calibration

class deimos.calibration.CCSCalibration

Performs calibration and stores result to enable convenient application.

buffer_mass

Mass of the buffer gas used in ion mobility experiment.

Type:

float

beta

Slope of calibration curve.

Type:

float

tfix

Intercept of calibration curve.

Type:

float

fit

Fit parameters of calibration curve.

Type:

dict of float

_check()

Helper method to check for calibration parameters.

arrival2ccs(mz, ta, q=1)

Calculates collision cross section (CCS) from arrival time, m/z, and nominal charge, according to calibration parameters.

Parameters:

• mz (float or list of float) – Feature mass-to-charge ratio.

• ta (float or list of float) – Feature arrival time (ms).

• q (int or list of int) – Feature nominal charge.

Returns:

Feature collision cross section (A^2).

Return type:

array

calibrate(mz=None, ta=None, ccs=None, q=None, beta=None, tfix=None, buffer_mass=28.013, power=False)

Performs calibration if mz, ta, ccs, and q arrays are provided, otherwise calibration parameters beta and tfix must be supplied directly.

Parameters:

• mz (array) – Calibration mass-to-charge ratios.

• ta (array) – Calibration arrival times.

• ccs (array) – Calibration collision cross sections.

• q (array) – Calibration nominal charges.

• beta (float) – Provide calibration parameter “beta” (slope) directly.

• tfix (float) – Provide calibration parameter “tfix” (intercept) directly.

• buffer_mass (float) – Mass of the buffer gas.

• power (bool) – Indicate whether to use linearize power function for calibration, i.e. in traveling wave ion moblility spectrometry.

ccs2arrival(mz, ccs, q=1)

Calculates arrival time from collsion cross section (CCS), m/z, and nominal charge, according to calibration parameters.

Parameters:

• mz (float or list of float) – Feature mass-to-charge ratio.

• ccs (float or list of float) – Feature collision cross section (A^2).

• q (int or list of int) – Feature nominal charge.

Returns:

Feature arrival time (ms).

Return type:

array

deimos.calibration.calibrate_ccs(mz=None, ta=None, ccs=None, q=None, beta=None, tfix=None, buffer_mass=28.013, power=False)

Convenience function for CCSCalibration. Performs calibration if mz, ta, ccs, and q arrays are provided, otherwise calibration parameters beta and tfix must be supplied directly.

Parameters:

• mz (array) – Calibration mass-to-charge ratios.

• ta (array) – Calibration arrival times.

• ccs (array) – Calibration collision cross sections.

• q (array) – Calibration nominal charges.

• beta (float) – Provide calibration parameter “beta” (slope) directly.

• tfix (float) – Provide calibration parameter “tfix” (intercept) directly.

• buffer_mass (float) – Mass of the buffer gas.

• power (bool) – Indicate whether to use linearize power function for calibration, i.e. in traveling wave ion moblility spectrometry.

Returns:

Instance of calibrated ~deimos.calibration.CCSCalibration object.

Return type:

CCSCalibration

deimos.calibration.tunemix(features, mz=[112.985587, 301.998139, 601.978977, 1033.988109, 1333.968947, 1633.949786], ccs=[108.4, 139.8, 179.9, 254.2, 283.6, 317.7], q=[1, 1, 1, 1, 1, 1], buffer_mass=28.013, mz_tol=0.0002, dt_tol=0.04, power=False)

Provided tune mix data with known calibration ions (i.e. known m/z, CCS, and nominal charge), determine the arrival time for each to define a CCS calibration.

Parameters:

• mz (array) – Calibration mass-to-charge ratios.

• ccs (array) – Calibration collision cross sections.

• q (array) – Calibration nominal charges.

• buffer_mass (float) – Mass of the buffer gas.

• mz_tol (float) – Tolerance in ppm to isolate tune ion.

• dt_tol (float) – Fractional tolerance to define drift time window bounds.

• power (bool) – Indicate whether to use linearize power function for calibration, i.e. in traveling wave ion moblility spectrometry.

Returns:

Instance of calibrated ~deimos.calibration.CCSCalibration object.

Return type:

CCSCalibration