays::StringDataArray & | ion_names,
|  | AASequence & | peptide,
|  | Size | link_pos,
|  | double | precursor_mass,
|  | bool | frag_alpha,
|  | int | charge
| ) |  | const

protected virtual

Adds one-residue-linked ion peaks, that are specific to XLMS.

These fragments consist of one whole peptide, the cross-linker and a part of the linked residue from the second peptide. The residue fragment on the linker is an internal ion from a y- and an a-fragmentation with the length of one residue. The function is called KLinked for now, but instead of K it is whatever the linker is attached to.

Parameters

  spectrum | The spectrum to which the peaks are added
  charges | A DataArray collecting the charges of the added peaks
  ion_names | A DataArray collecting the ion names of the added peaks
  peptide | The fragmented peptide
  link_pos | position of the linker on the fragmented peptide
  precursor_mass | The mass of the whole cross-link candidate or the precursor mass of the experimental MS2 spectrum.
  frag_alpha | True, if the fragmented peptide is the Alpha peptide. Used for ion-name annotation.
  charge | The charge of the ion

## ◆ addLinearIonLosses_()

virtual void addLinearIonLosses_ | ( | PeakSpectrum & | spectrum,
|  | DataArrays::IntegerDataArray & | charges,
|  | DataArrays::StringDataArray & | ion_names,
|  | double | mono_weight,
|  | Residue::ResidueType | res_type,
|  | Size | frag_index,
|  | double | intensity,
|  | int | charge,
|  | String | ion_type,
|  | LossIndex & | losses
| ) |  | const

protected virtual

Adds losses for a linear ion.

Parameters

  spectrum | The spectrum to which the new peak is added
  charges | A DataArray collecting the charges of the added peaks
  ion_names | A DataArray collecting the ion names of the added peaks
  mono_weight | monoisotopic mass of the current ion
  res_type | The ion type of the current ion
  frag_index | The index of the ion (fragmentation position)
  intensity |
  charge | The charge of the ion
  ion_type | Another cross-linking specific ion-type
  losses | a set of LossMasses with which to modify the current ion

## ◆ addLinearPeaks_()

virtual void addLinearPeaks_ | ( | PeakSpectrum & | spectrum,
|  | DataArrays::IntegerDataArray & | charges,
|  | DataArrays::StringDataArray & | ion_names,
|  | AASequence & | peptide,
|  | Size | link_pos,
|  | bool | frag_alpha,
|  | Residue::ResidueType | res_type,
|  | std::vector< LossIndex > & | forward_losses,
|  | std::vector< LossIndex > & | backward_losses,
|  | int | charge = `1`,
|  | Size | link_pos_2 = `0`
| ) |  | const

protected virtual

Adds cross-link-less ions of a specific ion type and charge to a spectrum and adds ion name and charge annotations to the DataArrays.

Parameters

  spectrum | The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it.
  charges | A DataArray collecting the charges of the added peaks
  ion_names | A DataArray collecting the ion names of the added peaks
  peptide | The peptide to fragment
  link_pos | The position of the cross-linker on the given peptide
  frag_alpha | True, if the fragmented peptide is the Alpha peptide. Used for ion-name annotation.
  res_type | The ion type of the added peaks
  forward_losses | vector of sets of losses generated by getForwardLosses_
  backward_losses | vector of sets of losses generated by getBackwardLosses_
  charge | The charge of the added peaks
  link_pos_2 | A second position for the linker, in case it is a loop link

## ◆ addPeak_()

virtual void addPeak_ | ( | PeakSpectrum & | spectrum,
|  | DataArrays::IntegerDataArray & | charges,
|  | DataArrays::StringDataArray & | ion_names,
|  | double | pos,
|  | double | intensity,
|  | Residue::ResidueType | res_type,
|  | Size | ion_index,
|  | int | charge,
|  | String | ion_type
| ) |  | const

protected virtual

Adds a single peak to a spectrum and its charge and ion name to the given DataArrays.

The ion_type is a string in this form: "alpha|xi", the first word can be either "alpha" or "beta" and indicates the fragmented peptide, the two letters at the end are either "ci" or "xi" for linear ion or cross-linked ion.

