| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
RawTandemMSSignalSimulation Class Reference
Simulation

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

`#include <OpenMS/SIMULATION/RawTandemMSSignalSimulation.h>`

Inheritance diagram for RawTandemMSSignalSimulation:

## Public Member Functions

RawTandemMSSignalSimulation & | operator= (const RawTandemMSSignalSimulation &source)
void | generateRawTandemSignals (const SimTypes::FeatureMapSim &, SimTypes::MSSimExperiment &, SimTypes::MSSimExperiment &)
Constructors and Destructors
| 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...
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

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)
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

SimTypes::MutableSimRandomNumberGeneratorPtr | rnd_gen_
| Random number generator. 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

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:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
status | string | disabled | disabled, precursor, MS^E | Create Tandem-MS scans?
tandem_mode | int | 0 | min: 0 max: 2 | Algorithm to generate the tandem-MS spectra. 0 - fixed intensities, 1 - SVC prediction (abundant/missing), 2 - SVR prediction of peak intensity
svm_model_set_file | string | examples/simulation/SvmModelSet.model |  | File containing the filenames of SVM Models for different charge variants
ionization_type | string | ESI | MALDI, ESI | Type of Ionization (MALDI or ESI)
Precursor:ms2_spectra_per_rt_bin | int | 5 | min: 1 | Number of allowed MS/MS spectra in a retention time bin.
Precursor:min_mz_peak_distance | float | 2.0 | min: 1.0e-04 | The 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 | float | 2.0 | min: 0.0 | All peaks within a mass window (in Th) of a selected peak are also selected for fragmentation.
Precursor:exclude_overlapping_peaks | string | false | true, false | If true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection.
Precursor:charge_filter | int list | [2, 3] | min: 1 max: 5 | Charges considered for MS2 fragmentation.
Precursor:Exclusion:use_dynamic_exclusion | string | false | true, false | If true dynamic exclusion is applied.
Precursor:Exclusion:exclusion_time | float | 100.0 | min: 0.0 | The time (in seconds) a feature is excluded.
Precursor:ProteinBasedInclusion:max_list_size | int | 1000 | min: 1 | The maximal number of precursors in the inclusion list.
Precursor:ProteinBasedInclusion:rt:min_rt | float | 960.0 | min: 0.0 | Minimal rt in seconds.
Precursor:ProteinBasedInclusion:rt:max_rt | float | 3840.0 | min: 0.0 | Maximal rt in seconds.
Precursor:ProteinBasedInclusion:rt:rt_step_size | float | 30.0 | min: 1.0 | rt step size in seconds.
Precursor:ProteinBasedInclusion:rt:rt_window_size | int | 100 | min: 1 | rt window size in seconds.
Precursor:ProteinBasedInclusion:thresholds:min_protein_id_probability | float | 0.95 | min: 0.0 max: 1.0 | Minimal protein probability for a protein to be considered identified.
Precursor:ProteinBasedInclusion:thresholds:min_pt_weight | float | 0.5 | min: 0.0 max: 1.0 | Minimal pt weight of a precursor
Precursor:ProteinBasedInclusion:thresholds:min_mz | float | 500.0 | min: 0.0 | Minimal mz to be considered in protein based LP formulation.
Precursor:ProteinBasedInclusion:thresholds:max_mz | float | 5000.0 | min: 0.0 | Minimal mz to be considered in protein based LP formulation.
Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule | string | false | true, false | Use peptide rule instead of minimal protein id probability
Precursor:ProteinBasedInclusion:thresholds:min_peptide_ids | int | 2 | min: 1 | If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id
Precursor:ProteinBasedInclusion:thresholds:min_peptide_probability | float | 0.95 | min: 0.0 max: 1.0 | If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified
MS_E:add_single_spectra | string | false | true, false | If 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 | string | none | none, coarse, fine | Model 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 | int | 2 |  | Defines the maximal isotopic peak which is added if 'isotope_model' is 'coarse'
TandemSim:Simple:max_isotope_probability | float | 0.05 |  | Defines the maximal isotopic probability to cover if 'isotope_model' is 'fine'
TandemSim:Simple:add_metainfo | string | false | true, false | Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++
TandemSim:Simple:add_losses | string | false | true, false | Adds common losses to those ion expect to have them, only water and ammonia loss is considered
TandemSim:Simple:sort_by_position | string | true | true, false | Sort output by position
