imspy.chemistry package

Submodules

imspy.chemistry.amino_acids module

imspy.chemistry.constants module

imspy.chemistry.elements module

imspy.chemistry.mobility module

imspy.chemistry.mobility.ccs_to_one_over_k0(ccs, mz, charge, mass_gas=28.013, temp=31.85, t_diff=273.15)

Convert CCS to reduced ion mobility (1/k0).

Parameters:

  • ccs – collision cross-section

  • mz – mass-over-charge of the ion

  • charge – charge state of the ion

  • mass_gas – mass of drift gas

  • temp – temperature of the drift gas in C°

  • t_diff – factor to translate from C° to K

Returns:

reduced ion mobility

Return type:

float

imspy.chemistry.mobility.ccs_to_one_over_k0_par(ccs, mz, charge, mass_gas=28.013, temp=31.85, t_diff=273.15, num_threads=-1)

Convert CCS to reduced ion mobility (1/k0) in parallel.

Parameters:

  • ccs (ndarray[Any, dtype[TypeVar(_ScalarType_co, bound= generic, covariant=True)]]) – collision cross-section

  • mz (ndarray[Any, dtype[TypeVar(_ScalarType_co, bound= generic, covariant=True)]]) – mass-over-charge of the ion

  • charge (ndarray[Any, dtype[TypeVar(_ScalarType_co, bound= generic, covariant=True)]]) – charge state of the ion

  • mass_gas (float) – mass of drift gas

  • temp (float) – temperature of the drift gas in C°

  • t_diff (float) – factor to translate from C° to K

  • num_threads (int) – number of threads

Returns:

reduced ion mobility

Return type:

NDArray

imspy.chemistry.mobility.one_over_k0_to_ccs(one_over_k0, mz, charge, mass_gas=28.013, temp=31.85, t_diff=273.15)

Convert reduced ion mobility (1/k0) to CCS.

Parameters:

  • one_over_k0 – reduced ion mobility

  • mz – mass-over-charge of the ion

  • charge – charge state of the ion

  • mass_gas – mass of drift gas

  • temp – temperature of the drift gas in C°

  • t_diff – factor to translate from C° to K

Returns:

collision cross-section

Return type:

float

imspy.chemistry.mobility.one_over_k0_to_ccs_par(one_over_k0, mz, charge, mass_gas=28.013, temp=31.85, t_diff=273.15, num_threads=-1)

Convert reduced ion mobility (1/k0) to CCS in parallel.

Parameters:

  • one_over_k0 (ndarray[Any, dtype[TypeVar(_ScalarType_co, bound= generic, covariant=True)]]) – reduced ion mobility

  • mz (ndarray[Any, dtype[TypeVar(_ScalarType_co, bound= generic, covariant=True)]]) – mass-over-charge of the ion

  • charge (ndarray[Any, dtype[TypeVar(_ScalarType_co, bound= generic, covariant=True)]]) – charge state of the ion

  • mass_gas (float) – mass of drift gas

  • temp (float) – temperature of the drift gas in C°

  • t_diff (float) – factor to translate from C° to K

  • num_threads (int) – number of threads

Returns:

collision cross-section

Return type:

NDArray

imspy.chemistry.sum_formula module

imspy.chemistry.unimod module

imspy.chemistry.utility module

imspy.chemistry.utility.calculate_mz(mass, charge)

Calculate m/z value.

Parameters:

  • mass (float) – Mass.

  • charge (int) – Charge.

Returns:

m/z value.

Return type:

float

imspy.chemistry.utility.calculate_transmission_dependent_fragment_ion_isotope_distribution(target_spec, complement_spec, transmitted_isotopes, max_isotope)

Calculate transmission dependent fragment ion isotope distribution.

Parameters:

  • target_spec (MzSpectrum) – Target spectrum.

  • complement_spec (MzSpectrum) – Complement spectrum.

  • transmitted_isotopes (MzSpectrum) – Transmitted isotopes.

  • max_isotope (int) – Maximum isotope.

Returns:

Transmission dependent fragment ion isotope distribution.

Return type:

MzSpectrum

Module contents