A roadmap for the XCMS family of software solutions in metabolomics. (February 2016)

• Record Type: Journal Article
• Authors: Mahieu, Nathaniel G; Genenbacher, Jessica Lloyd; Patti, Gary J
• Is Part Of: Current opinion in chemical biology. Volume 30(2016)
• Page Start: 87
• Page End: 93
• Publication Date: 2016-02
• Subjects: Bioorganic chemistry -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Clinical biochemistry -- Periodicals; Biochemistry -- Periodicals; Chimie bio-organique -- Périodiques; Biologie -- Périodiques; 572.05
• DOI: 10.1016/j.cbpa.2015.11.009
• Languages: English
• ISSNs: 1367-5931

Abstract

Highlights: XCMS implements four algorithms for processing metabolomic data. There are many published algorithms yet to be implemented or tested within XCMS. The major roles of XCMS are feature detection and correspondence determination. The XCMS peaks and groups tables are used by other programs with advanced functions. 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, X 13 CMS, and XCMS Online. Together, these informatic technologies can accommodate most cutting-edge metabolomic applications and offer unique advantages when compared to the original XCMS program.