imspy.data package

Submodules

imspy.data.peptide module

class imspy.data.peptide.PeptideIon(sequence, charge, intensity, peptide_id=None)

Bases: RustWrapperObject

property atomic_composition

calculate_isotopic_spectrum(mass_tolerance=0.001, abundance_threshold=1e-08, max_result=200, intensity_min=0.0001)

Calculate the isotopic spectrum of the peptide ion.

Parameters:

• mass_tolerance (float) – The mass tolerance for the isotopic spectrum calculation.

• abundance_threshold (float) – The abundance threshold for the isotopic spectrum calculation.

• max_result (int) – The maximum number of results to return.

• intensity_min (float) – The minimum intensity of the isotopic spectrum.

Return type:

MzSpectrum

Returns:

The isotopic spectrum of the peptide ion.

calculate_isotopic_spectrum_annotated(mass_tolerance=0.001, abundance_threshold=1e-08, max_result=200, intensity_min=0.0001)

Calculate the isotopic spectrum of the peptide ion.

Parameters:

• mass_tolerance (float) – The mass tolerance for the isotopic spectrum calculation.

• abundance_threshold (float) – The abundance threshold for the isotopic spectrum calculation.

• max_result (int) – The maximum number of results to return.

• intensity_min (float) – The minimum intensity of the isotopic spectrum.

Return type:

MzSpectrumAnnotated

Returns:

The isotopic spectrum of the peptide ion.

property charge: int

classmethod from_py_ptr(ion)

get_py_ptr()

property intensity: float

property mz: float

property peptide_id: None | int

property sequence: PeptideSequence

to_json()

Return type:

str

class imspy.data.peptide.PeptideProductIon(kind, sequence, charge=1, intensity=1.0, peptide_id=None)

Bases: RustWrapperObject

atomic_composition()

property charge: int

classmethod from_py_ptr(product_ion)

get_py_ptr()

property intensity: float

isotope_distribution(mass_tolerance=0.001, abundance_threshold=1e-08, max_result=200, intensity_min=0.0001)

Calculate the isotope distribution of the product ion.

Parameters:

• mass_tolerance (float) – The mass tolerance for the isotope distribution calculation.

• abundance_threshold (float) – The abundance threshold for the isotope distribution calculation.

• max_result (int) – The maximum number of results to return.

• intensity_min (float) – The minimum intensity of the isotope distribution.

Return type:

List[Tuple[float, float]]

Returns:

The isotope distribution of the product ion.

property kind: str

property mono_isotopic_mass: float

property mz: float

property sequence: str

to_json()

Return type:

str

class imspy.data.peptide.PeptideProductIonSeries(charge, n_ions, c_ions)

Bases: RustWrapperObject

property c_ions: List[PeptideProductIon]

property charge: int

classmethod from_py_ptr(series)

get_py_ptr()

property n_ions: List[PeptideProductIon]

to_json()

Return type:

str

class imspy.data.peptide.PeptideProductIonSeriesCollection(series)

Bases: RustWrapperObject

find_series(charge)

Find the product ion series with the given charge.

Parameters:

charge (int) – The charge of the product ion series.

Return type:

Optional[PeptideProductIonSeries]

Returns:

The product ion series with the given charge, or None if not found.

classmethod from_py_ptr(collection)

generate_isotopic_spectrum(mass_tolerance=0.001, abundance_threshold=1e-06, max_result=2000, intensity_min=1e-06)

Calculate the isotope distribution of the product ion series collection.

Parameters:

• mass_tolerance (float) – The mass tolerance for the isotope distribution calculation.

• abundance_threshold (float) – The abundance threshold for the isotope distribution calculation.

• max_result (int) – The maximum number of results to return.

• intensity_min (float) – The minimum intensity of the isotope distribution.

Return type:

MzSpectrum

Returns:

The isotope distribution of the product ion series collection.

generate_isotopic_spectrum_annotated(mass_tolerance=0.001, abundance_threshold=1e-06, max_result=2000, intensity_min=1e-06)

Calculate the isotope distribution of the product ion series collection.

Parameters:

• mass_tolerance (float) – The mass tolerance for the isotope distribution calculation.

• abundance_threshold (float) – The abundance threshold for the isotope distribution calculation.

• max_result (int) – The maximum number of results to return.

