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Calculate kinetics data

calculate_kinetics.Rd

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].

Value

a data.frame object.

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.

See also

read_hdx calculate_state_uptake plot_uptake_curve

Examples

# by default: for the first peptide
calculate_kinetics(alpha_dat)
#>     Protein    Sequence Start End       State time_chosen Exposure Modification
#> 1 db_eEF1Ba GFGDLKSPAGL     1  11 ALPHA_Gamma       0.167    0.167           NA
#> 2 db_eEF1Ba GFGDLKSPAGL     1  11 ALPHA_Gamma       1.000    1.000           NA
#> 3 db_eEF1Ba GFGDLKSPAGL     1  11 ALPHA_Gamma       5.000    5.000           NA
#> 4 db_eEF1Ba GFGDLKSPAGL     1  11 ALPHA_Gamma      25.000   25.000           NA
#> 5 db_eEF1Ba GFGDLKSPAGL     1  11 ALPHA_Gamma     150.000  150.000           NA
#>   frac_deut_uptake err_frac_deut_uptake deut_uptake err_deut_uptake
#> 1         30.64852            0.2215405    1.665053     0.003059254
#> 2         52.33080            0.7419739    2.842995     0.035068821
#> 3         66.17980            1.1520437    3.595375     0.057318502
#> 4         86.30034            1.4632251    4.688471     0.072421134
#> 5         98.61253            1.6349417    5.357359     0.080539467
#>   theo_frac_deut_uptake err_theo_frac_deut_uptake theo_deut_uptake
#> 1              17.33535                0.03749574         1.414381
#> 2              31.77278                0.42982083         2.592322
#> 3              40.99432                0.70252393         3.344702
#> 4              54.39185                0.88762927         4.437798
#> 5              62.59008                0.98713157         5.106687
#>   err_theo_deut_uptake Med_Sequence
#> 1          0.003059254            6
#> 2          0.035068821            6
#> 3          0.057318502            6
#> 4          0.072421134            6
#> 5          0.080539467            6