SimpleTSGXLMS#

class pyopenms.SimpleTSGXLMS#

Bases: object

Cython implementation of _SimpleTSGXLMS

Original C++ documentation is available here: – Inherits from [‘DefaultParamHandler’]

__init__()#

Overload:

__init__(self) → None

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

Overload:

__init__(self, in_0: SimpleTSGXLMS) → None

Methods

`__init__`	Overload:
`getDefaults`(self)	Returns the default parameters
`getLinearIonSpectrum`(self, spectrum, ...)	Generates fragment ions not containing the cross-linker for one peptide
`getName`(self)	Returns the name
`getParameters`(self)	Returns the parameters
`getSubsections`(self)
`getXLinkIonSpectrum`	Overload:
`setName`(self, in_0)	Sets the name
`setParameters`(self, param)	Sets the parameters

getDefaults(self) → Param#: Returns the default parameters

getLinearIonSpectrum(self, spectrum: List[SimplePeak], peptide: AASequence, link_pos: int, charge: int, link_pos_2: int) → None#

Generates fragment ions not containing the cross-linker for one peptide

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

Parameters:

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
charge – The maximal charge of the ions
link_pos_2 – A second position for the linker, in case it is a loop link

getName(self) → bytes | str | String#: Returns the name

getParameters(self) → Param#: Returns the parameters

getSubsections(self) → List[bytes]#

getXLinkIonSpectrum()#

Overload:

getXLinkIonSpectrum(self, spectrum: List[SimplePeak], peptide: AASequence, link_pos: int, precursor_mass: float, mincharge: int, maxcharge: int, link_pos_2: int) → None

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:

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
mincharge – The minimal charge of the ions
maxcharge – 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

Overload:

getXLinkIonSpectrum(self, spectrum: List[SimplePeak], crosslink: ProteinProteinCrossLink, frag_alpha: bool, mincharge: int, maxcharge: int) → None

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:

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
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
frag_alpha – True, if the fragmented peptide is the Alpha peptide
mincharge – The minimal charge of the ions
maxcharge – The maximal charge of the ions, it should be the precursor charge and is used to generate precursor ion peaks

setName(self, in_0: bytes | str | String) → None#: Sets the name

setParameters(self, param: Param) → None#: Sets the parameters