calculate_kinetics: Calculate kinetics data

In HaDeX2: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

Calculate kinetics data

Description

Calculate kinetics of the hydrogen-deuteration exchange for given peptide in given state.

Usage

calculate_kinetics(
  dat,
  protein = dat[["Protein"]][1],
  sequence = dat[["Sequence"]][1],
  state = dat[["State"]][1],
  start = dat[["Start"]][1],
  end = dat[["End"]][1],
  time_0 = min(dat[["Exposure"]]),
  time_100 = max(dat[["Exposure"]]),
  deut_part = 0.9
)

Arguments

dat	dat data imported by the read_hdx function.
protein	protein chosen protein.
sequence	sequence of chosen peptide.
state	biological state of chosen peptide.
start	start position of chosen peptide.
end	end position of chosen peptide.
time_0	minimal exchange control time point of measurement.
time_100	maximal exchange control time point of measurement.
deut_part	deuterium percentage in solution used in experiment, value from range [0, 1].

Details

The function calculates deuteration data for all available data points for given peptide in chosen biological state.. All four variants (relative & theoretical combinations) of deuterium uptake computations are supported. Manual correction of percentage of deuterium the protein was exposed to during the exchange in theoretical calculations is provided. To visualize obtained data we recommend using plot_uptake_curve function. The first version doesn't support filled Modification and Fragment columns. IMPORTANT! The kinetic data is often described as deuterium uptake curve data. We use this terms interchangeable.

Value

a data.frame object.

See Also

read_hdx calculate_state_uptake plot_uptake_curve

Examples

# by default: for the first peptide
calculate_kinetics(alpha_dat)
       

HaDeX2 documentation built on Feb. 9, 2026, 5:07 p.m.