Parameters

  spectrum | The spectrum to which the new peak is added
  charges | A DataArray collecting the charges of the added peaks
  ion_names | A DataArray collecting the ion names of the added peaks
  pos |
  intensity |
  res_type | The ion type of the added peak
  ion_index | The index of the ion (fragmentation position)
  charge | The charge of the ion
  ion_type | Another cross-linking specific ion-type

## ◆ addPrecursorPeaks_()

virtual void addPrecursorPeaks_ | ( | PeakSpectrum & | spectrum,
|  | DataArrays::IntegerDataArray & | charges,
|  | DataArrays::StringDataArray & | ion_names,
|  | double | precursor_mass,
|  | int | charge
| ) |  | const

protected virtual

Adds precursor masses including neutral losses for the given charge and adds charge and ion name to the given DataArrays.

Parameters

  spectrum | The spectrum to which the peaks are added
  charges | A DataArray collecting the charges of the added peaks
  ion_names | A DataArray collecting the ion names of the added peaks
  precursor_mass | The mass of the uncharged precursor
  charge | The charge of the precursor

## ◆ addXLinkIonLosses_()

virtual void addXLinkIonLosses_ | ( | PeakSpectrum & | spectrum,
|  | DataArrays::IntegerDataArray & | charges,
|  | DataArrays::StringDataArray & | ion_names,
|  | double | mono_weight,
|  | double | intensity,
|  | int | charge,
|  | String | ion_name,
|  | LossIndex & | losses
| ) |  | const

protected virtual

Adds losses for a cross-linked ion.

Parameters

  spectrum | The spectrum to which the new peak is added
  charges | A DataArray collecting the charges of the added peaks
  ion_names | A DataArray collecting the ion names of the added peaks
  mono_weight | monoisotopic mass of the current ion
  res_type | The ion type of the current ion
  frag_index | The index of the ion (fragmentation position)
  intensity |
  charge | The charge of the ion
  ion_type | Another cross-linking specific ion-type
  losses | a set of LossMasses with which to modify the current ion

## ◆ addXLinkIonPeaks_() [1/2]

virtual void addXLinkIonPeaks_ | ( | PeakSpectrum & | spectrum,
|  | DataArrays::IntegerDataArray & | charges,
|  | DataArrays::StringDataArray & | ion_names,
|  | AASequence & | peptide,
|  | Size | link_pos,
|  | double | precursor_mass,
|  | bool | frag_alpha,
|  | Residue::ResidueType | res_type,
|  | std::vector< LossIndex > & | forward_losses,
|  | std::vector< LossIndex > & | backward_losses,
|  | int | charge,
|  | Size | link_pos_2 = `0`
| ) |  | const

protected virtual

Adds cross-linked ions of a specific ion type and charge to a spectrum and adds ion name and charge annotations to the DataArrays.

This version of the function is for mono-links and loop-links.

Parameters

  spectrum | The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it.
  charges | A DataArray collecting the charges of the added peaks
  ion_names | A DataArray collecting the ion names of the added peaks
  peptide | The peptide to fragment
  link_pos | The position of the cross-linker on the given peptide
  precursor_mass | The mass of the whole cross-link candidate or the precursor mass of the experimental MS2 spectrum.
  frag_alpha | True, if the fragmented peptide is the Alpha peptide. Used for ion-name annotation.
  res_type | The ion type of the added peaks
  forward_losses | vector of sets of losses generated by getForwardLosses_
  backward_losses | vector of sets of losses generated by getBackwardLosses_
  charge | The charge of the added peaks
  link_pos_2 | A second position for the linker, in case it is a loop link

## ◆ addXLinkIonPeaks_() [2/2]

virtual void addXLinkIonPeaks_ | ( | PeakSpectrum & | spectrum,
|  | DataArrays::IntegerDataArray & | charges,
|  | DataArrays::StringDataArray & | ion_names,
|  | OPXLDataStructs::ProteinProteinCrossLink & | crosslink,
|  | bool | frag_alpha,
|  | Residue::ResidueType | res_type,
|  | std::vector< LossIndex > & | forward_losses,
|  | std::vector< LossIndex > & | backward_losses,
|  | LossIndex & | losses_peptide2,
|  | int | charge
| ) |  | const

protected virtual

Adds cross-linked ions of a specific ion type and charge to a spectrum and adds ion name and charge annotations to the DataArrays.

