`pyms.Spectrum`

Classes to model Mass Spectra and Scans.

Classes:

`CompositeMassSpectrum`(mass_list, intensity_list)	Represents a composite mass spectrum.
`MassSpectrum`(mass_list, intensity_list)	Models a binned mass spectrum.
`Scan`(mass_list, intensity_list)	Generic object for a single Scan's raw data.

Data:

`_C`	Invariant `TypeVar` bound to `pyms.Spectrum.CompositeMassSpectrum`.
`_M`	Invariant `TypeVar` bound to `pyms.Spectrum.MassSpectrum`.
`_S`	Invariant `TypeVar` bound to `pyms.Spectrum.Scan`.

Functions:

`array_as_numeric`(array)	Convert the given numpy array to a numeric data type.
`normalize_mass_spec`(mass_spec[, ...])	Normalize the intensities in the given Mass Spectrum to values between `0` and `max_intensity`, which by default is `100.0`.

class CompositeMassSpectrum(mass_list, intensity_list)[source]

Bases: MassSpectrum

Represents a composite mass spectrum.

Parameters

mass_list (Union[Sequence[float], ndarray]) – mass values
intensity_list (Union[Sequence[float], ndarray]) – intensity values

Author

Dominic Davis-Foster

Methods:

`__copy__`()	Returns a copy of the object.
`__eq__`(other)	Return whether this object is equal to another object.
`__len__`()	Returns the length of the object.
`crop`([min_mz, max_mz, inplace])	Crop the Mass Spectrum between the given mz values.
`dump`(file_name[, protocol])	Dumps an object to a file through `pickle.dump()`.
`from_dict`(dictionary)	Create a `Scan` from a dictionary.
`from_jcamp`(file_name)	Create a MassSpectrum from a JCAMP-DX file.
`from_mz_int_pairs`(mz_int_pairs)	Construct a MassSpectrum from a list of (m/z, intensity) tuples.
`from_spectra`(spectra)	Construct a `CompositeMassSpectrum` from multiple `MassSpectrum` objects.
`get_intensity_for_mass`(mass)	Returns the intensity for the given mass.
`get_mass_for_intensity`(intensity)	Returns the mass for the given intensity.
`icrop`([min_index, max_index, inplace])	Crop the Mass Spectrum between the given indices.
`iter_peaks`()	Iterate over the peaks in the mass spectrum.
`n_largest_peaks`(n)	Returns the indices of the `n` largest peaks in the Mass Spectrum.

Attributes:

`intensity_list`	Returns a copy of the intensity list.
`mass_list`	Returns a list of the masses.
`mass_spec`	Returns the intensity list.
`max_mass`	Returns the maximum m/z value in the spectrum.
`min_mass`	Returns the minimum m/z value in the spectrum.
`size`	The number of mass spectra combined to create this composite spectrum.

__copy__()

Returns a copy of the object.

Return type: Scan

__eq__(other)

Return whether this object is equal to another object.

Parameters: other (Any) – The other object to test equality with.
Return type: bool

__len__()

Returns the length of the object.

Authors: Andrew Isaac, Qiao Wang, Vladimir Likic
Return type: int

crop(min_mz=None, max_mz=None, inplace=False)

Crop the Mass Spectrum between the given mz values.

Parameters

min_mz (Optional[float]) – The minimum mz for the new mass spectrum. Default None.
max_mz (Optional[float]) – The maximum mz for the new mass spectrum. Default None.
inplace (bool) – Whether the cropping should be applied this instance or to a copy (default behaviour). Default False.

Return type

~_M

Returns

The cropped Mass Spectrum

dump(file_name, protocol=3)

Dumps an object to a file through pickle.dump().

Parameters

file_name (Union[str, Path, PathLike]) – Filename to save the dump as.
protocol (int) – The pickle protocol to use. Default 3.

Authors

Vladimir Likic, Dominic Davis-Foster (pathlib and pickle protocol support)

classmethod from_dict(dictionary)

Create a Scan from a dictionary.

The dictionary’s keys must match the arguments taken bt the class’s constructor.