• intensity_min (float) – The minimum intensity of the isotope distribution.

Return type:

MzSpectrumAnnotated

Returns:

The isotope distribution of the product ion series collection.

get_py_ptr()

property series: List[PeptideProductIonSeries]

to_json()

Return type:

str

class imspy.data.peptide.PeptideSequence(sequence, peptide_id=None)

Bases: RustWrapperObject

property amino_acid_count: int

associate_fragment_ion_series_with_prosit_intensities(flat_intensities, charge, fragment_type='b', normalize=True, half_charge_one=True)

Associate the peptide sequence with predicted intensities from Prosit intensity prediction.

Parameters:

• flat_intensities (List[float]) – The flat intensities.

• TODO (#) – check how charge should be handled

• charge (int) – The charge of the product ions.

• fragment_type (str) – The type of the product ions, must be one of ‘a’, ‘b’, ‘c’, ‘x’, ‘y’, ‘z’.

• normalize (bool) – Whether to normalize the intensities.

• half_charge_one (bool) – Whether to use half charge one.

Return type:

PeptideProductIonSeriesCollection

Returns:

The b and y product ion series of the peptide sequence.

property atomic_composition

calculate_isotopic_product_ion_spectrum_annotated(charge=1, fragment_type='b', mass_tolerance=0.001, abundance_threshold=1e-08, max_result=200, intensity_min=0.0001)

Calculate the isotopic product ion spectrum of the peptide sequence.

Parameters:

• intensity_min (float)

• max_result (int)

• abundance_threshold (float)

• mass_tolerance (float)

• charge (int) – The charge of the product ions.

• fragment_type (str) – The type of the product ions, must be one of ‘a’, ‘b’, ‘c’, ‘x’, ‘y’, ‘z’.

Return type:

MzSpectrumAnnotated

Returns:

The isotopic product ion spectrum of the peptide sequence.

calculate_mono_isotopic_product_ion_spectrum(charge=1, fragment_type='b')

Calculate the mono-isotopic product ion spectrum of the peptide sequence.

Parameters:

• charge (int) – The charge of the product ions.

• fragment_type (str) – The type of the product ions, must be one of ‘a’, ‘b’, ‘c’, ‘x’, ‘y’, ‘z’.

Return type:

MzSpectrum

Returns:

The mono-isotopic product ion spectrum of the peptide sequence.

calculate_mono_isotopic_product_ion_spectrum_annotated(charge=1, fragment_type='b')

Calculate the mono-isotopic product ion spectrum of the peptide sequence.

Parameters:

• charge (int) – The charge of the product ions.

• fragment_type (str) – The type of the product ions, must be one of ‘a’, ‘b’, ‘c’, ‘x’, ‘y’, ‘z’.

Return type:

MzSpectrumAnnotated

Returns:

The mono-isotopic product ion spectrum of the peptide sequence.

calculate_product_ion_series(charge=1, fragment_type='b')

Calculate the b and y product ion series of the peptide sequence.

Parameters:

• charge (int) – The charge of the product ions.

• fragment_type (str) – The type of the product ions, must be one of ‘a’, ‘b’, ‘c’, ‘x’, ‘y’, ‘z’.

Return type:

Tuple[List[PeptideProductIon], List[PeptideProductIon]]

Returns:

The b and y product ion series of the peptide sequence.

classmethod from_py_ptr(obj)

get_py_ptr()

property mono_isotopic_mass: float

property peptide_id: None | int

property sequence: str

to_json()

Return type:

str

to_sage_representation()

Return type:

Tuple[str, List[float]]

to_tokens(group_modifications=True)

Return type:

List[str]

imspy.data.spectrum module

class imspy.data.spectrum.IndexedMzSpectrum(index, mz, intensity)

Bases: RustWrapperObject

property df: DataFrame

Data.

Returns:

Data.

Return type:

pd.DataFrame

filter(mz_min=0.0, mz_max=2000.0, intensity_min=0.0, intensity_max=1000000000.0)

Filter the spectrum for a given m/z range and intensity range.

Parameters:

• mz_min (float) – Minimum m/z value.

• mz_max (float) – Maximum m/z value.

• intensity_min (float, optional) – Minimum intensity value. Defaults to 0.0.

• intensity_max (float, optional) – Maximum intensity value. Defaults to 1e9.