This version of the function is for cross-linked peptide pairs.

Parameters

  spectrum | The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it.
  charges | A DataArray collecting the charges of the added peaks
  ion_names | A DataArray collecting the ion names of the added peaks
  crosslink | The ProteinProteinCrossLink to be fragmented
  link_pos | The position of the cross-linker on the given peptide
  precursor_mass | The mass of the whole cross-link candidate or the precursor mass of the experimental MS2 spectrum.
  frag_alpha | True, if the fragmented peptide is the Alpha peptide. Used for ion-name annotation.
  res_type | The ion type of the added peaks
  forward_losses | vector of sets of losses generated by getForwardLosses_ for the fragmented peptide
  backward_losses | vector of sets of losses generated by getBackwardLosses_ for the fragmented peptide
  losses_peptide2 | set of losses for the second, not fragmented peptide, e.g. last set from getForwardLosses_ for the second peptide
  charge | The charge of the added peaks

## ◆ getBackwardLosses_()

std::vector< LossIndex > getBackwardLosses_ | ( | AASequence & | peptide | ) | const

protected

Calculates sets of possible neutral losses for each position in the given peptide.

This function generates a vector of sets. Each set contains the possible neutral losses for a specific suffix of the peptide.

Parameters

  peptide | The peptide or ion for which to collect possible losses

## ◆ getForwardLosses_()

std::vector< LossIndex > getForwardLosses_ | ( | AASequence & | peptide | ) | const

protected

Calculates sets of possible neutral losses for each position in the given peptide.

This function generates a vector of sets. Each set contains the possible neutral losses for a specific prefix of the peptide.

Parameters

  peptide | The peptide or ion for which to collect possible losses

## ◆ getLinearIonSpectrum()

virtual void getLinearIonSpectrum | ( | PeakSpectrum & | spectrum,
|  | AASequence & | peptide,
|  | Size | link_pos,
|  | bool | frag_alpha,
|  | int | charge = `1`,
|  | Size | link_pos_2 = `0`
| ) |  | const

virtual

Generates fragment ions not containing the cross-linker for one peptide.

B-ions are generated from the beginning of the peptide up to the first linked position, y-ions are generated from the second linked position up the end of the peptide. If link_pos_2 is 0, a mono-link or cross-link is assumed and the second position is the same as the first position. For a loop-link two different positions can be set and link_pos_2 must be larger than link_pos. The generated ion types and other additional settings are determined by the tool parameters.

Parameters

  spectrum | The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it.
  peptide | The peptide to fragment
  link_pos | The position of the cross-linker on the given peptide
  frag_alpha | True, if the fragmented peptide is the Alpha peptide. Used for ion-name annotation.
  charge | The maximal charge of the ions
  link_pos_2 | A second position for the linker, in case it is a loop link

## ◆ getXLinkIonSpectrum() [1/2]

virtual void getXLinkIonSpectrum | ( | PeakSpectrum & | spectrum,
|  | AASequence & | peptide,
|  | Size | link_pos,
|  | double | precursor_mass,
|  | bool | frag_alpha,
|  | int | mincharge,
|  | int | maxcharge,
|  | Size | link_pos_2 = `0`
| ) |  | const

virtual

Generates fragment ions containing the cross-linker for one peptide.

B-ions are generated from the first linked position up to the end of the peptide, y-ions are generated from the beginning of the peptide up to the second linked position. If link_pos_2 is 0, a mono-link or cross-link is assumed and the second position is the same as the first position. For a loop-link two different positions can be set and link_pos_2 must be larger than link_pos. Since in the case of a cross-link a whole second peptide is attached to the other side of the cross-link, a precursor mass for the two peptides and the linker is needed. In the case of a loop link the precursor mass is the mass of the only peptide and the linker. Although this function is more general, currently it is mainly used for loop-links and mono-links, because residues in the second, unknown peptide cannot be considered for possible neutral losses. The generated ion types and other additional settings are determined by the tool parameters.

