get_observed_iso_dist: Get observed distribution of ions

In hadexversum/powerHDX: Efficient Simulation of HDX-MS Data and Tools for the Statistical Analysis

Get observed distribution of ions

Description

Calculate isotopic probabilities (intensity).

Usage

get_observed_iso_dist(HDmatrix, isotopic_distribution, maxD)

Arguments

HDmatrix	simulated matrix after hydrogen-deuterium-exchange
isotopic_distribution	vector of isotopic probabilities of a peptide
maxD	length of the sequence - amount of prolines

Details

The exchangeable-hydrogen distribution describing the increase of the mass is obtained from the exchange matrix from get_HD_matrices or get_HD_matrices_using_markov and the number of exchangeable hydrogens n_exchangeable. First, the numbers of hydrogens exchanged in each molecule are calculated as sums of rows of the exchange matrix. Next, a vector of the counts is built and stored in a vector of length n_exchangeable plus one (for the lack of exchange). To obtain fractions counts are averaged.

The isotopic probabilities for the deuterated peptide are computed as the convolution of obtained distribution and the isotopic distribution for the undeuterated peptide (isotopic_distribution) as it is a sum of those variables (Claesen and Burzykowski 2017, Deconvolution-Based Approach). Namely

M_delta = M_{mol} - M_{mon}

where M_mol is the random variable describing molecular mass, M_mon is the random variable describing monoisotopic mass and M_delta is the random variable describing the increase in mass.

Value

a vector of observed isotopic distribution (observed_dist) and the observed peaks for mass spectrum (observed isotopic probabilities).

hadexversum/powerHDX documentation built on Aug. 31, 2022, 7:47 p.m.