powerHaDeX (version 1.0)

simulate_theoretical_spectra: Simulate theoretical spectra of a deuterated peptide over time

Description

Simulate theoretical spectra of a deuterated peptide over time

Usage

simulate_theoretical_spectra(
  sequence,
  charge = NULL,
  protection_factor = 1,
  times = c(60, 600),
  pH = 7.5,
  temperature = 15,
  n_molecules = 100,
  time_step_const = 1,
  if_corr = FALSE,
  min_probability = 1e-04,
  use_markov = TRUE
)

Arguments

sequence

amino acid sequence of a peptide as a single string

charge

vector of charges of the peptide ion. If NULL, one value is sampled from vector 2:6. Default NULL.

protection_factor

protection factor. If a single number of provided, same protection factor will be assumed for each amide. Default value: 1 (indicates that the exchange rate is equal to the intristic exchange rate)

times

a vector of times at which deuteration levels will be measured (seconds)

pH

pH of the reaction. Default to 7.5.

temperature

temperature of the reaction (Celsius)

n_molecules

number of peptide molecules. Default to 100.

time_step_const

time step constant. Default value: $1$. Value that indicates the length of the time step of the simulation. The bigger the time step, the fewer time points are simulated (the fewer iterations in case of Zhong-Yuan Kan's approach).

if_corr

logical. PH correction indicator. Default value FALSE. The value of pH is equal to pD. If there is correction, the pD = pH + 0.4. (Conelly et al 1993)

min_probability

smallest isotopic probability to consider

use_markov

logical. If TRUE algorithm basing on Markov chain will be used. If FALSE simulation provided by Zhong-Yuan Kan will be executed. Default to TRUE, as it fastens the calculation

Value

a data table of variables:

- Exposure - time point of a measurement,

- Mz - mass-to-charge ratio,

- Intensity - isotopic probabilities larger than min_probability(the smaller ones are zeroes)

and the variables provided by user

- Sequence,

- PF,

- Charge,

- PH.

Details

To the results calculated by get_iso_probs_deut is added a minimal exchange control - for time point 0 (directly after adding a buffer). The m/z values are obtained as a ratio of the peptide_mass magnified by proton mass and the peptide charge. The distribution of undeuterated peptide is the intensities vector.

See Also

The algorithm that is used to simulate theoretical spectra is based on Zhong-Yuan Kan's implementation in Matlab. The original version of codes is located in the repository https://github.com/kanzy/HX-MS-Simulations (as at 29.06.2020). In the powerHaDeX package can be found the Kan's algorithm re-implemented in R (using Rcpp) and the accelerated implementation (that uses Markov chains' properties). Moreover, the package powerHaDeX allows the user to simulate spectra for more than one exposure time for both (Rcpp and Markov) approaches.

Examples

# NOT RUN {
simulate_theoretical_spectra(sequence = "LVRKDLQN",
                             charge = c(3, 5),
                             protection_factor = 100,
                             times = c(0.167, 5),
                             pH = 7.5,
                             temperature = 15,
                             n_molecules = 500,
                             time_step_const = 1,
                             use_markov = TRUE)

# }