| OpenMS 2.5.0

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

Central class for simulation of mass spectrometry experiments. More...

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

Inheritance diagram for MSSim:

## Public Member Functions

void | simulate (SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen, SimTypes::SampleChannels &peptides)
| General purpose function to simulate a mass spectrometry run. More...
const SimTypes::MSSimExperiment & | getExperiment () const
| Access the simulated experiment. More...
const SimTypes::FeatureMapSim & | getSimulatedFeatures () const
| Access the simulated features. More...
ConsensusMap & | getChargeConsensus ()
| Access the charge consensus map of simulated features. More...
const SimTypes::FeatureMapSim & | getContaminants () const
| Access the contaminants feature map of simulated features. More...
ConsensusMap & | getLabelingConsensus ()
| Access the labeling consensus map of simulated features. More...
const SimTypes::MSSimExperiment & | getPeakMap () const
| Access the picked (centroided) experiment. More...
void | getIdentifications (std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides) const
| Access the simulated identifications (proteins and peptides) More...
void | getMS2Identifications (std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides) const
| Access the simulated MS2 identifications (proteins and peptides) More...
void | getFeatureIdentifications (std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides) const
| Access the simulated identifications (proteins and peptides) from feature annotations. More...
Param | getParameters () const
| Returns the default parameters for simulation including the labeling technique with name `labeling_name`. More...
Constructors and Destructors
| MSSim ()
| Default constructor. More...
| ~MSSim () 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...
Public Member Functions inherited from ProgressLogger
| ProgressLogger ()
| Constructor. More...
| ~ProgressLogger ()
| Destructor. More...
| ProgressLogger (const ProgressLogger &other)
| Copy constructor. More...
ProgressLogger & | operator= (const ProgressLogger &other)
| Assignment Operator. More...
void | setLogType (LogType type) const
| Sets the progress log that should be used. The default type is NONE! More...
LogType | getLogType () const
| Returns the type of progress log being used. More...
void | startProgress (SignedSize begin, SignedSize end, const String &label) const
| Initializes the progress display. More...
void | setProgress (SignedSize value) const
| Sets the current progress. More...
void | endProgress () const
| Ends the progress display. More...
void | nextProgress () const
| increment progress by 1 (according to range begin-end) More...

## Protected Member Functions

void | syncParams_ (Param &p, bool to_outer)
| handle global params More...
void | createFeatureMap_ (const SimTypes::SampleProteins &peptides, SimTypes::FeatureMapSim &features, Size map_index)
| Convert a list of peptides with given abundance values into a FeatureMap. More...
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...

## Private Attributes

SimTypes::MSSimExperiment | experiment_
| Holds the simulated data. More...
SimTypes::MSSimExperiment | peak_map_
| Holds the ground-truth on generated peaks positions and intensities. More...
SimTypes::FeatureMapSimVector | feature_maps_
| Holds the ground-truth on generated features. More...
ConsensusMap | consensus_map_
| Holds consensus ground-truth about the charge associations. More...
SimTypes::FeatureMapSim | contaminants_map_
| Holds the ground-truth on generated contaminants. More...
BaseLabeler * | labeler_
| Labeling functionality. More...

## Additional Inherited Members

Public Types inherited from ProgressLogger
enum | LogType { CMD, GUI, NONE }
| Possible log types. More...
Static Protected Member Functions inherited from ProgressLogger
static String | logTypeToFactoryName_ (LogType type)
| Return the name of the factory product used for this log type. 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...
Protected Attributes inherited from ProgressLogger
LogType | type_
time_t | last_invoke_
ProgressLoggerImpl * | current_logger_
Static Protected Attributes inherited from ProgressLogger
static int | recursion_depth_

## Detailed Description

Central class for simulation of mass spectrometry experiments.

This implementation is an extended and rewritten version of the concepts and ideas presented in:

Ole Schulz-Trieglaff, Nico Pfeifer, Clemens Gropl, Oliver Kohlbacher, and Knut Reinert.
LC-MSsim - A simulation software for liquid chromatography mass spectrometry data.
BMC Bioinformatics 9:423, 2008.

