Apply interference correction — correct

This function corrects lipidomics feature intensities by subtracting interference (e.g., isotope overlap or in-source fragments). The correction is applied using the following formula: $$value\_corrected = value\_raw - value\_raw\_interfering\_feature \times interference\_contribution$$

The interfering features and their relative contributions must be defined in the feature metadata.

By default, a chain of interferences (e.g., isotopic M+2 interferences of PC 34:2 > PC 34:1 > PC 34:0) is corrected sequentially: each feature is corrected using the already-corrected signal of its interfering feature, so the correction propagates along the chain. To disable this and instead correct each feature independently from the raw (uncorrected) signal of its interfering feature, set sequential_correction = FALSE.

Usage

correct_interferences(
  data = NULL,
  variable = "feature_intensity",
  sequential_correction = TRUE,
  neg_to_na = FALSE
)

Arguments

data: MRMhubExperiment object containing lipidomics data.
variable: Name of the variable to be corrected. Default: feature_intensity.
sequential_correction: Logical. If TRUE (the default), a chain of interferences is corrected sequentially, so that each feature is corrected using the already-corrected signal of its interfering feature (the correction propagates along the chain). If FALSE, each feature is corrected independently using the raw (uncorrected) signal of its interfering feature, without propagation.
neg_to_na: If TRUE, negative or zero values after correction will be replaced with NA. Default: FALSE.

Value

MRMhubExperiment object with feature intensities corrected for interferences.

Details

For isotopic interference correction of MRM/PRM data, the relative isotope abundances needed for the calculation (interference_contribution) can be calculated using the LICAR application (Gao et al., 2021), see below.

References

Gao L., Ji S, Burla B, Wenk MR, Torta F, Wenk MR, & Cazenave-Gassiot A (2021). LICAR: An Application for Isotopic Correction of Targeted Lipidomic Data Acquired with Class-Based Chromatographic Separations Using Multiple Reaction Monitoring. Analytical Chemistry, 93(6), 3163-3171. https://doi.org/10.1021/acs.analchem.0c04565