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.MSCalResult(name=None, mol=None, mass=None, cal_type=None, F=None)[source]

A class for a mass spec ms_calibration result.

FIXME: I think that something inheriting directly from Saveable does not belong in

a technique module.

class ixdat.techniques.ms.MSCalibration(name=None, date=None, tstamp=None, setup=None, ms_cal_results=None, signal_bgs=None, technique='MS', measurement=None)[source]

Class for mass spec calibrations. TODO: replace with powerful external package

calibrate_series(key, measurement=None)[source]

Return a calibrated series for key if possible.

If key starts with “n_”, it is interpreted as a molecule flux. This method then searches the calibration for a sensitivity factor for that molecule uses it to divide the relevant mass signal from the measurement. Example acceptable keys: “n_H2”, “n_dot_H2”. If the key does not start with “n_”, or the calibration can’t find a relevant sensitivity factor and mass signal, this method returns None.

export(path_to_file=None)[source]

Export an ECMSCalibration as a json-formatted text file

get_F(mol, mass)[source]

Return the sensitivity factor for mol at mass

get_mass_and_F(mol)[source]

Return the mass and sensitivity factor to use for simple quant. of mol

classmethod read(path_to_file)[source]

Read an MSCalibration from a json-formatted text file

scaled_to(ms_cal_result)[source]

Return a new ms_calibration w scaled sensitivity factors to match one given

class ixdat.techniques.ms.MSInlet(*, l_cap=0.001, w_cap=6e-06, h_cap=6e-06, gas='He', T=298.15, p=100000.0, verbose=True)[source]

A class for describing the inlet to the mass spec

Every MSInlet describes the rate and composition of the gas entering a mass spectrometer. The default is a Spectro Inlets EC-MS chip.

calc_l_cap_eff(n_dot_measured, gas=None, w_cap=None, h_cap=None, T=None, p=None)[source]

Calculate gas specific effective length of the capillary in [m] and add {gas:value} to l_cap_eff (dict)

Parameters
  • w_cap (float) – Capillary width [m], defaults to self.w_cap

  • h_cap (float) – Capillary height [m], defaults to self.h_cap

  • n_dot_measured (float) – Measured flux of gas [mol/s]

  • gas (dict or str) – The gas in the chip, defaults to self.gas

  • T (float) – Temperature [K], if to be updated

  • p (float) – Pressure [Pa], if to be updated

Returns

Gas specific effective length in [m]

Return type

float

calc_n_dot_0(gas=None, w_cap=None, h_cap=None, l_cap=None, T=None, p=None)[source]

Calculate the total molecular flux through the capillary in [s^-1]

Uses Equation 4.10 of Trimarco, 2017. “Real-time detection of sub-monolayer desorption phenomena during electrochemical reactions: Instrument development and applications.” PhD Thesis, Technical University of Denmark.

Parameters
  • w_cap (float) – Capillary width [m], defaults to self.w_cap

  • h_cap (float) – Capillary height [m], defaults to self.h_cap

  • l_cap (float) – Capillary length [m], defaults to self.l_cap

  • gas (dict or str) – The gas in the chip, defaults to self.gas

  • T (float) – Temperature [K], if to be updated

  • p (float) – Pressure [Pa], if to be updated

Returns

The total molecular flux in [s^-1] through the capillary

Return type

float

update_l_cap(gases=None)[source]

Update self.l_cap from average of values in dict l_cap_eff

Parameters

gases (list) – List of gases to average l_cap, default all

Returns

Averaged effective capilllary length in [m]

Return type

float

class ixdat.techniques.ms.MSMeasurement(name, **kwargs)[source]

Class implementing raw MS functionality

cut(**kwargs)

Return a new measurement with the data in the given time interval

Parameters
  • tspan (iter of float) – The time interval to use, relative to self.tstamp tspan[0] is the start time of the interval, and tspan[-1] is the end time of the interval. Using tspan[-1] means you can directly use a long time vector that you have at hand to describe the time interval you’re looking for.

