A roadmap for the XCMS family of software solutions in metabolomics

Abstract

Global profiling of metabolites in biological samples by liquid chromatography/mass spectrometry results in datasets too large to evaluate manually. Fortunately, a variety of software programs are now available to automate the data analysis. Selection of the appropriate processing solution is dependent upon experimental design. Most metabolomic studies a decade ago had a relatively simple experimental design in which the intensities of compounds were compared between only two sample groups. More recently, however, increasingly sophisticated applications have been pursued. Examples include comparing compound intensities between multiple sample groups and unbiasedly tracking the fate of specific isotopic labels. The latter types of applications have necessitated the development of new software programs, which have introduced additional functionalities that facilitate data analysis. The objective of this review is to provide an overview of the freely available bioinformatic solutions that are either based upon or are compatible with the algorithms in XCMS, which we broadly refer to here as the “XCMS family” of software. These include CAMERA, credentialing, Warpgroup, metaXCMS, X13CMS, and XCMS Online. Together, these informatic technologies can accommodate most cutting-edge metabolomic applications and offer some advantages when compared to the original XCMS program.

Metabolite Measurement: Pitfalls to Avoid and Practices to Follow

“…With knowledge of the retention time of targeted metabolites, it is possible to read their peaks directly off the high-resolution MS chromatograms. Moreover, it is possible to compare all peaks across biological conditions to find ones that change significantly in response to a biological perturbation and thus merit identification (46–48). …”

A Protocol to Compare Methods for Untargeted Metabolomics

“…1. In this protocol, we detail a method using XCMS for feature detection, since it is commonly used in untargeted metabolomics [14]. We also include details on how to use other data-processing pipelines with credentialing .…”

Review of emerging metabolomic tools and resources: 2015–2016

“…In another update on various forms (X) of chromatography mass spectrometry (XCMS) family of software solutions, the authors discuss the integral tools such as, CAMERA, credentialing, Warpgroup, metaXCMS, X13CMS, and XCMS Online . In this review, the authors shed light on the role of CAMERA in annotating common isotopologues, adducts, clusters and neutral losses, role of warpgroup in improving quantitation with consensus integration bounds, role of credentialing in annotating artefacts, of metaXCMS in finding shared alterations among multiple sample classes, and of X13CMS in unbiased mapping of isotopic fates and XCMS Online for taking metabolomics to the cloud.…”