Parameters of this class are:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
Digestion:enzyme | string | Trypsin | PepsinA, Alpha-lytic protease, 2-iodobenzoate, Asp-N, Chymotrypsin, iodosobenzoate, Lys-C, staphylococcal protease/D, proline-endopeptidase/HKR, Lys-N, TrypChymo, Formic_acid, Trypsin/P, V8-DE, V8-E, Trypsin, CNBr, Lys-C/P, Asp-N_ambic, Asp-N/B, leukocyte elastase, Chymotrypsin/P, proline endopeptidase, Arg-C, Arg-C/P, glutamyl endopeptidase, PepsinA + P, Glu-C+P, Clostripain/P, cyanogen-bromide, elastase-trypsin-chymotrypsin, no cleavage, unspecific cleavage | Enzyme to use for digestion (select 'no cleavage' to skip digestion)
Digestion:model | string | naive | trained, naive | The cleavage model to use for digestion. 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u).
Digestion:min_peptide_length | int | 3 | min: 1 | Minimum peptide length after digestion (shorter ones will be discarded)
Digestion:model_trained:threshold | float | 0.5 | min: -2.0 max: 4.0 | Model threshold for calling a cleavage. Higher values increase the number of cleavages. -2 will give no cleavages, +4 almost full cleavage.
Digestion:model_naive:missed_cleavages | int | 1 | min: 0 | Maximum number of missed cleavages considered. All possible resulting peptides will be created.
RT:rt_column | string | HPLC | none, HPLC, CE | Modelling of an RT or CE column
RT:auto_scale | string | true | true, false | Scale predicted RT's/MT's to given 'total_gradient_time'? If 'true', for CE this means that 'CE:lenght_d', 'CE:length_total', 'CE:voltage' have no influence.
RT:total_gradient_time | float | 2500.0 | min: 1.0e-05 | The duration [s] of the gradient.
RT:sampling_rate | float | 2.0 | min: 0.01 max: 60.0 | Time interval [s] between consecutive scans
RT:scan_window:min | float | 500.0 | min: 0.0 | Start of RT Scan Window [s]
RT:scan_window:max | float | 1500.0 | min: 1.0 | End of RT Scan Window [s]
RT:variation:feature_stddev | int | 3 |  | Standard deviation of shift in retention time [s] from predicted model (applied to every single feature independently)
RT:variation:affine_offset | int | 0 |  | Global offset in retention time [s] from predicted model
RT:variation:affine_scale | int | 1 |  | Global scaling in retention time from predicted model
RT:column_condition:distortion | int | 0 | min: 0 max: 10 | Distortion of the elution profiles. Good presets are 0 for a perfect elution profile, 1 for a slightly distorted elution profile etc... For trapping instruments (e.g. Orbitrap) distortion should be >4.
RT:profile_shape:width:value | float | 9.0 | min: 0.0 | Width of the Exponential Gaussian Hybrid distribution shape of the elution profile. This does not correspond directly to the width in [s].
RT:profile_shape:width:variance | float | 1.6 | min: 0.0 | Random component of the width (set to 0 to disable randomness), i.e. scale parameter for the lorentzian variation of the variance (Note: The scale parameter has to be >= 0).
RT:profile_shape:skewness:value | float | 0.1 |  | Asymmetric component of the EGH. Higher absolute(!) values lead to more skewness (negative values cause fronting, positive values cause tailing). Tau parameter of the EGH, i.e. time constant of the exponential decay of the Exponential Gaussian Hybrid distribution shape of the elution profile.
RT:profile_shape:skewness:variance | float | 0.3 | min: 0.0 | Random component of skewness (set to 0 to disable randomness), i.e. scale parameter for the lorentzian variation of the time constant (Note: The scale parameter has to be > 0).
RT:HPLC:model_file | string | examples/simulation/RTPredict.model |  | SVM model for retention time prediction
RT:CE:pH | float | 3.0 | min: 0.0 max: 14.0 | pH of buffer
RT:CE:alpha | float | 0.5 | min: 0.0 max: 1.0 | Exponent Alpha used to calculate mobility
RT:CE:mu_eo | float | 0.0 | min: 0.0 max: 5.0 | Electroosmotic flow
RT:CE:lenght_d | float | 70.0 | min: 0.0 max: 1000.0 | Length of capillary [cm] from injection site to MS
RT:CE:length_total | float | 75.0 | min: 0.0 max: 1000.0 | Total length of capillary [cm]
RT:CE:voltage | float | 1000.0 | min: 0.0 | Voltage applied to capillary