Returns:

Filtered spectrum.

Return type:

IndexedMzSpectrum

classmethod from_py_ptr(spec)

Create a IndexedMzSpectrum from a PyIndexedMzSpectrum.

Parameters:

spec (pims.PyIndexedMzSpectrum) – PyIndexedMzSpectrum to create the IndexedMzSpectrum from.

Returns:

IndexedMzSpectrum created from the PyIndexedMzSpectrum.

Return type:

IndexedMzSpectrum

get_py_ptr()

Get the spec_ptr.

Returns:

spec_ptr.

Return type:

pims.PyIndexedMzSpectrum

property index: ndarray[Any, dtype[int32]]

Index.

Returns:

Index.

Return type:

NDArray[np.int32]

property intensity: ndarray[Any, dtype[float64]]

Intensity.

Returns:

Intensity.

Return type:

NDArray[np.float64]

property mz: ndarray[Any, dtype[float64]]

m/z.

Returns:

m/z.

Return type:

NDArray[np.float64]

class imspy.data.spectrum.MzSpectrum(mz, intensity)

Bases: RustWrapperObject

add_mz_noise_normal(noise_ppm)

Add normal noise to the intensity values of the spectrum.

Parameters:

noise_ppm (float) – Noise ppm, noise will be sampled from a normal distribution with mean 0 and std noise_ppm / 3.0.

Returns:

Spectrum with added noise.

Return type:

MzSpectrum

add_mz_noise_uniform(noise_ppm, right_drag=False)

Add uniform noise to the m/z values of the spectrum.

Parameters:

• noise_ppm (float) – Noise ppm, noise will be sampled from a uniform distribution with mean 0 and std noise_ppm.

• right_drag (bool, optional) – If true, the noise will be shifted to the right. Defaults to False.

Returns:

Spectrum with added noise.

Return type:

MzSpectrum

property df: DataFrame

Data.

Returns:

Data.

Return type:

pd.DataFrame

filter(mz_min=0.0, mz_max=2000.0, intensity_min=0.0, intensity_max=1000000000.0)

Filter the spectrum for a given m/z range and intensity range.

Parameters:

• mz_min (float) – Minimum m/z value.

• mz_max (float) – Maximum m/z value.

• intensity_min (float, optional) – Minimum intensity value. Defaults to 0.0.

• intensity_max (float, optional) – Maximum intensity value. Defaults to 1e9.

Returns:

Filtered spectrum.

Return type:

MzSpectrum

classmethod from_jsons(jsons)

Return type:

MzSpectrum

classmethod from_mz_spectra_list(spectra_list, resolution)

Generates a convoluted mass spectrum by adding all spectra in the given list.

Parameters:

• spectra_list (List[MzSpectrum]) – List of mass spectra.

• resolution (int) – Desired resolution of returned spectrum.

Returns:

Convoluted spectrum.

Return type:

MzSpectrum

classmethod from_py_ptr(spec)

Create a MzSpectrum from a PyMzSpectrum.

Parameters:

spec (pims.PyMzSpectrum) – PyMzSpectrum to create the MzSpectrum from.

Returns:

MzSpectrum created from the PyMzSpectrum.

Return type:

MzSpectrum

get_py_ptr()

Get the spec_ptr.

Returns:

spec_ptr.

Return type:

pims.PyMzSpectrum

property intensity: ndarray[Any, dtype[float64]]

Intensity.

Returns:

Intensity.

Return type:

NDArray[np.float64]

property mz: ndarray[Any, dtype[float64]]

m/z.

Returns:

m/z.

Return type:

NDArray[np.float64]

to_centroided(baseline_noise_level=0.0, sigma=0.1, normalize=True)

Convert the spectrum to a centroided spectrum.

Returns:

Centroided spectrum.

Return type:

MzSpectrum

to_jsons()

generates json string representation of MzSpectrum

Return type:

str

to_resolution(resolution)

Bins the spectrum’s m/z values to a given resolution and sums the intensities.

Parameters:

resolution (int) – Negative decadic logarithm of bin size.

Returns:

A new MzSpectrum where m/z values are binned according to the given resolution.

Return type:

MzSpectrum

to_windows(window_length=10, overlapping=True, min_num_peaks=5, min_intensity=1)

Convert the spectrum to a list of windows.

