Calculate kinetics dataset
calculate_peptide_kinetics.RdCalculate kinetics of the hydrogen-deuteration exchange for given peptide in multiple biological states.
Arguments
- dat
dat data imported by the
read_hdxfunction.- protein
chosen protein.
- sequence
sequence of chosen peptide.
- states
vector of states (for chosen protein), for which the calculations are done.
- 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
Function calculate_peptide_kinetics calculates
kinetic data for chosen peptide in chosen biological states.
It is a wrapper for calculate_kinetics but for mutltiple
states.
The output of this function can be visualized using plot_uptake_curve.
IMPORTANT! The kinetic data is often described as deuterium uptake curve data.
We use this terms interchangeable.
Examples
# by default calculated for the first peptide from the peptide pool
calculate_peptide_kinetics(alpha_dat)
#> Protein Sequence Start End State time_chosen Exposure
#> 1 db_eEF1Ba GFGDLKSPAGL 1 11 ALPHA_Gamma 0.167 0.167
#> 2 db_eEF1Ba GFGDLKSPAGL 1 11 ALPHA_Gamma 1.000 1.000
#> 3 db_eEF1Ba GFGDLKSPAGL 1 11 ALPHA_Gamma 5.000 5.000
#> 4 db_eEF1Ba GFGDLKSPAGL 1 11 ALPHA_Gamma 25.000 25.000
#> 5 db_eEF1Ba GFGDLKSPAGL 1 11 ALPHA_Gamma 150.000 150.000
#> 6 db_eEF1Ba GFGDLKSPAGL 1 11 ALPHA_beta_gamma 0.167 0.167
#> 7 db_eEF1Ba GFGDLKSPAGL 1 11 ALPHA_beta_gamma 1.000 1.000
#> 8 db_eEF1Ba GFGDLKSPAGL 1 11 ALPHA_beta_gamma 5.000 5.000
#> 9 db_eEF1Ba GFGDLKSPAGL 1 11 ALPHA_beta_gamma 25.000 25.000
#> 10 db_eEF1Ba GFGDLKSPAGL 1 11 ALPHA_beta_gamma 150.000 150.000
#> 11 db_eEF1Ba GFGDLKSPAGL 1 11 Alpha_KSCN 0.167 0.167
#> 12 db_eEF1Ba GFGDLKSPAGL 1 11 Alpha_KSCN 1.000 1.000
#> 13 db_eEF1Ba GFGDLKSPAGL 1 11 Alpha_KSCN 5.000 5.000
#> 14 db_eEF1Ba GFGDLKSPAGL 1 11 Alpha_KSCN 25.000 25.000
#> 15 db_eEF1Ba GFGDLKSPAGL 1 11 Alpha_KSCN 150.000 150.000
#> Modification frac_deut_uptake err_frac_deut_uptake deut_uptake
#> 1 NA 30.64852 0.2215405 1.665053
#> 2 NA 52.33080 0.7419739 2.842995
#> 3 NA 66.17980 1.1520437 3.595375
#> 4 NA 86.30034 1.4632251 4.688471
#> 5 NA 98.61253 1.6349417 5.357359
#> 6 NA 29.41361 0.4376162 1.590581
#> 7 NA 44.59159 0.4601648 2.411351
#> 8 NA 59.18888 0.4376175 3.200719
#> 9 NA 76.89181 1.5591714 4.158029
#> 10 NA 97.83217 1.1677838 5.290407
#> 11 NA 32.40425 1.1841232 1.760438
#> 12 NA 51.02357 1.1197261 2.771976
#> 13 NA 62.88876 0.9298826 3.416581
#> 14 NA 84.59564 0.7741527 4.595859
#> 15 NA 96.98272 0.7264052 5.268816
#> err_deut_uptake theo_frac_deut_uptake err_theo_frac_deut_uptake
#> 1 0.003059254 17.33535 0.03749574
#> 2 0.035068821 31.77278 0.42982083
#> 3 0.057318502 40.99432 0.70252393
#> 4 0.072421134 54.39185 0.88762927
#> 5 0.080539467 62.59008 0.98713157
#> 6 0.020535773 16.42258 0.25169660
#> 7 0.017359706 26.48234 0.21276916
#> 8 0.000000000 36.15723 0.00000000
#> 9 0.078509790 47.89049 0.96225485
#> 10 0.049576933 61.76948 0.60763943
#> 11 0.063142057 18.50443 0.77390031
#> 12 0.057662478 30.90235 0.70673987
#> 13 0.044514766 38.80294 0.54559501
#> 14 0.027139060 53.25675 0.33262975
#> 15 0.014163676 61.50485 0.17359702
#> theo_deut_uptake err_theo_deut_uptake Med_Sequence
#> 1 1.414381 0.003059254 6
#> 2 2.592322 0.035068821 6
#> 3 3.344702 0.057318502 6
#> 4 4.437798 0.072421134 6
#> 5 5.106687 0.080539467 6
#> 6 1.339908 0.020535773 6
#> 7 2.160678 0.017359706 6
#> 8 2.950046 0.000000000 6
#> 9 3.907356 0.078509790 6
#> 10 5.039734 0.049576933 6
#> 11 1.509765 0.063142057 6
#> 12 2.521304 0.057662478 6
#> 13 3.165908 0.044514766 6
#> 14 4.345186 0.027139060 6
#> 15 5.018144 0.014163676 6