Parameters: dictionary (Mapping)
Return type: ~_S

classmethod from_jcamp(file_name)

Create a MassSpectrum from a JCAMP-DX file.

Parameters: file_name (Union[str, Path, PathLike]) – Path of the file to read.
Authors: Qiao Wang, Andrew Isaac, Vladimir Likic, David Kainer, Dominic Davis-Foster
Return type: ~_M

classmethod from_mz_int_pairs(mz_int_pairs)

Construct a MassSpectrum from a list of (m/z, intensity) tuples.

Parameters: mz_int_pairs (Sequence[Tuple[float, float]])
Return type: ~_M

classmethod from_spectra(spectra)[source]

Construct a CompositeMassSpectrum from multiple MassSpectrum objects.

If no MassSpectrum objects are given an empty CompositeMassSpectrum is returned.

Parameters: spectra (Iterable[MassSpectrum])
Return type: ~_C

get_intensity_for_mass(mass)

Returns the intensity for the given mass.

Parameters: mass (float)
Return type: float

get_mass_for_intensity(intensity)

Returns the mass for the given intensity. If more than one mass has the given intensity, the first mass is returned.

Parameters: intensity (float)
Return type: float

icrop(min_index=0, max_index=-1, inplace=False)

Crop the Mass Spectrum between the given indices.

Parameters

min_index (int) – The minimum index for the new mass spectrum. Default 0.
max_index (int) – The maximum index for the new mass spectrum. Default -1.
inplace (bool) – Whether the cropping should be applied this instance or to a copy (default behaviour). Default False.

Return type

~_M

Returns

The cropped Mass Spectrum

property intensity_list

Returns a copy of the intensity list.

Authors: Qiao Wang, Andrew Isaac, Vladimir Likic
Return type: List

iter_peaks()

Iterate over the peaks in the mass spectrum.

Return type: Iterator[Tuple[float, float]]

property mass_list

Returns a list of the masses.

Authors: Qiao Wang, Andrew Isaac, Vladimir Likic
Return type: List[float]

property mass_spec

Returns the intensity list.

Authors: Qiao Wang, Andrew Isaac, Vladimir Likic
Return type: List

property max_mass

Returns the maximum m/z value in the spectrum.

Author: Andrew Isaac
Return type: Optional[float]

property min_mass

Returns the minimum m/z value in the spectrum.

Author: Andrew Isaac
Return type: Optional[float]

n_largest_peaks(n)

Returns the indices of the n largest peaks in the Mass Spectrum.

Parameters: n (int) – The number of peaks to return the indices for.
Return type: List[int]

size: int = 1: The number of mass spectra combined to create this composite spectrum.

class MassSpectrum(mass_list, intensity_list)[source]

Bases: Scan

Models a binned mass spectrum.

Parameters

mass_list (Union[Sequence[float], ndarray]) – mass values
intensity_list (Union[Sequence[float], ndarray]) – intensity values

Authors

Andrew Isaac, Qiao Wang, Vladimir Likic, Dominic Davis-Foster

Methods:

`__copy__`()	Returns a copy of the object.
`__eq__`(other)	Return whether this object is equal to another object.
`__len__`()	Returns the length of the object.
`crop`([min_mz, max_mz, inplace])	Crop the Mass Spectrum between the given mz values.
`dump`(file_name[, protocol])	Dumps an object to a file through `pickle.dump()`.
`from_dict`(dictionary)	Create a `Scan` from a dictionary.
`from_jcamp`(file_name)	Create a MassSpectrum from a JCAMP-DX file.
`from_mz_int_pairs`(mz_int_pairs)	Construct a MassSpectrum from a list of (m/z, intensity) tuples.
`get_intensity_for_mass`(mass)	Returns the intensity for the given mass.
`get_mass_for_intensity`(intensity)	Returns the mass for the given intensity.
`icrop`([min_index, max_index, inplace])	Crop the Mass Spectrum between the given indices.
`iter_peaks`()	Iterate over the peaks in the mass spectrum.
`n_largest_peaks`(n)	Returns the indices of the `n` largest peaks in the Mass Spectrum.

