X13CMS

Version: 1.4

Website

http://pattilab.wustl.edu/software/x13cms/x13cms.php

Description

This is an extension of XCMS that provides support for isotopic labelling. It requires two biologically identical samples to be prepared, with isotopic labelling being applied to one of them. XCMS is used for peak detection and retention time alignment, with the table of putative detected peaks being forwarded to X13CMS. X13CMS function getIsoLabelReport() can then be used to detect which metabolites have been enriched with isotopic labelling. This function detects the difference in mass between labelled and unlabelled samples and outputs a table of isotopologues that have statistically significant isotopic labelling. It requires that the mean intensity of the labelled peak be less than the unlabelled peak. getIsoDiffReport() then compares labelling between different biological conditions, to find significant biological differences between them (using a Welch's t-test).

Functionality

• Preprocessing

Instrument Data Type

• MS/LC-MS

Approaches

• Untargeted
• Isotopic Labelling Analysis

Computer Skills

Advanced

Software Type

R Package

Interface

Command line interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R

Dependencies

xcms, mzR, Rcpp, BioGenerics, Biobase

Input Formats - Open

mzData, mzML, mzXML, netCDF

Input Formats - Proprietary

N/A

Published

2014

Last Updated

2014

License

Paper

http://www.ncbi.nlm.nih.gov/pubmed/24397582

PMID

24397582