  • t_zero (float or str) – The time in the measurement to set to t=0. If a float, it is interpreted as wrt the original tstamp. String options include “start”, which puts t=0 at the start of the cut interval.

default_plotter

alias of MSPlotter

gas_flux_calibration(mol, mass, inlet=None, chip=None, tspan=None, tspan_bg=None, ax=None, carrier_mol=None, mol_conc_ppm=None)[source]

Fit mol’s sensitivity at mass based on one period with steady gas composition.

Parameters
  • mol (str) – The name of the molecule to calibrate

  • mass (str) – The mass to calibrate at

  • inlet (MSInlet) – An object with a calc_n_dot_0 method for total flux to the vacuum chamber containing the mass spectrometer.

  • chip (MSInlet) – DEPRECATED. Old name for inlet.

  • tspan (iter) – The timespan to average the signal over. Defaults to all

  • tspan_bg (iter) – Optional timespan at which the signal is at its background.

  • ax (matplotlib axis) – The axis on which to indicate what signal is used with a thicker line. Defaults to none

  • carrier_mol (str) – The name of the molecule of the carrier gas if a dilute analyte is used. Calibration assumes total flux of the capillary is the same as the flux of pure carrier gas. Defaults to None.

  • mol_conc_ppm (float) – Concentration of the dilute analyte in the carrier gas in ppm. Defaults to None.

Returns MSCalResult: a MS calibration result containing the sensitivity factor

for mol at mass

gas_flux_calibration_curve(mol, mass, inlet=None, chip=None, tspan_list=None, carrier_mol=None, mol_conc_ppm=None, p_inlet=None, tspan_bg=None, ax='new', axis_measurement=None, remove_bg_on_axis_measurement=True, return_ax=False)[source]

Fit mol’s sensitivity at mass from 2+ periods of steady gas composition.

Parameters
  • inlet (MSInlet) – An object with a calc_n_dot_0 method for total flux to the vacuum chamber containing the mass spectrometer.

  • mol (str) – Name of the molecule to calibrate

  • mass (str) – Name of the mass at which to calibrate

  • inlet – An object with a calc_n_dot_0 method for total flux to the vacuum chamber containing the mass spectrometer.

  • chip (MSInlet) – DEPRECATED. Old name for inlet.

  • tspan_list (list of tspan) – The timespans of steady concentration or pressure

  • carrier_mol (str) – The name of the molecule of the carrier gas if a dilute analyte is used. Calibration assumes total flux of the capillary is the same as the flux of pure carrier gas. Defaults to None.

  • mol_conc_ppm (float or list) – Concentration of the dilute analyte in the carrier gas in ppm. Defaults to None. Accepts float (for pressure calibration) or list for concentration calibration. If list needs to be same length as tspan_list or selector_list.

  • p_inlet (float, list) – Pressure at the inlet (Pa). Overwrites the pressure inherent to self (i.e. the MSInlet object). Accepts float (for conc. calibration) or list for pressure calibration. If list, then needs to be same length as tspan_list or selector_list.

  • tspan_bg (tspan) – The time to use as a background

  • ax (Axis) – The axis on which to plot the ms_calibration curve result. Defaults to a new axis.

  • axis_measurement (Axis) – The MS plot axes to highlight the ms_calibration on. Defaults to None.

  • remove_bg_on_axis_measurement (bool) – Whether the plot on axis_measurement is showing raw data or bg subtracted data. Defaults to True, i.e. plotting data with the same bg subtraction as used for the calibration.

  • return_ax (bool) – Whether to return the axis on which the calibration curve is plotted together with the MSCalResult. Defaults to False.

Return MSCalResult(, Axis): The result of the MS calibration (and calibration

curve axis if requested) based on flux calculation during selected time periods.

TODO: automatically recognize the pressure from measurement (if available)

get_flux_series(mol)[source]

Return a ValueSeries with the calibrated flux of mol

grab(item, tspan=None, tspan_bg=None, include_endpoints=False, remove_background=False)[source]

Returns t, S where S is raw signal in [A] for a given signal name (ie mass)

Parameters
  • item (str) – Name of the signal. If item has the form f”n_dot_{mol}”, then grab_flux(mol) is returned.

  • 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. This is special to MSMeasurement. Defaults to False, but in grab_flux it defaults to True.

