OpenMS
RawTandemMSSignalSimulation Class Reference

Simulates tandem MS signals for a given set of peptides. More...

#include <OpenMS/SIMULATION/RawTandemMSSignalSimulation.h>

Inheritance diagram for RawTandemMSSignalSimulation:
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Collaboration diagram for RawTandemMSSignalSimulation:
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Constructors and Destructors

SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen_
 Random number generator. More...
 
 RawTandemMSSignalSimulation ()
 Default constructor (hidden) More...
 
 RawTandemMSSignalSimulation (SimTypes::MutableSimRandomNumberGeneratorPtr rng)
 Constructor taking a random generator. More...
 
 RawTandemMSSignalSimulation (const RawTandemMSSignalSimulation &source)
 Copy constructor. More...
 
 ~RawTandemMSSignalSimulation () override
 Destructor. More...
 
RawTandemMSSignalSimulationoperator= (const RawTandemMSSignalSimulation &source)
 
void generateRawTandemSignals (const SimTypes::FeatureMapSim &, SimTypes::MSSimExperiment &, SimTypes::MSSimExperiment &)
 
void initParam_ ()
 initialize param_ class More...
 
void generateMSESpectra_ (const SimTypes::FeatureMapSim &features, const SimTypes::MSSimExperiment &experiment, SimTypes::MSSimExperiment &ms2)
 
void generatePrecursorSpectra_ (const SimTypes::FeatureMapSim &features, const SimTypes::MSSimExperiment &experiment, SimTypes::MSSimExperiment &ms2)
 

Additional Inherited Members

- 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...
 
DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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 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 Member Functions inherited from DefaultParamHandler
virtual void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. 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< Stringsubsections_
 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

Simulates tandem MS signals for a given set of peptides.

