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.
| 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 |
min: 0.0001 | 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 |
min: 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 |
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_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 |
| 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 |
Public Member Functions inherited from DefaultParamHandler
1.8.14