  • include_endpoints (bool) – Whether to ensure tspan[0] and tspan[-1] are in t

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.

grab_for_t(item, t, tspan_bg=None, remove_background=False)[source]

Return a numpy array with the value of item interpolated to time t

Parameters
  • item (str) – The name of the value to grab

  • t (np array) – The time vector to grab the value for

  • tspan_bg (iterable) – Optional. A timespan defining when item is at its baseline level. The average value of item in this interval will be subtracted from what is returned.

  • remove_background (bool) – Whether to remove a pre-set background if available. This is special to MSMeasurement. Defaults to False, but in grab_flux it defaults to True.

grab_signal(*args, **kwargs)[source]

Alias for grab()

grab_siq_fluxes(tspan=None, tspan_bg=None, remove_background=False, include_endpoints=False)[source]

Return a time vector and a dictionary with all the quantified fluxes

Parameters
  • 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..

  • include_endpoints (bool) – Whether to interpolate for tspan[0] and tspan[-1]

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

multicut(**kwargs)

Return a selection of the measurement including each of the given tspans

reset_bg(mass_list=None)[source]

Reset background values for the masses in mass_list

set_bg(tspan_bg=None, mass_list=None)[source]

Set background values for mass_list to the average signal during tspan_bg.

set_siq_quantifier(quantifier=None, calibration=None, mol_list=None, mass_list=None, carrier='He')[source]

Set the spectro_inlets_quantification quantifier.

The Quantifier is an object with the method calc_n_dot, which takes a dictionary of signals or signal vectors in [A] and return a dictionary of molecular fluxes in [mol/s]. The quantifier typically does this by solving the linear equations of S_M = sum_i ( F_M^i * n_dot^i ) Where n_dot^i is the flux to the vacuum chamber of molecule i in [mol/s], S_M is the signal at mass M in [A], and F_M^i is the sensitivity factor of molecule i at mass M. The quantifier thus needs access to a set of sensitivity factors.

The quantifier can be built in this method (avoiding explicit import of the spectro_inlets_quantification package) by providing the sensitivity factors in the form of a Calibration (which can be obtained from e.g. MSMeasurement.multicomp_gas_flux_cal) and the specification of which ones to use by mol_list and mass_list. The quantifier will always use all the masses in mass_list to solve for the flux of all the mols in mol_list.

The argument carrier is required by some quantifiers but only used if partial pressures before the MS inlet are required (quantifier.calc_pp)

Quantification is only as accurate as your sensitivity factors!

Parameters
  • quantifier (Quantifier) – The quantifier, if prepared before method call. No additional arguments needed. Otherwise, the following three are needed:

  • calibration (Calibration) – The calibration to build the quantifier with

  • mol_list (list of str) – The list of molecules to use in flux calculations. These should all be represented in the Calibration. If not provided, we’ll use all the mols in the Calibration.

  • mass_list (list of str) – The list of masses to use in flux calculations. These should all be represented in the Calibration. If not provided, we’ll use all the masses in the Calibration.

  • carrier (optional, str) – The carrier gas in the experiment. Defaults to “He”.

siq_gas_flux_calibration(mol, mass, tspan, chip=None)[source]

Simple pure-gas flux calibration, using spectro_inlets_quantification

Parameters
  • mol (str) – Name of molecule to be calibrated (e.g. “He”)

  • mass (str) – Mass at which to calibrate it (e.g. “M4”)

  • tspan (timespan) – A timespan during which the pure gas is in the chip

  • chip (Chip, optional) – An object defining the capillary inlet, if different than the standard chip assumed by the external package.

Returns CalPoint: An object from spectro_inlets_quantification,

representing the calibration result

siq_gas_flux_calibration_curve(mol, mass, chip=None, tspan_list=None, carrier_mol=None, mol_conc_ppm=None, p_inlet=None, tspan_bg=None, ax='new', axis_measurement=None, remove_bg_on_axis_measurement=True, return_ax=False)[source]

Fit mol’s sensitivity at mass from 2+ periods of steady gas composition.

Parameters
  • mol (str) – Name of the molecule to calibrate

  • mass (str) – Name of the mass at which to calibrate

  • tspan_list (list of tspan) – The timespans of steady concentration or pressure

  • carrier_mol (str) – The name of the molecule of the carrier gas if a dilute analyte is used. Calibration assumes total flux of the capillary is the same as the flux of pure carrier gas. Defaults to None.

