Skip to contents

Parameters for CCS calculation

Source: R/utils-exported.R
getCCSParams.Rd

Configuration and description of parameters used for CCS calculation.

Usage

getCCSParams(method, ..., calibrant = NULL)

Source

The calculation formulas was derived from (Haler et al. 2017) , (George et al. 2024) and the implementation used by MS-DIAL (Tsugawa et al. 2020) . (MobilityToCrossSection method from the IonMobilityUtility class).

Arguments

method, calibrant

Sets the CCS calculation method and the calibrant data (only required if method="agilent"). See details.

...

optional named arguments that override defaults.

Details

The following parameters exist to configure the CCS calculation:

  • method The CCS calculation method. Should be "bruker", "mason-schamp_k", "mason-schamp_1/k" or "agilent". See details below.

  • defaultCharge The default charge of the ions. This is used when no charge information is available.

  • temperature,massGas The temperature (Kelvin) and exact mass of the drift gas. See calculation details below.

  • MasonSchampConstant The Mason-Schamp constant. See calculation details below.

  • calibrant If method="agilent": the calibrant data to be used for CCS calculation. This should either be

    • A path to an Agilent .d file.

    • A path to an OverrideImsCal.xml file (found in sample.d/AcqData).

    • A named list with the elements massGas, TFix and beta.

The CCS calculation depends on the method parameter:

  • bruker: uses the Bruker TDF-SDK for calculations. See msdata for configuration options. Only applicable to TIMS data.

  • mason-schamp_k: uses the Mason-Schamp equation: $$CCS = C \cdot \frac{charge}{\sqrt{u \cdot T}} \cdot \frac{1}{mobility}$$

    With

    • C the Mason-Schamp constant, can be changed by setting the MasonSchampConstant parameter. See (George et al. 2024) for details.

    • u the reduced mass of the drift gas and the ion: $$u = \frac{m_{gas} \cdot m_{ion}}{m_{gas} + m_{ion}}$$ The mass of the drift gas is defined by the massGas parameter.

    • T the temperature (Kelvin) as defined by the temperature parameter.

  • mason-schamp_1/k: as mason-schamp_k but assuming an inversed mobility (\(\frac{1}{k}\)). This is meant for TIMS data. Compared to method="bruker", this doesn't rely on the TDF-SDK but may produce results with very minor differences (George et al. 2024) .

  • agilent: uses Agilent calibration data with the following equation:

    $$CCS = (mobility - t_{fix}) \cdot \frac{charge}{\beta} \cdot \frac{1}{\sqrt{\frac{m_{ion}}{m_{ion} + m_{gas}}}}$$

    With \(t_{fix}\) and \(\beta\) the TFix and beta values from the calibration data. The massGas parameter sets the \(m_{gas}\) value.

The getCCSParams function generates such parameter list with defaults.

References

George AC, Schmitz I, Rouviere F, Alves S, Colsch B, Heinisch S, Afonso C, Fenaille F, Loutelier-Bourhis C (2024). “Interplatform comparison between three ion mobility techniques for human plasma lipid collision cross sections.” Analytica Chimica Acta, 1304, 342535. ISSN 0003-2670. doi:10.1016/j.aca.2024.342535 . http://dx.doi.org/10.1016/j.aca.2024.342535.

Haler JRN, Kune C, Massonnet P, Comby-Zerbino C, Jordens J, Honing M, Mengerink Y, Far J, De Pauw E (2017). “Comprehensive Ion Mobility Calibration: Poly(ethylene oxide) Polymer Calibrants and General Strategies.” Analytical Chemistry, 89(22), 12076–12086. ISSN 1520-6882. doi:10.1021/acs.analchem.7b02564 . http://dx.doi.org/10.1021/acs.analchem.7b02564.

Tsugawa H, Ikeda K, Takahashi M, Satoh A, Mori Y, Uchino H, Okahashi N, Yamada Y, Tada I, Bonini P, Higashi Y, Okazaki Y, Zhou Z, Zhu Z, Koelmel J, Cajka T, Fiehn O, Saito K, Arita M, Arita M (2020). “A lipidome atlas in MS-DIAL 4.” Nature Biotechnology, 38(10), 1159–1163. ISSN 1546-1696. doi:10.1038/s41587-020-0531-2 . http://dx.doi.org/10.1038/s41587-020-0531-2.