biocontainers/ramid repository overview

⁠RaMID

Version: 1.0

⁠Short description

R-program to read CDF files, created by mass spectrometry machine, and evaluate the mass spectra of 13C-labeled metabolites

⁠Description

Here a docker image of RaMID can be created. RaMID is a computer program designed to read the machine-generated files saved in netCDF format containing registered time course of m/z chromatograms. It evaluates the peaks of mass isotopomer distribution (MID) making them ready for further correction for natural isotope occurrence. To create the docker image the github repository "https://github.com/seliv55/RaMID⁠" is used.

⁠Key features

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

⁠Functionality

• Preprocessing of raw data
• initiation of workflows

⁠Approaches

• Isotopic Labeling Analysis / 13C

⁠Instrument Data Types

• MS

⁠Data Analysis

• RaMID reads the CDF files presented in the working directory, and then
• separates the time courses for selected m/z peaks corresponding to specific mass isotopomers;
• corrects baseline for each selected mz;
• choses the time points where the distribution of peaks is less contaminated by other compounds and thus is the most representative of the real analyzed distribution of mass isotopomers;
• evaluates this distribution, and saves it in files readable by MIDcor, a program, which performs the next step of analysis, i.e. correction of the RaMID spectra for natural isotope occurrence, which is necessary to perform a fluxomic 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

⁠Tool Authors

• Vitaly Selivanov (Universitat de Barcelona)

⁠Container Contributors

• Pablo Moreno⁠

⁠Website

• N/A

⁠Git Repository

• https://github.com/seliv55/RaMID-docker⁠

⁠Installation

• go to the directory where the dockerfile is.
• create container from dockerfile: ''' sudo docker build -t ramid:0.1 . '''

⁠Usage Instructions

• To run RaMID as a docker image, execute

''' sudo docker run -i -t -v $PWD:/data ramid:0.1 -i /data/ramidin.csv -o /data/ramidout.csv -z /data/wd.zip '''

⁠Publications