TheoreticalSpectrumGeneratorXLMS

class pyopenms.TheoreticalSpectrumGeneratorXLMS

Bases: object

Cython implementation of _TheoreticalSpectrumGeneratorXLMS

Original C++ documentation is available here

– Inherits from [‘DefaultParamHandler’]

__init__()

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: TheoreticalSpectrumGeneratorXLMS) → 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: MSSpectrum, peptide: AASequence, link_pos: int, frag_alpha: bool, 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

• frag_alpha – True, if the fragmented peptide is the Alpha peptide. Used for ion-name annotation

• 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: MSSpectrum, peptide: AASequence, link_pos: int, precursor_mass: float, frag_alpha: bool, 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

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

Overload:

getXLinkIonSpectrum(self, spectrum: MSSpectrum, 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 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(self, in_0: bytes | str | String) → None

Sets the name

setParameters(self, param: Param) → None

Sets the parameters