IMTypes Class Reference

#include <OpenMS/IONMOBILITY/IMTypes.h>

Collaboration diagram for IMTypes:

Static Public Member Functions
static IMFormat	determineIMFormat (const MSExperiment &exp, int ms_level)
static IMFormat	determineIMFormat (const MSSpectrum &spec)
	Checks for existence of a single driftTime (using spec.getDriftTime()) or an ion-mobility float data array (using spec.hasIMData())
static DIM_UNIT	fromIMUnit (const DriftTimeUnit from)
	Convert a DriftTimeUnit to the more general DIM_UNIT.
static double	oneOverK0ToCCS (double one_over_k0, double mz, int charge, double buffer_gas_mass=N2_BUFFER_GAS_MASS)
	Convert a reduced inverse ion mobility (1/K0) to a collision cross section (CCS) via the Mason-Schamp relation.
static double	ccsToOneOverK0 (double ccs, double mz, int charge, double buffer_gas_mass=N2_BUFFER_GAS_MASS)
	Inverse of oneOverK0ToCCS - convert a collision cross section (CCS) back to reduced inverse ion mobility (1/K0).

Static Public Attributes
static constexpr double	DRIFTTIME_NOT_SET = -1.0
	If drift time for a spectrum is unavailable (i.e. not an IM spectrum), it will have this value.
static constexpr double	N2_BUFFER_GAS_MASS = 28.0

Member Function Documentation

ccsToOneOverK0()

static double ccsToOneOverK0 ( double  ccs, double  mz, int  charge, double  buffer_gas_mass = N2_BUFFER_GAS_MASS  )

static

Inverse of oneOverK0ToCCS - convert a collision cross section (CCS) back to reduced inverse ion mobility (1/K0).

Parameters

[in]	ccs	Collision cross section in square Angstrom (Angstrom^2); must be > 0.
[in]	mz	Precursor m/z of the ion; must be > 0.
[in]	charge	Precursor charge; the sign is ignored (|charge| is used) and it must be non-zero.
[in]	buffer_gas_mass	Drift-gas mass in Da; defaults to N2 (N2_BUFFER_GAS_MASS).

Returns

Reduced inverse ion mobility 1/K0 in V*s/cm^2.

Exceptions

Exception::InvalidValue

if ccs <= 0, mz <= 0, or charge == 0.

determineIMFormat() [1/2]

static IMFormat determineIMFormat ( const MSExperiment &  exp, int  ms_level  )

static

Checks only spectra of the given MS level for their IM format and returns the common type. If no spectra of ms_level exist or none have IM data, IMFormat::NONE is returned.

Exceptions

Exception::InvalidValue

if spectra of the given MS level have different IM formats

determineIMFormat() [2/2]

static IMFormat determineIMFormat ( const MSSpectrum &  spec )

static

Checks for existence of a single driftTime (using spec.getDriftTime()) or an ion-mobility float data array (using spec.hasIMData())

If neither is found, IMFormat::NONE is returned. If a single drift time (== IMFormat::IM_SPECTRUM) is found, but no unit, a warning is issued.

Exceptions

Exception::InvalidValue

if IM values are annotated as single drift time and float array in the given spectrum

fromIMUnit()

static DIM_UNIT fromIMUnit ( const DriftTimeUnit  from )

static

Convert a DriftTimeUnit to the more general DIM_UNIT.

Parameters

[in]

from

Drift unit to convert from

Returns

A more general DIM_UNIT

Exceptions

Exception::ConversionError

if from has an invalid value (e.g. 'NONE')

Referenced by TOPPViewBase::showCurrentPeaksAsIonMobility().

oneOverK0ToCCS()

static double oneOverK0ToCCS ( double  one_over_k0, double  mz, int  charge, double  buffer_gas_mass = N2_BUFFER_GAS_MASS  )

static

Convert a reduced inverse ion mobility (1/K0) to a collision cross section (CCS) via the Mason-Schamp relation.

Uses the conventional single-temperature form CCS = (C * |charge| / sqrt(mu)) * (1/K0) with the Bruker calibration constant C = 1059.62245 (validated against alphatims and MaxQuant CCS values for an N2 drift gas at the usual calibration temperature). mu is the ion-gas reduced mass mu = (m_ion * m_gas) / (m_ion + m_gas), with the ion mass approximated as m_ion = mz * |charge|.

Parameters

[in]	one_over_k0	Reduced inverse ion mobility 1/K0 in V*s/cm^2; must be > 0.
[in]	mz	Precursor m/z of the ion; must be > 0.
[in]	charge	Precursor charge; the sign is ignored (|charge| is used) and it must be non-zero.
[in]	buffer_gas_mass	Drift-gas mass in Da; defaults to N2 (N2_BUFFER_GAS_MASS).

Returns

Collision cross section in square Angstrom (Angstrom^2).

Exceptions

Exception::InvalidValue

if one_over_k0 <= 0, mz <= 0, or charge == 0.

Member Data Documentation

DRIFTTIME_NOT_SET

constexpr double DRIFTTIME_NOT_SET = -1.0

inlinestaticconstexpr

If drift time for a spectrum is unavailable (i.e. not an IM spectrum), it will have this value.

N2_BUFFER_GAS_MASS

constexpr double N2_BUFFER_GAS_MASS = 28.0

inlinestaticconstexpr

Mass of N2 (the most common drift/buffer gas) in Da; default buffer gas for the CCS conversions below. The rounded value 28.0 is used (rather than 28.006148) to match the calibration constant below, which was validated against the Bruker/alphatims and MaxQuant CCS values.