Parameters

  spectrum | The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it.
  peptide | The peptide to fragment
  link_pos | The position of the cross-linker on the given peptide
  precursor_mass | The mass of the whole cross-link candidate or the precursor mass of the experimental MS2 spectrum.
  frag_alpha | True, if the fragmented peptide is the Alpha peptide. Used for ion-name annotation.
  mincharge | The minimal charge of the ions
  maxcharge | The maximal charge of the ions, it should be the precursor charge and is used to generate precursor ion peaks
  link_pos_2 | A second position for the linker, in case it is a loop link

## ◆ getXLinkIonSpectrum() [2/2]

virtual void getXLinkIonSpectrum | ( | PeakSpectrum & | spectrum,
|  | OPXLDataStructs::ProteinProteinCrossLink & | crosslink,
|  | bool | frag_alpha,
|  | int | mincharge,
|  | int | maxcharge
| ) |  | const

virtual

Generates fragment ions containing the cross-linker for a pair of peptides.

B-ions are generated from the first linked position up to the end of the peptide, y-ions are generated from the beginning of the peptide up to the second linked position. This function generates neutral loss ions by considering both linked peptides. Only one of the peptides, decided by , is fragmented. This function is not suitable to generate fragments for mono-links or loop-links. This simplifies the function, but it has to be called twice to get all fragments of a peptide pair. The generated ion types and other additional settings are determined by the tool parameters.

Parameters

  spectrum | The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it.
  crosslink | ProteinProteinCrossLink to be fragmented
  link_pos | The position of the cross-linker on the given peptide
  precursor_mass | The mass of the whole cross-link candidate or the precursor mass of the experimental MS2 spectrum.
  frag_alpha | True, if the fragmented peptide is the Alpha peptide.
  mincharge | The minimal charge of the ions
  maxcharge | The maximal charge of the ions, it should be the precursor charge and is used to generate precursor ion peaks

## ◆ operator=()

TheoreticalSpectrumGeneratorXLMS& operator= | ( | const TheoreticalSpectrumGeneratorXLMS & | tsg | ) |

assignment operator

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override virtual

overwrite

Reimplemented from DefaultParamHandler.

## Member Data Documentation

## ◆ a_intensity_

double a_intensity_

protected

## ◆ add_a_ions_

bool add_a_ions_

protected

## ◆ add_abundant_immonium_ions_

bool add_abundant_immonium_ions_

protected

## ◆ add_b_ions_

bool add_b_ions_

protected

## ◆ add_c_ions_

bool add_c_ions_

protected

## ◆ add_charges_

bool add_charges_

protected

## ◆ add_first_prefix_ion_

bool add_first_prefix_ion_

protected

## ◆ add_isotopes_

bool add_isotopes_

protected

## ◆ add_k_linked_ions_

bool add_k_linked_ions_

protected

## ◆ add_losses_

bool add_losses_

protected

## ◆ add_metainfo_

bool add_metainfo_

protected

## ◆ add_precursor_peaks_

bool add_precursor_peaks_

protected

## ◆ add_x_ions_

bool add_x_ions_

protected

## ◆ add_y_ions_

bool add_y_ions_

protected

## ◆ add_z_ions_

bool add_z_ions_

protected

## ◆ b_intensity_

double b_intensity_

protected

## ◆ c_intensity_

double c_intensity_

protected

## ◆ loss_db_

std::map< String, LossIndex > loss_db_

protected

## ◆ loss_H2O_

double loss_H2O_ = 0

protected

## ◆ loss_NH3_

double loss_NH3_ = 0

protected

## ◆ max_isotope_

Int max_isotope_

protected

## ◆ pre_int_

double pre_int_

protected

## ◆ pre_int_H2O_

double pre_int_H2O_

protected

## ◆ pre_int_NH3_

double pre_int_NH3_

protected

## ◆ rel_loss_intensity_

double rel_loss_intensity_

protected

## ◆ x_intensity_

double x_intensity_

protected

## ◆ y_intensity_

double y_intensity_

protected

## ◆ z_intensity_

double z_intensity_

protected