Attributes:

`intensity_list`	Returns a copy of the intensity list.
`mass_list`	Returns a list of the masses.
`mass_spec`	Returns the intensity list.
`max_mass`	Returns the maximum m/z value in the spectrum.
`min_mass`	Returns the minimum m/z value in the spectrum.

__copy__()

Returns a copy of the object.

Return type: Scan

__eq__(other)

Return whether this object is equal to another object.

Parameters: other (Any) – The other object to test equality with.
Return type: bool

__len__()

Returns the length of the object.

Authors: Andrew Isaac, Qiao Wang, Vladimir Likic
Return type: int

crop(min_mz=None, max_mz=None, inplace=False)[source]

Crop the Mass Spectrum between the given mz values.

Parameters

min_mz (Optional[float]) – The minimum mz for the new mass spectrum. Default None.
max_mz (Optional[float]) – The maximum mz for the new mass spectrum. Default None.
inplace (bool) – Whether the cropping should be applied this instance or to a copy (default behaviour). Default False.

Return type

~_M

Returns

The cropped Mass Spectrum

dump(file_name, protocol=3)

Dumps an object to a file through pickle.dump().

Parameters

file_name (Union[str, Path, PathLike]) – Filename to save the dump as.
protocol (int) – The pickle protocol to use. Default 3.

Authors

Vladimir Likic, Dominic Davis-Foster (pathlib and pickle protocol support)

classmethod from_dict(dictionary)

Create a Scan from a dictionary.

The dictionary’s keys must match the arguments taken bt the class’s constructor.

Parameters: dictionary (Mapping)
Return type: ~_S

classmethod from_jcamp(file_name)[source]

Create a MassSpectrum from a JCAMP-DX file.

Parameters: file_name (Union[str, Path, PathLike]) – Path of the file to read.
Authors: Qiao Wang, Andrew Isaac, Vladimir Likic, David Kainer, Dominic Davis-Foster
Return type: ~_M

classmethod from_mz_int_pairs(mz_int_pairs)[source]

Construct a MassSpectrum from a list of (m/z, intensity) tuples.

Parameters: mz_int_pairs (Sequence[Tuple[float, float]])
Return type: ~_M

get_intensity_for_mass(mass)[source]

Returns the intensity for the given mass.

Parameters: mass (float)
Return type: float

get_mass_for_intensity(intensity)[source]

Returns the mass for the given intensity. If more than one mass has the given intensity, the first mass is returned.

Parameters: intensity (float)
Return type: float

icrop(min_index=0, max_index=-1, inplace=False)[source]

Crop the Mass Spectrum between the given indices.

Parameters

min_index (int) – The minimum index for the new mass spectrum. Default 0.
max_index (int) – The maximum index for the new mass spectrum. Default -1.
inplace (bool) – Whether the cropping should be applied this instance or to a copy (default behaviour). Default False.

Return type

~_M

Returns

The cropped Mass Spectrum

property intensity_list

Returns a copy of the intensity list.

Authors: Qiao Wang, Andrew Isaac, Vladimir Likic
Return type: List

iter_peaks()

Iterate over the peaks in the mass spectrum.

Return type: Iterator[Tuple[float, float]]

property mass_list

Returns a list of the masses.

Authors: Qiao Wang, Andrew Isaac, Vladimir Likic
Return type: List[float]

property mass_spec

Returns the intensity list.

Authors: Qiao Wang, Andrew Isaac, Vladimir Likic
Return type: List

property max_mass

Returns the maximum m/z value in the spectrum.

Author: Andrew Isaac
Return type: Optional[float]

property min_mass

Returns the minimum m/z value in the spectrum.

Author: Andrew Isaac
Return type: Optional[float]

n_largest_peaks(n)[source]

Returns the indices of the n largest peaks in the Mass Spectrum.

Parameters: n (int) – The number of peaks to return the indices for.
Return type: List[int]

class Scan(mass_list, intensity_list)[source]

Bases: pymsBaseClass, MassListMixin

Generic object for a single Scan’s raw data.