Detectability:dt_simulation_on | string | false | true, false | Modelling detectibility enabled? This can serve as a filter to remove peptides which ionize badly, thus reducing peptide count
Detectability:min_detect | float | 0.5 |  | Minimum peptide detectability accepted. Peptides with a lower score will be removed
Detectability:dt_model_file | string | examples/simulation/DTPredict.model |  | SVM model for peptide detectability prediction
Ionization:esi:ionized_residues | string list | [Arg, Lys, His] | Ala, Cys, Asp, Glu, Phe, Gly, His, Ile, Lys, Leu, Met, Asn, Pro, Gln, Arg, Sec, Ser, Thr, Val, Trp, Tyr | List of residues (as three letter code) that will be considered during ES ionization. The N-term is always assumed to carry a charge. This parameter will be ignored during MALDI ionization
Ionization:esi:charge_impurity | string list | [H+:1] |  | List of charged ions that contribute to charge with weight of occurrence (their sum is scaled to 1 internally), e.g. ['H:1'] or ['H:0.7' 'Na:0.3'], ['H:4' 'Na:1'] (which internally translates to ['H:0.8' 'Na:0.2'])
Ionization:esi:max_impurity_set_size | int | 3 |  | Maximal @#combinations of charge impurities allowed (each generating one feature) per charge state. E.g. assuming charge=3 and this parameter is 2, then we could choose to allow '3H+, 2H+Na+' features (given a certain 'charge_impurity' constraints), but no '3H+, 2H+Na+, 3Na+'
Ionization:esi:ionization_probability | float | 0.8 |  | Probability for the binomial distribution of the ESI charge states
Ionization:maldi:ionization_probabilities | float list | [0.9, 0.1, 0.0] |  | List of probabilities for different charge states (starting at charge=1, 2, ...) during MALDI ionization (the list must sum up to 1.0)
Ionization:mz:lower_measurement_limit | float | 200.0 | min: 0.0 | Lower m/z detector limit
Ionization:mz:upper_measurement_limit | float | 1200.0 | min: 0.0 | Upper m/z detector limit
RawSignal:enabled | string | true | true, false | Enable RAW signal simulation? (select 'false' if you only need feature-maps)
RawSignal:peak_shape | string | Gaussian | Gaussian, Lorentzian | Peak Shape used around each isotope peak (be aware that the area under the curve is constant for both types, but the maximal height will differ (~ 2:3 = Lorentz:Gaussian) due to the wider base of the Lorentzian
RawSignal:resolution:value | int | 50000 |  | Instrument resolution at 400 Th
RawSignal:resolution:type | string | linear | constant, linear, sqrt | How does resolution change with increasing m/z?! QTOFs usually show 'constant' behavior, FTs have linear degradation, and on Orbitraps the resolution decreases with square root of mass
RawSignal:baseline:scaling | float | 0.0 | min: 0.0 | Scale of baseline. Set to 0 to disable simulation of baseline
RawSignal:baseline:shape | float | 0.5 | min: 0.0 | The baseline is modeled by an exponential probability density function (pdf) with f(x) = shape*e^(- shape*x)
RawSignal:mz:sampling_points | int | 3 | min: 2 | Number of raw data points per FWHM of the peak
RawSignal:contaminants:file | string | examples/simulation/contaminants.csv |  | Contaminants file with sum formula and absolute RT interval. See 'OpenMS/examples/simulation/contaminants.txt' for details
RawSignal:variation:mz:error_mean | float | 0.0 |  | Average systematic m/z error (in Da)
RawSignal:variation:mz:error_stddev | float | 0.0 |  | Standard deviation for m/z errors. Set to 0 to disable simulation of m/z errors
RawSignal:variation:intensity:scale | float | 100.0 | min: 0.0 | Constant scale factor of the feature intensity. Set to 1.0 to get the real intensity values provided in the FASTA file
RawSignal:variation:intensity:scale_stddev | float | 0.0 | min: 0.0 | Standard deviation of peak intensity (relative to the scaled peak height). Set to 0 to get simple rescaled intensities
RawSignal:noise:shot:rate | float | 0.0 | min: 0.0 | Poisson rate of shot noise per unit m/z (random peaks in m/z, where the number of peaks per unit m/z follows a Poisson distribution). Set this to 0 to disable simulation of shot noise
