TheoreticalSpectrumGeneratorXLMS

class pyopenms.TheoreticalSpectrumGeneratorXLMS

Bases: object

Cython implementation of _TheoreticalSpectrumGeneratorXLMS

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1TheoreticalSpectrumGeneratorXLMS.html

– Inherits from [‘DefaultParamHandler’]

__init__()

• Cython signature: void TheoreticalSpectrumGeneratorXLMS()

• Cython signature: void TheoreticalSpectrumGeneratorXLMS(TheoreticalSpectrumGeneratorXLMS &)

Methods

__init__	Cython signature: void TheoreticalSpectrumGeneratorXLMS()
getDefaults	Cython signature: Param getDefaults() Returns the default parameters
getLinearIonSpectrum	Cython signature: void getLinearIonSpectrum(MSSpectrum & spectrum, AASequence peptide, size_t link_pos, bool frag_alpha, int charge, size_t link_pos_2)
getName	Cython signature: String getName() Returns the name
getParameters	Cython signature: Param getParameters() Returns the parameters
getSubsections	Cython signature: libcpp_vector[String] getSubsections()
getXLinkIonSpectrum	Cython signature: void getXLinkIonSpectrum(MSSpectrum & spectrum, AASequence peptide, size_t link_pos, double precursor_mass, bool frag_alpha, int mincharge, int maxcharge, size_t link_pos_2)
setName	Cython signature: void setName(const String &) Sets the name
setParameters	Cython signature: void setParameters(Param & param) Sets the parameters

getDefaults()

Cython signature: Param getDefaults() Returns the default parameters

getLinearIonSpectrum()

Cython signature: void getLinearIonSpectrum(MSSpectrum & spectrum, AASequence peptide, size_t link_pos, bool frag_alpha, int charge, size_t link_pos_2)

B-ions are generated from the beginning of the peptide up to the first linked position, y-ions are generated from the second linked position up the end of the peptide. 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 The generated ion types and other additional settings are determined by the tool parameters —– :param spectrum: The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it :param peptide: The peptide to fragment :param link_pos: The position of the cross-linker on the given peptide :param frag_alpha: True, if the fragmented peptide is the Alpha peptide. Used for ion-name annotation :param charge: The maximal charge of the ions :param link_pos_2: A second position for the linker, in case it is a loop link

getName()

Cython signature: String getName() Returns the name

getParameters()

Cython signature: Param getParameters() Returns the parameters

getSubsections()

Cython signature: libcpp_vector[String] getSubsections()

getXLinkIonSpectrum()

• Cython signature: void getXLinkIonSpectrum(MSSpectrum & spectrum, AASequence peptide, size_t link_pos, double precursor_mass, bool frag_alpha, int mincharge, int maxcharge, size_t link_pos_2)

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 —– :param spectrum: The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it :param peptide: The peptide to fragment :param link_pos: The position of the cross-linker on the given peptide :param precursor_mass: The mass of the whole cross-link candidate or the precursor mass of the experimental MS2 spectrum. :param frag_alpha: True, if the fragmented peptide is the Alpha peptide. Used for ion-name annotation. :param mincharge: The minimal charge of the ions :param maxcharge: The maximal charge of the ions, it should be the precursor charge and is used to generate precursor ion peaks :param link_pos_2: A second position for the linker, in case it is a loop link

• Cython signature: void getXLinkIonSpectrum(MSSpectrum & spectrum, ProteinProteinCrossLink crosslink, bool frag_alpha, int mincharge, int maxcharge)

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 function is not suitable to generate fragments for mono-links or loop-links. 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 —– :param spectrum: The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it :param crosslink: ProteinProteinCrossLink to be fragmented :param link_pos: The position of the cross-linker on the given peptide :param precursor_mass: The mass of the whole cross-link candidate or the precursor mass of the experimental MS2 spectrum :param frag_alpha: True, if the fragmented peptide is the Alpha peptide :param mincharge: The minimal charge of the ions :param maxcharge: The maximal charge of the ions, it should be the precursor charge and is used to generate precursor ion peaks

setName()

Cython signature: void setName(const String &) Sets the name

setParameters()

Cython signature: void setParameters(Param & param) Sets the parameters