Parameters:

• window_length (float, optional) – Window length. Defaults to 10.

• overlapping (bool, optional) – Whether the windows should overlap. Defaults to True.

• min_num_peaks (int, optional) – Minimum number of peaks in a window. Defaults to 5.

• min_intensity (float, optional) – Minimum intensity of a peak in a window. Defaults to 1.

Returns:

List of windows.

Return type:

Tuple[NDArray, List[MzSpectrum]]

vectorized(resolution=2)

Convert the spectrum to a vectorized spectrum.

Parameters:

resolution (int, optional) – Resolution. Defaults to 2.

Returns:

Vectorized spectrum.

Return type:

MzSpectrumVectorized

class imspy.data.spectrum.MzSpectrumVectorized(indices, values, resolution)

Bases: RustWrapperObject

classmethod from_py_ptr(spec)

Create a MzSpectrum from a PyMzSpectrum.

Parameters:

spec (pims.PyMzSpectrum) – PyMzSpectrum to create the MzSpectrum from.

Returns:

MzSpectrum created from the PyMzSpectrum.

Return type:

MzSpectrum

get_py_ptr()

Get the spec_ptr.

Returns:

spec_ptr.

Return type:

pims.PyMzSpectrumVectorized

property indices: ndarray[Any, dtype[int32]]

m/z.

Returns:

m/z.

Return type:

NDArray[np.float64]

property resolution: float

Resolution.

Returns:

Resolution.

Return type:

float

to_centroided(integrate_method=<function get_peak_integral>)

Convert the spectrum to a centroided spectrum.

Returns:

Centroided spectrum.

Return type:

MzSpectrum

property values: ndarray[Any, dtype[float64]]

Intensity.

Returns:

Intensity.

Return type:

NDArray[np.float64]

class imspy.data.spectrum.TimsSpectrum(frame_id, scan, retention_time, mobility, ms_type, index, mz, intensity)

Bases: RustWrapperObject

property df: DataFrame

Data.

Returns:

Data.

Return type:

pd.DataFrame

filter(mz_min=0.0, mz_max=2000.0, intensity_min=0.0, intensity_max=1000000000.0)

Filter the spectrum for a given m/z range and intensity range.

Parameters:

• mz_min (float) – Minimum m/z value.

• mz_max (float) – Maximum m/z value.

• intensity_min (float, optional) – Minimum intensity value. Defaults to 0.0.

• intensity_max (float, optional) – Maximum intensity value. Defaults to 1e9.

Returns:

Filtered spectrum.

Return type:

TimsSpectrum

property frame_id: int

Frame ID.

Returns:

Frame ID.

Return type:

int

classmethod from_py_ptr(spec)

Create a TimsSpectrum from a PyTimsSpectrum.

Parameters:

spec (pims.PyTimsSpectrum) – PyTimsSpectrum to create the TimsSpectrum from.

Returns:

TimsSpectrum created from the PyTimsSpectrum.

Return type:

TimsSpectrum

get_py_ptr()

Get the spec_ptr.

Returns:

spec_ptr.

Return type:

pims.PyTimsSpectrum

property index: ndarray[Any, dtype[int32]]

Index.

Returns:

Index.

Return type:

NDArray[np.int32]

property intensity: ndarray[Any, dtype[float64]]

Intensity.

Returns:

Intensity.

Return type:

NDArray[np.float64]

property mobility: float

Inverse mobility.

Returns:

Inverse mobility.

Return type:

float

property ms_type: str

MS type.

Returns:

MS type.

Return type:

str

property mz: ndarray[Any, dtype[float64]]

m/z.

Returns:

m/z.

Return type:

NDArray[np.float64]

property mz_spectrum: MzSpectrum

Get the MzSpectrum.

Returns:

Spectrum.

Return type:

MzSpectrum

property retention_time: float

Retention time.

Returns:

Retention time.

Return type:

float

property scan: int

Scan.

Returns:

Scan.

Return type:

int

imspy.data.spectrum.get_peak_integral(peaks, peak_info)

Calculates the integral of the peaks in a spectrum.

Parameters:

• peaks (NDArray[np.int32]) – Peak indices.

• peak_info (dict) – Peak info.

Returns:

Peak integrals.

Return type:

NDArray[np.float64]

Module contents