create_p_diff_uptake_dataset: Create differential uptake dataset with p-value

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

Create differential uptake dataset with p-value

Description

Creates differential deuterium uptake dataset with P-value from t-Student test for selected two biological states.

Usage

create_p_diff_uptake_dataset(
  dat,
  diff_uptake_dat = NULL,
  protein = unique(dat[["Protein"]])[1],
  state_1 = unique(dat[["State"]])[1],
  state_2 = unique(dat[["State"]])[2],
  p_adjustment_method = "none",
  confidence_level = 0.98,
  time_0 = min(dat[["Exposure"]]),
  time_100 = max(dat[["Exposure"]]),
  deut_part = 0.9
)

Arguments

dat	data imported by the read_hdx function.
diff_uptake_dat	differential uptake data
protein	chosen protein.
state_1	biological state for chosen protein. From this state values the second state values are subtracted to get the deuterium uptake difference.
state_2	biological state for chosen protein. This state values are subtracted from the first state values to get the deuterium uptake difference.
p_adjustment_method	method of adjustment P-values for multiple comparisons. Possible methods: "BH" (Benjamini & Hochberg correction), "bonferroni" (Bonferroni correction) and "none" (default).
confidence_level	confidence level for the t-test.
time_0	minimal exchange control time point of measurement [min].
time_100	maximal exchange control time point of measurement [min].
deut_part	deuterium percentage in solution used in experiment, value from range [0, 1].

Details

For peptides in all of the time points of measurement (except for minimal and maximal exchange control) the deuterium uptake difference between state_1 and state_2 is calculated, with its uncertainty (combined and propagated as described in 'Data processing' article). For each peptide in time point the P-value is calculated using unpaired t-test. The deuterium uptake difference is calculated as the difference of measured masses in a given time point for two states. The tested hypothesis is that the mean masses for states from the replicates of the experiment are similar. The P-values indicates if the null hypothesis can be rejected - rejection of the hypothesis means that the difference between states is statistically significant at provided confidence level. The P-values can be adjusted using the provided method.

Value

a data.frame object with calculated deuterium uptake difference in different forms with their uncertainty, P-value and -log(P-value) for the peptides from the provided data.

References

Hageman, T. S. & Weis, D. D. Reliable Identification of Significant Differences in Differential Hydrogen Exchange-Mass Spectrometry Measurements Using a Hybrid Significance Testing Approach. Anal Chem 91, 8008–8016 (2019).

See Also

read_hdx calculate_exp_masses_per_replicate

Examples

p_diff_uptake_dat <- create_p_diff_uptake_dataset(alpha_dat)
head(p_diff_uptake_dat)

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