For the correction of isotopologue distributions for MS tracing data.
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README.md

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MIDcor

Version: 1.0

Short Description

“R”-program that corrects 13C mass isotopomers spectra of metabolites for natural occurring isotopes and peaks overlapping

Description

“midcor.R” is an “R”-program that performs a primary analysis of isotopic isomers (isotopomers) distribution obtained by Gas Cromatography coupled with Mass Spectrometry (GCMS). The aim of this analysis is to have a correct distribution of isotopes originated from substrates that are artificially enriched with specific isotopes (usually 13C). To this end the program performs a correction for natural occurring isotopes and also correction for “impurities” of the assay media that give peaks overlapping with the spectra of analyzed labeled metabolites. This program offers two ways of corrections of “impurities” resulted from overlapping the assayed mass isotopomer distribution with peaks produced either by unknown metabolites in the media, or by different fragments produced by the assayed metabolite.

Key features

  • primary processing of 13C mass isotopomer data obtained with GCMS

Functionality

  • Preprocessing
  • Statistical Analysis
  • Workflows

Approaches

  • Isotopic Labelling Analysis / 13C

Instrument Data Types

  • MS

Data Analysis

  • correction for H+ loss produced by electron impact, natural occurring isotopes, and peaks overlapping

Screenshots

  • screenshot of input data (format Metabolights), output is the same format with one more column added: corrected mass spectrum

screenshot

Tool Authors

Container Contributors

Website

  • N/A

Git Repository

Installation

To create the Docker container:

  • go to the directory where the dockerfile is;
  • create container from dockerfile:
docker build -t midcor:0.1 .

Alternatively, pull directly from the repo

docker pull container-registry.phenomenal-h2020.eu/phnmnl/midcor

Usage Instructions

To run MIDcor as a docker image, execute

docker run -it -v $PWD:/data container-registry.phenomenal-h2020.eu/phnmnl/midcor -i /data/input.csv -o /data/output.csv

An example of input file is provided as "outin.csv"

Publications

  • “MIDcor”, an R-program for deciphering mass interferences in mass spectra of metabolites enriched in stable isotopes. Submitted to BMC bioinformatics.