Simulates tandem MS signals for a given set of peptides, with charge annotation, given detectabilities, predicted retention times and charge values.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
status stringdisabled disabled, precursor, MS^ECreate Tandem-MS scans?
tandem_mode int0 min: 0 max: 2Algorithm to generate the tandem-MS spectra. 0 - fixed intensities, 1 - SVC prediction (abundant/missing), 2 - SVR prediction of peak intensity
svm_model_set_file stringSIMULATION/SvmModelSet.model  File containing the filenames of SVM Models for different charge variants
ionization_type stringESI MALDI, ESIType of Ionization (MALDI or ESI)
Precursor:ms2_spectra_per_rt_bin int5 min: 1Number of allowed MS/MS spectra in a retention time bin.
Precursor:min_mz_peak_distance float2.0 min: 1.0e-04The minimal distance (in Th) between two peaks for concurrent selection for fragmentation. Also used to define the m/z width of an exclusion window (distance +/- from m/z of precursor). If you set this lower than the isotopic envelope of a peptide, you might get multiple fragment spectra pointing to the same precursor.
Precursor:mz_isolation_window float2.0 min: 0.0All peaks within a mass window (in Th) of a selected peak are also selected for fragmentation.
Precursor:exclude_overlapping_peaks stringfalse true, falseIf true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection.
Precursor:charge_filter int list[2, 3] min: 1 max: 5Charges considered for MS2 fragmentation.
Precursor:Exclusion:use_dynamic_exclusion stringfalse true, falseIf true dynamic exclusion is applied.
Precursor:Exclusion:exclusion_time float100.0 min: 0.0The time (in seconds) a feature is excluded.
Precursor:ProteinBasedInclusion:max_list_size int1000 min: 1The maximal number of precursors in the inclusion list.
Precursor:ProteinBasedInclusion:rt:min_rt float960.0 min: 0.0Minimal rt in seconds.
Precursor:ProteinBasedInclusion:rt:max_rt float3840.0 min: 0.0Maximal rt in seconds.
Precursor:ProteinBasedInclusion:rt:rt_step_size float30.0 min: 1.0rt step size in seconds.
Precursor:ProteinBasedInclusion:rt:rt_window_size int100 min: 1rt window size in seconds.
Precursor:ProteinBasedInclusion:thresholds:min_protein_id_probability float0.95 min: 0.0 max: 1.0Minimal protein probability for a protein to be considered identified.
Precursor:ProteinBasedInclusion:thresholds:min_pt_weight float0.5 min: 0.0 max: 1.0Minimal pt weight of a precursor
Precursor:ProteinBasedInclusion:thresholds:min_mz float500.0 min: 0.0Minimal mz to be considered in protein based LP formulation.
Precursor:ProteinBasedInclusion:thresholds:max_mz float5000.0 min: 0.0Minimal mz to be considered in protein based LP formulation.
Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule stringfalse true, falseUse peptide rule instead of minimal protein id probability
Precursor:ProteinBasedInclusion:thresholds:min_peptide_ids int2 min: 1If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id
Precursor:ProteinBasedInclusion:thresholds:min_peptide_probability float0.95 min: 0.0 max: 1.0If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified
MS_E:add_single_spectra stringfalse true, falseIf true, the MS2 spectra for each peptide signal are included in the output (might be a lot). They will have a meta value 'MSE_DebugSpectrum' attached, so they can be filtered out. Native MS_E spectra will have 'MSE_Spectrum' instead.
TandemSim:Simple:isotope_model stringnone none, coarse, fineModel to use for isotopic peaks ('none' means no isotopic peaks are added, 'coarse' adds isotopic peaks in unit mass distance, 'fine' uses the hyperfine isotopic generator to add accurate isotopic peaks. Note that adding isotopic peaks is very slow.
TandemSim:Simple:max_isotope int2  Defines the maximal isotopic peak which is added if 'isotope_model' is 'coarse'
TandemSim:Simple:max_isotope_probability float0.05  Defines the maximal isotopic probability to cover if 'isotope_model' is 'fine'
TandemSim:Simple:add_metainfo stringfalse true, falseAdds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++
TandemSim:Simple:add_losses stringfalse true, falseAdds common losses to those ion expect to have them, only water and ammonia loss is considered
TandemSim:Simple:sort_by_position stringtrue true, falseSort output by position
TandemSim:Simple:add_precursor_peaks stringfalse true, falseAdds peaks of the unfragmented precursor ion to the spectrum
TandemSim:Simple:add_all_precursor_charges stringfalse true, falseAdds precursor peaks with all charges in the given range