TandemSim:Simple:add_precursor_peaks | string | false | true, false | Adds peaks of the unfragmented precursor ion to the spectrum
TandemSim:Simple:add_all_precursor_charges | string | false | true, false | Adds precursor peaks with all charges in the given range
TandemSim:Simple:add_abundant_immonium_ions | string | false | true, false | Add most abundant immonium ions
TandemSim:Simple:add_first_prefix_ion | string | false | true, false | If set to true e.g. b1 ions are added
TandemSim:Simple:add_y_ions | string | true | true, false | Add peaks of y-ions to the spectrum
TandemSim:Simple:add_b_ions | string | true | true, false | Add peaks of b-ions to the spectrum
TandemSim:Simple:add_a_ions | string | false | true, false | Add peaks of a-ions to the spectrum
TandemSim:Simple:add_c_ions | string | false | true, false | Add peaks of c-ions to the spectrum
TandemSim:Simple:add_x_ions | string | false | true, false | Add peaks of x-ions to the spectrum
TandemSim:Simple:add_z_ions | string | false | true, false | Add peaks of z-ions to the spectrum
TandemSim:Simple:y_intensity | float | 1.0 |  | Intensity of the y-ions
TandemSim:Simple:b_intensity | float | 1.0 |  | Intensity of the b-ions
TandemSim:Simple:a_intensity | float | 1.0 |  | Intensity of the a-ions
TandemSim:Simple:c_intensity | float | 1.0 |  | Intensity of the c-ions
TandemSim:Simple:x_intensity | float | 1.0 |  | Intensity of the x-ions
TandemSim:Simple:z_intensity | float | 1.0 |  | Intensity of the z-ions
TandemSim:Simple:relative_loss_intensity | float | 0.1 |  | Intensity of loss ions, in relation to the intact ion intensity
TandemSim:Simple:precursor_intensity | float | 1.0 |  | Intensity of the precursor peak
TandemSim:Simple:precursor_H2O_intensity | float | 1.0 |  | Intensity of the H2O loss peak of the precursor
TandemSim:Simple:precursor_NH3_intensity | float | 1.0 |  | Intensity of the NH3 loss peak of the precursor
TandemSim:SVM:add_isotopes | string | false | true, false | If set to 1 isotope peaks of the product ion peaks are added
TandemSim:SVM:max_isotope | int | 2 |  | Defines the maximal isotopic peak which is added, add_isotopes must be set to 1
TandemSim:SVM:add_metainfo | string | false | true, false | Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++
TandemSim:SVM:add_first_prefix_ion | string | false | true, false | If set to true e.g. b1 ions are added
TandemSim:SVM:hide_y_ions | string | false | true, false | Add peaks of y-ions to the spectrum
TandemSim:SVM:hide_y2_ions | string | false | true, false | Add peaks of y-ions to the spectrum
TandemSim:SVM:hide_b_ions | string | false | true, false | Add peaks of b-ions to the spectrum
TandemSim:SVM:hide_b2_ions | string | false | true, false | Add peaks of b-ions to the spectrum
TandemSim:SVM:hide_a_ions | string | false | true, false | Add peaks of a-ions to the spectrum
TandemSim:SVM:hide_c_ions | string | false | true, false | Add peaks of c-ions to the spectrum
TandemSim:SVM:hide_x_ions | string | false | true, false | Add peaks of x-ions to the spectrum
TandemSim:SVM:hide_z_ions | string | false | true, false | Add peaks of z-ions to the spectrum
TandemSim:SVM:hide_losses | string | false | true, false | Adds common losses to those ion expect to have them, only water and ammonia loss is considered
TandemSim:SVM:y_intensity | float | 1.0 |  | Intensity of the y-ions
TandemSim:SVM:b_intensity | float | 1.0 |  | Intensity of the b-ions
TandemSim:SVM:a_intensity | float | 1.0 |  | Intensity of the a-ions
TandemSim:SVM:c_intensity | float | 1.0 |  | Intensity of the c-ions
TandemSim:SVM:x_intensity | float | 1.0 |  | Intensity of the x-ions
TandemSim:SVM:z_intensity | float | 1.0 |  | Intensity of the z-ions
TandemSim:SVM:relative_loss_intensity | float | 0.1 |  | 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]

RawTandemMSSignalSimulation | ( |  | ) |

Default constructor (hidden)

## ◆ RawTandemMSSignalSimulation() [2/3]

RawTandemMSSignalSimulation | ( | SimTypes::MutableSimRandomNumberGeneratorPtr | rng | ) |

explicit

Constructor taking a random generator.

## ◆ RawTandemMSSignalSimulation() [3/3]

RawTandemMSSignalSimulation | ( | const RawTandemMSSignalSimulation & | source | ) |

Copy constructor.

## ◆ ~RawTandemMSSignalSimulation()

~RawTandemMSSignalSimulation | ( |  | ) |

override

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=()

RawTandemMSSignalSimulation& operator= | ( | const RawTandemMSSignalSimulation & | source | ) |

## Member Data Documentation

## ◆ rnd_gen_

SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen_

protected

Random number generator.