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bool | add_b_ions_ |
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bool | add_y_ions_ |
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bool | add_a_ions_ |
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bool | add_c_ions_ |
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bool | add_x_ions_ |
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bool | add_z_ions_ |
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bool | add_first_prefix_ion_ |
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bool | add_losses_ |
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bool | add_charges_ |
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bool | add_isotopes_ |
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bool | add_precursor_peaks_ |
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bool | add_abundant_immonium_ions_ |
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Int | max_isotope_ |
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double | pre_int_ |
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double | pre_int_H2O_ |
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double | pre_int_NH3_ |
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bool | add_k_linked_ions_ |
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std::map< String, LossIndex > | loss_db_ |
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double | loss_H2O_ = 0 |
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double | loss_NH3_ = 0 |
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| SimpleTSGXLMS () |
| default constructor More...
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| SimpleTSGXLMS (const SimpleTSGXLMS &source) |
| copy constructor More...
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| ~SimpleTSGXLMS () override |
| destructor More...
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SimpleTSGXLMS & | operator= (const SimpleTSGXLMS &tsg) |
| assignment operator More...
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virtual void | getLinearIonSpectrum (std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, int charge=1, Size link_pos_2=0) const |
| Generates fragment ions not containing the cross-linker for one peptide. More...
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virtual void | getXLinkIonSpectrum (std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, double precursor_mass, int min_charge, int max_charge, Size link_pos_2=0) const |
| Generates fragment ions containing the cross-linker for one peptide. More...
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virtual void | getXLinkIonSpectrum (std::vector< SimplePeak > &spectrum, OPXLDataStructs::ProteinProteinCrossLink &crosslink, bool frag_alpha, int min_charge, int max_charge) const |
| Generates fragment ions containing the cross-linker for a pair of peptides. More...
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void | updateMembers_ () override |
| overwrite More...
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virtual void | addLinearPeaks_ (std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, Residue::ResidueType res_type, std::vector< LossIndex > &forward_losses, std::vector< LossIndex > &backward_losses, int charge=1, Size link_pos_2=0) const |
| Adds cross-link-less ions of a specific ion type and charge to a spectrum. More...
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virtual void | addPrecursorPeaks_ (std::vector< SimplePeak > &spectrum, double precursor_mass, int charge) const |
| Adds precursor masses including neutral losses for the given charge. More...
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virtual void | addLosses_ (std::vector< SimplePeak > &spectrum, double mono_weight, int charge, LossIndex &losses) const |
| Adds neutral losses for an ion to a spectrum. More...
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virtual void | addKLinkedIonPeaks_ (std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, double precursor_mass, int charge) const |
| Adds one-residue-linked ion peaks, that are specific to XLMS. More...
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virtual void | addXLinkIonPeaks_ (std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, double precursor_mass, Residue::ResidueType res_type, std::vector< LossIndex > &forward_losses, std::vector< LossIndex > &backward_losses, int charge, Size link_pos_2=0) const |
| Adds cross-linked ions of a specific ion type and charge to a spectrum. More...
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virtual void | addXLinkIonPeaks_ (std::vector< SimplePeak > &spectrum, OPXLDataStructs::ProteinProteinCrossLink &crosslink, bool frag_alpha, Residue::ResidueType res_type, std::vector< LossIndex > &forward_losses, std::vector< LossIndex > &backward_losses, LossIndex &losses_peptide2, int charge) const |
| Adds cross-linked ions of a specific ion type and charge to a spectrum. More...
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std::vector< LossIndex > | getForwardLosses_ (AASequence &peptide) const |
| Calculates sets of possible neutral losses for each position in the given peptide. More...
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std::vector< LossIndex > | getBackwardLosses_ (AASequence &peptide) const |
| Calculates sets of possible neutral losses for each position in the given peptide. More...
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Generates theoretical spectra for cross-linked peptides.
The spectra this class generates are vectors of SimplePeaks. This class generates the same peak types as TheoreticalSpectrumGeneratorXLMS and the interface is very similar, but it is simpler and faster. SimplePeak only contains an mz value and a charge. No intensity values or String annotations or other additional DataArrays are generated.