TandemSim:Simple:add_abundant_immonium_ions stringfalse true, falseAdd most abundant immonium ions (for Proline, Cystein, Iso/Leucine, Histidin, Phenylalanin, Tyrosine, Tryptophan)
TandemSim:Simple:add_first_prefix_ion stringfalse true, falseIf set to true e.g. b1 ions are added
TandemSim:Simple:add_y_ions stringtrue true, falseAdd peaks of y-ions to the spectrum
TandemSim:Simple:add_b_ions stringtrue true, falseAdd peaks of b-ions to the spectrum
TandemSim:Simple:add_a_ions stringfalse true, falseAdd peaks of a-ions to the spectrum
TandemSim:Simple:add_c_ions stringfalse true, falseAdd peaks of c-ions to the spectrum
TandemSim:Simple:add_x_ions stringfalse true, falseAdd peaks of x-ions to the spectrum
TandemSim:Simple:add_z_ions stringfalse true, falseAdd peaks of z-ions to the spectrum
TandemSim:Simple:y_intensity float1.0 min: 0.0Intensity of the y-ions
TandemSim:Simple:b_intensity float1.0 min: 0.0Intensity of the b-ions
TandemSim:Simple:a_intensity float1.0 min: 0.0Intensity of the a-ions
TandemSim:Simple:c_intensity float1.0 min: 0.0Intensity of the c-ions
TandemSim:Simple:x_intensity float1.0 min: 0.0Intensity of the x-ions
TandemSim:Simple:z_intensity float1.0 min: 0.0Intensity of the z-ions
TandemSim:Simple:relative_loss_intensity float0.1 min: 0.0 max: 1.0Intensity of loss ions, in relation to the intact ion intensity
TandemSim:Simple:precursor_intensity float1.0 min: 0.0Intensity of the precursor peak
TandemSim:Simple:precursor_H2O_intensity float1.0 min: 0.0Intensity of the H2O loss peak of the precursor
TandemSim:Simple:precursor_NH3_intensity float1.0 min: 0.0Intensity of the NH3 loss peak of the precursor
TandemSim:SVM:add_isotopes stringfalse true, falseIf set to 1 isotope peaks of the product ion peaks are added
TandemSim:SVM:max_isotope int2  Defines the maximal isotopic peak which is added, add_isotopes must be set to 1
TandemSim:SVM:add_metainfo stringfalse true, falseAdds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++
TandemSim:SVM:add_first_prefix_ion stringfalse true, falseIf set to true e.g. b1 ions are added
TandemSim:SVM:hide_y_ions stringfalse true, falseAdd peaks of y-ions to the spectrum
TandemSim:SVM:hide_y2_ions stringfalse true, falseAdd peaks of y-ions to the spectrum
TandemSim:SVM:hide_b_ions stringfalse true, falseAdd peaks of b-ions to the spectrum
TandemSim:SVM:hide_b2_ions stringfalse true, falseAdd peaks of b-ions to the spectrum
TandemSim:SVM:hide_a_ions stringfalse true, falseAdd peaks of a-ions to the spectrum
TandemSim:SVM:hide_c_ions stringfalse true, falseAdd peaks of c-ions to the spectrum
TandemSim:SVM:hide_x_ions stringfalse true, falseAdd peaks of x-ions to the spectrum
TandemSim:SVM:hide_z_ions stringfalse true, falseAdd peaks of z-ions to the spectrum
TandemSim:SVM:hide_losses stringfalse true, falseAdds common losses to those ion expect to have them, only water and ammonia loss is considered
TandemSim:SVM:y_intensity float1.0  Intensity of the y-ions
TandemSim:SVM:b_intensity float1.0  Intensity of the b-ions
TandemSim:SVM:a_intensity float1.0  Intensity of the a-ions
TandemSim:SVM:c_intensity float1.0  Intensity of the c-ions
TandemSim:SVM:x_intensity float1.0  Intensity of the x-ions
TandemSim:SVM:z_intensity float1.0  Intensity of the z-ions
TandemSim:SVM:relative_loss_intensity float0.1  Intensity of loss ions, in relation to the intact ion intensity

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

Constructor & Destructor Documentation

◆ RawTandemMSSignalSimulation() [1/3]

Default constructor (hidden)

◆ RawTandemMSSignalSimulation() [2/3]

Constructor taking a random generator.

◆ RawTandemMSSignalSimulation() [3/3]

Copy constructor.

◆ ~RawTandemMSSignalSimulation()

Destructor.

Member Function Documentation

◆ generateMSESpectra_()

void generateMSESpectra_ ( const SimTypes::FeatureMapSim features,
const SimTypes::MSSimExperiment experiment,
SimTypes::MSSimExperiment ms2 
)
protected

◆ generatePrecursorSpectra_()

void generatePrecursorSpectra_ ( const SimTypes::FeatureMapSim features,
const SimTypes::MSSimExperiment experiment,
SimTypes::MSSimExperiment ms2 
)
protected

◆ generateRawTandemSignals()

void generateRawTandemSignals ( const SimTypes::FeatureMapSim ,
SimTypes::MSSimExperiment ,
SimTypes::MSSimExperiment  
)

◆ initParam_()

void initParam_ ( )
protected

initialize param_ class

◆ operator=()

Member Data Documentation

◆ rnd_gen_

Random number generator.