Planned intervention: On Wednesday April 3rd 05:30 UTC Zenodo will be unavailable for up to 2-10 minutes to perform a storage cluster upgrade.
Published June 26, 2020 | Version 1.0.0
Other Open

Metabolomics data pre-processing using xcms

  • 1. Institute for Biomedicine, Eurac Research, Bolzano, Italy

Description

Workflow illustrating mass spectrometry (MS) data handling and access using Bioconductor’s MSnbase package (Gatto and Lilley 2012) and preprocessing of an (untargeted) LC-MS toy data set using the xcms package (Smith et al. 2006). The preprocessing comprises chromatographic peak detection, sample alignment and peak correspondence. Particular emphasis is given on defining data-set dependent values for the most important settings of popular preprocessing methods.

The source code of the workflow is available on github: https://github.com/jorainer/metabolomics2018

Files

Files (5.0 MB)

Name Size Download all
md5:71710b3bfc951f7bdb7ea46cf51bd3d6
5.0 MB Download