IsotopicLabelling: IsotopicLabelling-package

Description Details Block diagram Author(s)

Description

The IsotopicLabelling package allows to analyse the isotopic patterns in MS data obtained in isotopic labelling experiments. From the experimental patterns, the package estimates the isotopic abundance of the stable isotope employed in the labelling experiment (either ^2H or ^13C) inside a specified compound.

Details

Given a data frame of LC-MS or GC-MS peak intensities or areas (one column for each sample to analyse), the IsotopicLabelling package first extracts the isotopic patterns of the specified compound, and then performs an isotopic pattern analysis to estimate the isotopic abundance of the labelling isotope. This is performed through a weighted non-linear least squares fitting procedure, where the resulting estimate is the value for which the theoretical pattern best reproduces the experimental one. During the fitting, the experimental signals are given weights proportional to the square root of their intensity, to correct for the non uniform variance at different intensity levels. The theoretical patterns are computed using the ecipex R package.

Block diagram

The isotopic pattern analysis can be divided into the following steps:

  1. Starting from a class xcmsSet object (from the xcms R package), generate a data frame of peak signal intensities or areas, with each column corresponding to a sample. This step can be avoided if the data frame is already available (obtained by other means);

  2. Extract from the data frame the experimental isotopic patterns of the specified compound (one pattern for each sample). In the chemical formula of the compound, the element whose abundance is unknown is called "X";

  3. Normalise the patterns and estimate the abundance of the label through a weighted non-linear least squares fitting procedure.

  4. Summarize the results.

Author(s)

Ruggero Ferrazza, Pietro Franceschi


RuggeroFerrazza/IsotopicLabelling documentation built on May 10, 2017, 10:21 a.m.