RawSignal:noise:shot:intensity-mean | float | 1.0 |  | Shot noise intensity mean (exponentially distributed with given mean)
RawSignal:noise:white:mean | float | 0.0 |  | Mean value of white noise (Gaussian) being added to each *measured* signal intensity
RawSignal:noise:white:stddev | float | 0.0 |  | Standard deviation of white noise being added to each *measured* signal intensity
RawSignal:noise:detector:mean | float | 0.0 |  | Mean intensity value of the detector noise (Gaussian distribution)
RawSignal:noise:detector:stddev | float | 0.0 |  | Standard deviation of the detector noise (Gaussian distribution)
RawTandemSignal:status | string | disabled | disabled, precursor, MS^E | Create Tandem-MS scans?
RawTandemSignal: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
RawTandemSignal:svm_model_set_file | string | examples/simulation/SvmModelSet.model |  | File containing the filenames of SVM Models for different charge variants
RawTandemSignal:Precursor:ms2_spectra_per_rt_bin | int | 5 | min: 1 | Number of allowed MS/MS spectra in a retention time bin.
RawTandemSignal: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.
RawTandemSignal: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.
RawTandemSignal:Precursor:exclude_overlapping_peaks | string | false | true, false | If true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection.
RawTandemSignal:Precursor:charge_filter | int list | [2, 3] | min: 1 max: 5 | Charges considered for MS2 fragmentation.
RawTandemSignal:Precursor:Exclusion:use_dynamic_exclusion | string | false | true, false | If true dynamic exclusion is applied.
RawTandemSignal:Precursor:Exclusion:exclusion_time | float | 100.0 | min: 0.0 | The time (in seconds) a feature is excluded.
RawTandemSignal:Precursor:ProteinBasedInclusion:max_list_size | int | 1000 | min: 1 | The maximal number of precursors in the inclusion list.
RawTandemSignal:Precursor:ProteinBasedInclusion:rt:min_rt | float | 960.0 | min: 0.0 | Minimal rt in seconds.
RawTandemSignal:Precursor:ProteinBasedInclusion:rt:max_rt | float | 3840.0 | min: 0.0 | Maximal rt in seconds.
RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_step_size | float | 30.0 | min: 1.0 | rt step size in seconds.
RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_window_size | int | 100 | min: 1 | rt window size in seconds.
RawTandemSignal: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.
RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_pt_weight | float | 0.5 | min: 0.0 max: 1.0 | Minimal pt weight of a precursor
RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_mz | float | 500.0 | min: 0.0 | Minimal mz to be considered in protein based LP formulation.
RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:max_mz | float | 5000.0 | min: 0.0 | Minimal mz to be considered in protein based LP formulation.
RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule | string | false | true, false | Use peptide rule instead of minimal protein id probability
RawTandemSignal: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
RawTandemSignal: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
RawTandemSignal: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.
RawTandemSignal: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.
RawTandemSignal:TandemSim:Simple:max_isotope | int | 2 |  | Defines the maximal isotopic peak which is added if 'isotope_model' is 'coarse'
RawTandemSignal:TandemSim:Simple:max_isotope_probability | float | 0.05 |  | Defines the maximal isotopic probability to cover if 'isotope_model' is 'fine'
RawTandemSignal:TandemSim:Simple:add_metainfo | string | false | true, false | Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++
RawTandemSignal: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
RawTandemSignal:TandemSim:Simple:sort_by_position | string | true | true, false | Sort output by position
RawTandemSignal:TandemSim:Simple:add_precursor_peaks | string | false | true, false | Adds peaks of the unfragmented precursor ion to the spectrum
RawTandemSignal:TandemSim:Simple:add_all_precursor_charges | string | false | true, false | Adds precursor peaks with all charges in the given range
RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions | string | false | true, false | Add most abundant immonium ions
RawTandemSignal:TandemSim:Simple:add_first_prefix_ion | string | false | true, false | If set to true e.g. b1 ions are added
RawTandemSignal:TandemSim:Simple:add_y_ions | string | true | true, false | Add peaks of y-ions to the spectrum
RawTandemSignal:TandemSim:Simple:add_b_ions | string | true | true, false | Add peaks of b-ions to the spectrum
RawTandemSignal:TandemSim:Simple:add_a_ions | string | false | true, false | Add peaks of a-ions to the spectrum
RawTandemSignal:TandemSim:Simple:add_c_ions | string | false | true, false | Add peaks of c-ions to the spectrum
RawTandemSignal:TandemSim:Simple:add_x_ions | string | false | true, false | Add peaks of x-ions to the spectrum
RawTandemSignal:TandemSim:Simple:add_z_ions | string | false | true, false | Add peaks of z-ions to the spectrum
RawTandemSignal:TandemSim:Simple:y_intensity | float | 1.0 |  | Intensity of the y-ions
RawTandemSignal:TandemSim:Simple:b_intensity | float | 1.0 |  | Intensity of the b-ions
RawTandemSignal:TandemSim:Simple:a_intensity | float | 1.0 |  | Intensity of the a-ions
RawTandemSignal:TandemSim:Simple:c_intensity | float | 1.0 |  | Intensity of the c-ions
RawTandemSignal:TandemSim:Simple:x_intensity | float | 1.0 |  | Intensity of the x-ions
RawTandemSignal:TandemSim:Simple:z_intensity | float | 1.0 |  | Intensity of the z-ions
RawTandemSignal:TandemSim:Simple:relative_loss_intensity | float | 0.1 |  | Intensity of loss ions, in relation to the intact ion intensity
RawTandemSignal:TandemSim:Simple:precursor_intensity | float | 1.0 |  | Intensity of the precursor peak
RawTandemSignal:TandemSim:Simple:precursor_H2O_intensity | float | 1.0 |  | Intensity of the H2O loss peak of the precursor
RawTandemSignal:TandemSim:Simple:precursor_NH3_intensity | float | 1.0 |  | Intensity of the NH3 loss peak of the precursor
RawTandemSignal:TandemSim:SVM:add_isotopes | string | false | true, false | If set to 1 isotope peaks of the product ion peaks are added
RawTandemSignal:TandemSim:SVM:max_isotope | int | 2 |  | Defines the maximal isotopic peak which is added, add_isotopes must be set to 1
RawTandemSignal:TandemSim:SVM:add_metainfo | string | false | true, false | Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++
RawTandemSignal:TandemSim:SVM:add_first_prefix_ion | string | false | true, false | If set to true e.g. b1 ions are added
RawTandemSignal:TandemSim:SVM:hide_y_ions | string | false | true, false | Add peaks of y-ions to the spectrum
RawTandemSignal:TandemSim:SVM:hide_y2_ions | string | false | true, false | Add peaks of y-ions to the spectrum
RawTandemSignal:TandemSim:SVM:hide_b_ions | string | false | true, false | Add peaks of b-ions to the spectrum
RawTandemSignal:TandemSim:SVM:hide_b2_ions | string | false | true, false | Add peaks of b-ions to the spectrum
RawTandemSignal:TandemSim:SVM:hide_a_ions | string | false | true, false | Add peaks of a-ions to the spectrum
RawTandemSignal:TandemSim:SVM:hide_c_ions | string | false | true, false | Add peaks of c-ions to the spectrum
RawTandemSignal:TandemSim:SVM:hide_x_ions | string | false | true, false | Add peaks of x-ions to the spectrum
RawTandemSignal:TandemSim:SVM:hide_z_ions | string | false | true, false | Add peaks of z-ions to the spectrum
RawTandemSignal: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
RawTandemSignal:TandemSim:SVM:y_intensity | float | 1.0 |  | Intensity of the y-ions
RawTandemSignal:TandemSim:SVM:b_intensity | float | 1.0 |  | Intensity of the b-ions
RawTandemSignal:TandemSim:SVM:a_intensity | float | 1.0 |  | Intensity of the a-ions
RawTandemSignal:TandemSim:SVM:c_intensity | float | 1.0 |  | Intensity of the c-ions
RawTandemSignal:TandemSim:SVM:x_intensity | float | 1.0 |  | Intensity of the x-ions
RawTandemSignal:TandemSim:SVM:z_intensity | float | 1.0 |  | Intensity of the z-ions
RawTandemSignal:TandemSim:SVM:relative_loss_intensity | float | 0.1 |  | Intensity of loss ions, in relation to the intact ion intensity
Global:ionization_type | string | ESI | MALDI, ESI | Type of Ionization (MALDI or ESI)

