Natural Abundance Correction of Mass Spectrometer Data.

AccuCor - Isotope Natural Abundance Correction

AccuCor is an isotope natural abundance correction algorithm that is needed especially for high resolution mass spectrometers. AccuCor supports 13C, 2H and 15N isotope correction.

AccuCor accepts Excel (.xls and .xlsx), comma-separated text (.csv), or tab-separated test (.tsv) files.

Installation

install.packages("accucor")

Quickstart

library(accucor)

# Input file (example file included)
# Or use your own: carbon_input_file <- "/path/to/my/datafile.csv"

carbon_input_file <- system.file("extdata", "C_Sample_Input_Simple.csv", package = "accucor")


# Output is written to [input_file]_corrected.xlsx by default
# Be sure to specify the appropriate resolution.
# For Exactive, the resolution is 100000, defined at 200 Mw

carbon_corrected <- natural_abundance_correction(
  path = carbon_input_file,
  resolution = 100000)


# The results are also returned as a named list of dataframes for further processing in R
# "Original", "Corrected", "Normalized", "PoolBeforeDF", "PoolAfterDF"

carbon_corrected


# Purity is set to 0.99 for C and N, and 0.98 for H
# Be sure to specify purity if your samples differ
carbon_corrected <- natural_abundance_correction(
  path = carbon_input_file,
  resolution = 100000,
  purity = 0.97)

Introduction

Input files

Two types of input are accepted:

• Simple table including the compound, formula, isotope label, and values for the samples

• Classic Maven copy/paste along with a separate compound database (e.g. knowns.csv).

Simple table input must contain the following columns:

• Compound - The name of the compound.

• Formula - The chemical formula for the compound.

• IsotopeLabel - The isotope labeling. Currently C12 PARENT for the parent (unlabeled) peak group and C13-label-# for the labeled peak groups. D-label-# and N15-label- are also recognized for Deuterium and Nitrogen labeled data, respectively.

• Samples - One column for the intensity data for each sample.

• metaGroupId - OPTIONAL - Used to support multiple peak groups per compound. Exported from El-MAVEN (version 0.4.0 and greater).

Additional columns commonly exported from El-MAVEN will be automatically ignored.

NOTE - Previous versions required the compound database (KNOWNS.csv) as well as the output data. This is no longer necessary, as the formula is included the exported data from El-MAVEN.

Classic Maven input

• Data input file - one block per compound. The first row of a block is the compound name followed by sample names. The remaining rows in the block contain the isotope label (e.g.C12 PARENT, C13-label-1) in the first column followed by intensities for each sample.

• Compound database file - A comma separated (.csv) file with columns for the compound name (compound) and molecular formula (formula).

Input file formats

Input and output files may be Excel (.xls and .xlsx), comma-separated text (.csv), or tab-separated test (.tsv) files. The type is automatically determined by file extension.

Isotope support

The isotope for correction is automatically determined by the contents of the isotopeLabel column in your input data. AccuCor supports 13C, 2H and 15N isotope correction. Only single labeled experiments are supported. Be sure to turn off isotope detection for other isotopes (see El-MAVEN isotope detection documentation).

Citation

If you use this software in your research, please cite the following paper (also see citation("accucor")):

Su X, Lu W and Rabinowitz J (2017). "Metabolite Spectral Accuracy on Orbitraps." Analytical Chemistry, 89(11), pp. 5940-5948. doi: 10.1021/acs.analchem.7b00396 (URL: https://doi.org/10.1021/acs.analchem.7b00396), PMID: 28471646, R package version 0.2.3 (2018).

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Metabolite Spectral Accuracy on Orbitraps},
    author = {Xiaoyang Su and Wenyun Lu and Joshua D. Rabinowitz},
    journal = {Analytical Chemistry},
    doi = {10.1021/acs.analchem.7b00396},
    volume = {89},
    number = {11},
    pages = {5940-5948},
    year = {2017},
    note = {PMID: 28471646, R package version 0.2.3 (2018)},
    url = {https://doi.org/10.1021/acs.analchem.7b00396},
    eprint = {https://doi.org/10.1021/acs.analchem.7b00396},
  }