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 | 2.0 |
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 |
Public Member Functions inherited from DefaultParamHandler
1.8.16