Note:

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

See also
  DetectabilitySimulation
  DigestSimulation
  IonizationSimulation
  RawMSSignalSimulation
  RTSimulation

## Constructor & Destructor Documentation

## ◆ MSSim()

MSSim | ( |  | ) |

Default constructor.

## ◆ ~MSSim()

~MSSim | ( |  | ) |

override

Destructor.

## Member Function Documentation

## ◆ createFeatureMap_()

void createFeatureMap_ | ( | const SimTypes::SampleProteins & | peptides,
|  | SimTypes::FeatureMapSim & | features,
|  | Size | map_index
| ) |  |

protected

Convert a list of peptides with given abundance values into a FeatureMap.

## ◆ getChargeConsensus()

ConsensusMap& getChargeConsensus | ( |  | ) |

Access the charge consensus map of simulated features.

## ◆ getContaminants()

const SimTypes::FeatureMapSim& getContaminants | ( |  | ) | const

Access the contaminants feature map of simulated features.

## ◆ getExperiment()

const SimTypes::MSSimExperiment& getExperiment | ( |  | ) | const

Access the simulated experiment.

## ◆ getFeatureIdentifications()

void getFeatureIdentifications | ( | std::vector< ProteinIdentification > & | proteins,
|  | std::vector< PeptideIdentification > & | peptides
| ) |  | const

Access the simulated identifications (proteins and peptides) from feature annotations.

Parameters

  proteins | Will be filled with a single ProteinIdentification holding all ProteinHits.
  peptides | Will be filled with PeptideIdentifications for all simulated features.

## ◆ getIdentifications()

void getIdentifications | ( | std::vector< ProteinIdentification > & | proteins,
|  | std::vector< PeptideIdentification > & | peptides
| ) |  | const

Access the simulated identifications (proteins and peptides)

If an MS2 signal has been simulated, identifications are generated based on their corresponding MS2 spectra. If MS2 simulation has been disabled, peptide IDs are generated from feature annotations. Otherwise, the -out_id idXML file would be empty if MS2 simulation is disabled (which is the default).

Parameters

  proteins | Will be filled with a single ProteinIdentification holding all ProteinHits.
  peptides | Will be filled with PeptideIdentifications.

## ◆ getLabelingConsensus()

ConsensusMap& getLabelingConsensus | ( |  | ) |

Access the labeling consensus map of simulated features.

## ◆ getMS2Identifications()

void getMS2Identifications | ( | std::vector< ProteinIdentification > & | proteins,
|  | std::vector< PeptideIdentification > & | peptides
| ) |  | const

Access the simulated MS2 identifications (proteins and peptides)

Parameters

  proteins | Will be filled with a single ProteinIdentification holding all ProteinHits used in the simulated MS2 spectra.
  peptides | Will be filled with PeptideIdentifications for each simulated MS2 spectra holding all contributing peptides scored by their intensity contribution.

## ◆ getParameters()

Param getParameters | ( |  | ) | const

Returns the default parameters for simulation including the labeling technique with name `labeling_name`.

## ◆ getPeakMap()

const SimTypes::MSSimExperiment& getPeakMap | ( |  | ) | const

Access the picked (centroided) experiment.

## ◆ getSimulatedFeatures()

const SimTypes::FeatureMapSim& getSimulatedFeatures | ( |  | ) | const

Access the simulated features.

## ◆ simulate()

void simulate | ( | SimTypes::MutableSimRandomNumberGeneratorPtr | rnd_gen,
|  | SimTypes::SampleChannels & | peptides
| ) |  |

General purpose function to simulate a mass spectrometry run.

Parameters

  rnd_gen | random number generator which will be passed to the different classes
  peptides | List of peptides and abundances that will be simulated

## ◆ syncParams_()

void syncParams_ | ( | Param & | p,
|  | bool | to_outer
| ) |  |

protected

handle global params

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override protected virtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

## Member Data Documentation

## ◆ consensus_map_

ConsensusMap consensus_map_

private

Holds consensus ground-truth about the charge associations.

## ◆ contaminants_map_

SimTypes::FeatureMapSim contaminants_map_

private

Holds the ground-truth on generated contaminants.

## ◆ experiment_

SimTypes::MSSimExperiment experiment_

private

Holds the simulated data.

## ◆ feature_maps_

SimTypes::FeatureMapSimVector feature_maps_

private

Holds the ground-truth on generated features.

## ◆ labeler_

BaseLabeler* labeler_

private

Labeling functionality.

## ◆ peak_map_

SimTypes::MSSimExperiment peak_map_

private

Holds the ground-truth on generated peaks positions and intensities.