Simulates tandem MS signales for a given set of peptides. 
Simulates tandem MS signales for a given set of peptides, with charge annotation, given detectabilities, predicted retention times and charge values.
| 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_peak_distance | float | 3 | min: 0 | The minimal distance (in Da) of two peaks in one spectrum so that they can be selected. | 
  | Precursor:selection_window | float | 2 | min: 0 | All peaks within a mass window (in Da) 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_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 | min: 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 | min: 0 | Minimal rt in seconds. | 
  | Precursor:ProteinBasedInclusion:rt:max_rt | float | 3840 | min: 0 | Maximal rt in seconds. | 
  | Precursor:ProteinBasedInclusion:rt:rt_step_size | float | 30 | min: 1 | 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 max: 1 | Minimal protein probability for a protein to be considered identified. | 
  | Precursor:ProteinBasedInclusion:thresholds:min_pt_weight | float | 0.5 | min: 0 max: 1 | Minimal pt weight of a precursor | 
  | Precursor:ProteinBasedInclusion:thresholds:min_mz | float | 500 | min: 0 | Minimal mz to be considered in protein based LP formulation. | 
  | Precursor:ProteinBasedInclusion:thresholds:max_mz | float | 5000 | min: 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 max: 1 | 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:add_isotopes | string | false | true, false | If set to 1 isotope peaks of the product ion peaks are added | 
  | TandemSim:Simple:max_isotope | int | 2 |  | Defines the maximal isotopic peak which is added, add_isotopes must be set to 1 | 
  | 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:add_precursor_peaks | string | false | true, false | Adds peaks of the precursor to the spectrum, which happen to occur sometimes | 
  | 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 |  | Intensity of the y-ions | 
  | TandemSim:Simple:b_intensity | float | 1 |  | Intensity of the b-ions | 
  | TandemSim:Simple:a_intensity | float | 1 |  | Intensity of the a-ions | 
  | TandemSim:Simple:c_intensity | float | 1 |  | Intensity of the c-ions | 
  | TandemSim:Simple:x_intensity | float | 1 |  | Intensity of the x-ions | 
  | TandemSim:Simple:z_intensity | float | 1 |  | 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 |  | Intensity of the precursor peak | 
  | TandemSim:Simple:precursor_H2O_intensity | float | 1 |  | Intensity of the H2O loss peak of the precursor | 
  | TandemSim:Simple:precursor_NH3_intensity | float | 1 |  | 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 |  | Intensity of the y-ions | 
  | TandemSim:SVM:b_intensity | float | 1 |  | Intensity of the b-ions | 
  | TandemSim:SVM:a_intensity | float | 1 |  | Intensity of the a-ions | 
  | TandemSim:SVM:c_intensity | float | 1 |  | Intensity of the c-ions | 
  | TandemSim:SVM:x_intensity | float | 1 |  | Intensity of the x-ions | 
  | TandemSim:SVM:z_intensity | float | 1 |  | Intensity of the z-ions | 
  | TandemSim:SVM:relative_loss_intensity | float | 0.1 |  | Intensity of loss ions, in relation to the intact ion intensity |