Parameters of this class are:
Name | Type | Default | Restrictions | Description |
add_isotopes |
string | false |
true, false | If set to 1 isotope peaks of the product ion peaks are added |
max_isotope |
int | 2 |
| Defines the maximal isotopic peak which is added, add_isotopes must be set to 1 |
add_losses |
string | false |
true, false | Adds common losses to those ion expect to have them, only water and ammonia loss is considered |
add_precursor_peaks |
string | true |
true, false | Adds peaks of the precursor to the spectrum, which happen to occur sometimes |
add_abundant_immonium_ions |
string | false |
true, false | Add most abundant immonium ions |
add_k_linked_ions |
string | true |
true, false | Add RES-Linked ions, which are specific to XLMS |
add_first_prefix_ion |
string | true |
true, false | If set to true e.g. b1 ions are added |
add_y_ions |
string | true |
true, false | Add peaks of y-ions to the spectrum |
add_b_ions |
string | true |
true, false | Add peaks of b-ions to the spectrum |
add_a_ions |
string | true |
true, false | Add peaks of a-ions to the spectrum |
add_c_ions |
string | false |
true, false | Add peaks of c-ions to the spectrum |
add_x_ions |
string | false |
true, false | Add peaks of x-ions to the spectrum |
add_z_ions |
string | false |
true, false | Add peaks of z-ions to the spectrum |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
virtual void addKLinkedIonPeaks_ |
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std::vector< SimplePeak > & |
spectrum, |
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AASequence & |
peptide, |
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Size |
link_pos, |
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double |
precursor_mass, |
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int |
charge |
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protectedvirtual |
Adds one-residue-linked ion peaks, that are specific to XLMS.
These fragments consist of one whole peptide, the cross-linker and a part of the linked residue from the second peptide. The residue fragment on the linker is an internal ion from a y- and an a-fragmentation with the length of one residue. The function is called KLinked for now, but instead of K it is whatever residue the linker is bound to.
- Parameters
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spectrum | The spectrum to which the peaks are added |
peptide | The fragmented peptide |
link_pos | position of the linker on the fragmented peptide |
precursor_mass | The mass of the whole cross-link candidate or the precursor mass of the experimental MS2 spectrum. |
charge | The charge of the ion |
virtual void getXLinkIonSpectrum |
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std::vector< SimplePeak > & |
spectrum, |
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AASequence & |
peptide, |
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Size |
link_pos, |
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double |
precursor_mass, |
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int |
min_charge, |
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int |
max_charge, |
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Size |
link_pos_2 = 0 |
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virtual |
Generates fragment ions containing the cross-linker for one peptide.
B-ions are generated from the first linked position up to the end of the peptide, y-ions are generated from the beginning of the peptide up to the second linked position. If link_pos_2 is 0, a mono-link or cross-link is assumed and the second position is the same as the first position. For a loop-link two different positions can be set and link_pos_2 must be larger than link_pos. Since in the case of a cross-link a whole second peptide is attached to the other side of the cross-link, a precursor mass for the two peptides and the linker is needed. In the case of a loop link the precursor mass is the mass of the only peptide and the linker. Although this function is more general, currently it is mainly used for loop-links and mono-links, because residues in the second, unknown peptide cannot be considered for possible neutral losses. The generated ion types and other additional settings are determined by the tool parameters.
- Parameters
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spectrum | The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it. |
peptide | The peptide to fragment |
link_pos | The position of the cross-linker on the given peptide |
precursor_mass | The mass of the whole cross-link candidate or the precursor mass of the experimental MS2 spectrum. |
min_charge | The minimal charge of the ions |
max_charge | The maximal charge of the ions, it should be the precursor charge and is used to generate precursor ion peaks |
link_pos_2 | A second position for the linker, in case it is a loop link |
Generates fragment ions containing the cross-linker for a pair of peptides.
B-ions are generated from the first linked position up to the end of the peptide, y-ions are generated from the beginning of the peptide up to the second linked position. This function generates neutral loss ions by considering both linked peptides. Only one of the peptides, decided by frag_alpha
, is fragmented. This simplifies the function, but it has to be called twice to get all fragments of a peptide pair. The generated ion types and other additional settings are determined by the tool parameters. This function is not suitable to generate fragments for mono-links or loop-links.
- Parameters
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spectrum | The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it. |
crosslink | ProteinProteinCrossLink to be fragmented |
frag_alpha | True, if the fragmented peptide is the Alpha peptide. |
min_charge | The minimal charge of the ions |
max_charge | The maximal charge of the ions, it should be the precursor charge and is used to generate precursor ion peaks |