Mass Spectrometry
Mass spectrometry is commonly used in catalysis and electrocatalysis for two different types of data - spectra, where intensity is taken while scanning over m/z, and multiple ion detection (MID) where the intensity of a small set of m/z values are tracked in time.
The main TechniqueMeasurement class for MID data is the MSMeasurement
.
The position of spectra in ixdat is not completely set yet. Currently, they exist as Spectrum
base
class alongside Measurement
. For more details see Spectrum
The ms
module
Module for representation and analysis of MS measurements
- class ixdat.techniques.ms.MSMeasurement(name, **kwargs)[source]
Class implementing raw MS functionality
- default_exporter
alias of
MSExporter
- grab_flux(mol, tspan=None, tspan_bg=None, remove_background=True, removebackground=None, include_endpoints=False)[source]
Return the flux of mol (calibrated signal) in [mol/s]
Note: - With native ixdat quantification (use_siq=False),
grab_flux(mol, …) is identical to grab(f”n_dot_{mol}”, …) with remove_background=True by default. An MSCalibration does the maths.
With an external quantification package (use_siq=True), the maths are done here with the help of self.quantifier
- Parameters
mol (str or MSCalResult) – Name of the molecule or a ms_calibration thereof
tspan (list) – Timespan for which the signal is returned.
tspan_bg (list) – Timespan that corresponds to the background signal. If not given, no background is subtracted.
remove_background (bool) – Whether to remove a pre-set background if available Defaults to True.
removebackground (bool) – DEPRECATED. Use remove_background.
include_endpoints (bool) – Whether to interpolate for tspan[0] and tspan[-1]
- grab_flux_for_t(mol, t, tspan_bg=None, remove_background=False, removebackground=None)[source]
Return the flux of mol (calibrated signal) in [mol/s] for a given time vec
- Parameters
mol (str) – Name of the molecule.
t (np.array) – The time vector along which to give the flux
tspan_bg (tspan) – Timespan that corresponds to the background signal. If not given, no background is subtracted.
remove_background (bool) – Whether to remove a pre-set background if available
removebackground (bool) – DEPRECATED. Use remove_background.
- integrate_flux(mol, tspan, tspan_bg, ax=None)[source]
Integrate a calibrated ms signal with background subtraction and evt. plotting (copy of integrate_signal method)
- TODO: Should this, like grab_signal does now, have the option of using a
background saved in the object rather than calculating a new one?
TODO: Ensure fill_between considers the non-standard unit in the figure
- Parameters
mol (str) – The molecule name for which to integrate the signal
tspan (tspan) – The timespan over which to integrate
tspan_bg (tspan) – Timespan at which the signal is at its background value
ax (Axis) – axis to plot on. Defaults to None
- integrate_signal(mass, tspan, tspan_bg, ax=None)[source]
Integrate a ms signal with background subtraction and evt. plotting
- TODO: Should this, like grab_signal does now, have the option of using a
background saved in the object rather than calculating a new one?
- Parameters
mass (str) – The mass for which to integrate the signal
tspan (tspan) – The timespan over which to integrate
tspan_bg (tspan) – Timespan at which the signal is at its background value
ax (Axis) – axis to plot on. Defaults to None
- property mass_list
List of the masses for which ValueSeries are contained in the measurement
- class ixdat.techniques.ms.MSSpectroMeasurement(name, **kwargs)[source]
- default_exporter
alias of
MSSpectroExporter
- default_plotter
alias of
MSSpectroPlotter