Parameters

mass_list (Union[Sequence[float], ndarray]) – A sequence of mass values
intensity_list (Union[Sequence[float], ndarray]) – A sequence intensity values

Authors

Andrew Isaac, Qiao Wang, Vladimir Likic, Dominic Davis-Foster

Methods:

`__copy__`()	Returns a copy of the object.
`__eq__`(other)	Return whether this object is equal to another object.
`__len__`()	Returns the length of the object.
`dump`(file_name[, protocol])	Dumps an object to a file through `pickle.dump()`.
`from_dict`(dictionary)	Create a `Scan` from a dictionary.
`iter_peaks`()	Iterate over the peaks in the mass spectrum.

Attributes:

`intensity_list`	Returns a copy of the intensity list.
`mass_list`	Returns a list of the masses.
`mass_spec`	Returns the intensity list.
`max_mass`	Returns the maximum m/z value in the spectrum.
`min_mass`	Returns the minimum m/z value in the spectrum.

__copy__()[source]

Returns a copy of the object.

Return type: Scan

__eq__(other)[source]

Return whether this object is equal to another object.

Parameters: other (Any) – The other object to test equality with.
Return type: bool

__len__()[source]

Returns the length of the object.

Authors: Andrew Isaac, Qiao Wang, Vladimir Likic
Return type: int

dump(file_name, protocol=3)

Dumps an object to a file through pickle.dump().

Parameters

file_name (Union[str, Path, PathLike]) – Filename to save the dump as.
protocol (int) – The pickle protocol to use. Default 3.

Authors

Vladimir Likic, Dominic Davis-Foster (pathlib and pickle protocol support)

classmethod from_dict(dictionary)[source]

Create a Scan from a dictionary.

The dictionary’s keys must match the arguments taken bt the class’s constructor.

Parameters: dictionary (Mapping)
Return type: ~_S

property intensity_list

Returns a copy of the intensity list.

Authors: Qiao Wang, Andrew Isaac, Vladimir Likic
Return type: List

iter_peaks()[source]

Iterate over the peaks in the mass spectrum.

Return type: Iterator[Tuple[float, float]]

property mass_list

Returns a list of the masses.

Authors: Qiao Wang, Andrew Isaac, Vladimir Likic
Return type: List[float]

property mass_spec

Returns the intensity list.

Authors: Qiao Wang, Andrew Isaac, Vladimir Likic
Return type: List

property max_mass

Returns the maximum m/z value in the spectrum.

Author: Andrew Isaac
Return type: Optional[float]

property min_mass

Returns the minimum m/z value in the spectrum.

Author: Andrew Isaac
Return type: Optional[float]

_C = TypeVar(_C, bound=CompositeMassSpectrum)

Type: TypeVar

Invariant TypeVar bound to pyms.Spectrum.CompositeMassSpectrum.

_M = TypeVar(_M, bound=MassSpectrum)

Type: TypeVar

Invariant TypeVar bound to pyms.Spectrum.MassSpectrum.

_S = TypeVar(_S, bound=Scan)

Type: TypeVar

Invariant TypeVar bound to pyms.Spectrum.Scan.

array_as_numeric(array)[source]

Convert the given numpy array to a numeric data type.

If the data in the array is already in a numeric data type no changes will be made.

If array is a python Sequence then it will first be converted to a numpy array.

Parameters: array (Union[Sequence, ndarray])
Return type: ndarray

normalize_mass_spec(mass_spec, relative_to=None, inplace=False, max_intensity=100)[source]

Normalize the intensities in the given Mass Spectrum to values between 0 and max_intensity, which by default is 100.0.

Parameters

mass_spec (MassSpectrum) – The Mass Spectrum to normalize
relative_to (Optional[float]) – The largest intensity in the original data set. If not None the intensities are computed relative to this value. If None the value is calculated from the mass spectrum. This can be useful when normalizing several mass spectra to each other. Default None.
inplace (bool) – Whether the normalization should be applied to the MassSpectrum object given, or to a copy (default behaviour). Default False.
max_intensity (float) – The maximum intensity in the normalized spectrum. If omitted the range 0-100.0 is used. If an integer the normalized intensities will be integers. Default 100.

Return type

MassSpectrum

Returns

The normalized mass spectrum

pyms.Spectrum

`pyms.Spectrum`