  • mol_conc_ppm (float, list) – Concentration of the dilute analyte in the carrier gas in ppm. Defaults to None. Accepts float (for pressure calibration) or list for concentration calibration. If list needs to be same length as tspan_list or selector_list.

  • p_inlet (float, list) – Pressure at the inlet (Pa). Overwrites the pressure inherent to self (i.e. the MSInlet object). Accepts float (for conc. calibration) or list for pressure calibration. If list, then needs to be same length as tspan_list or selector_list.

  • tspan_bg (tspan) – The time to use as a background

  • ax (Axis) – The axis on which to plot the ms_calibration curve result. Defaults to a new axis.

  • axis_measurement (Axes) – The MS plot axes to highlight the ms_calibration on. Defaults to None. These axes are not returned.

  • remove_bg_on_axis_measurement (bool) – Whether the plot on axis_measurement is showing raw data or bg subtracted data. Defaults to True, i.e. plotting data with the same bg subtraction as used for the calibration.

  • return_ax (bool) – Whether to return the axis on which the calibration curve is plotted together with the MSCalResult. Defaults to False.

Returns CalPoint: An object from spectro_inlets_quantification,

representing the calibration result

TODO: automatically recognize the pressure from measurement (if available)

siq_multicomp_gas_flux_calibration(mol_list, mass_list, gas, tspan, gas_bg=None, tspan_bg=None, chip=None)[source]

Calibration of multiple components of a calibration gas simultaneously

Uses a matrix equation and the reference spectra in the molecule data files.

The results are only as accurate as the reference spectrum used. For this reason, this method is a last resort and it is recommended not to use a multicomponent calibration gas. Instead, get a separate calibration gas for each molecule to be calibrated.

Here is an explanation of the math used in this method:

The fundamental matrix equation is:

S_vec = F_mat @ n_dot_vec

Elementwise, this is:

S_M = sum_i ( F^i_M * n_dot^i )

Rewrite to show that sensitivity factors follow each molecule’s spectrum:

S_M = sum_i (F_weight_i * spectrum^i_M * n_dot^i)

And regroup the parts that only depend on the molecule (^i):

S_M = sum_i (spectrum^i_M * (F_weight^i * n_dot^i)) S_M = sum_i (spectrum^i_M * sensitivity_flux^i)

Change back into a matrix equation, and solve it:

S_vec = spectrum_mat @ sensitivity_flux_vec sensitivity_flux_vec = spectrum_mat^-1 @ S_vec # eq. 1

Ungroup the part we grouped before (the “sensitivity_flux”):

F_weight^i = sensitivity_flux^i / n_dot^i # eq. 2

And, in the end, each sensitivity factor is:

F_M^i = F_weight^i * spectrum^i_M # eq. 3

Equations 1, 2, and 3 are implemented in the code of this method.

Parameters
  • mol_list (list of str) – List of the names of the molecules to calibrate

  • mass_list (list of str) – List of the masses to calibrate

  • gas (Gas, dict, or str) – Composition of the calibration gas, e.g. {“Ar”: 0.95, “H2”: 0.05} for 5% H2 in Ar

  • tspan (Timespan) – Timespan during which the calibration gas is in the chip

  • gas_bg (Gas, dict, or str) – Composition of the background gas

  • tspan_bg (Timespan) – Timespan during which the background gas is in the chip

  • chip (Chip, optional) – object describing the MS capillary, if different than the standard chip in the MS quantification package

Returns Calibration: An object from spectro_inlets_quantification,

representing all the calibration results from the calibration.

class ixdat.techniques.ms.MSSpectrum(*, name, technique='spectrum', metadata=None, sample_name=None, reader=None, tstamp=None, field=None, field_id=None, duration=None)[source]

Nothing to add to normal Spectrum yet. TODO: Methods for co-plotting ref spectra from a database

class ixdat.techniques.ms.MSSpectrumSeries(*args, **kwargs)[source]

Nothing to add to normal SpectrumSeries yet.

class ixdat.techniques.ms.SpectroMSMeasurement(name, **kwargs)[source]
default_plotter

alias of SpectroMSPlotter