xMSanalyzer protocols

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xMSanalyzer statistics

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chevron_left Metabolite identification Spectral deconvolution Peak detection Quality control Spectral visualization Chromatogram alignment chevron_right
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xMSanalyzer specifications


Unique identifier OMICS_06039
Name xMSanalyzer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for xMSanalyzer

xMSanalyzer in pipelines

PMCID: 5863097
PMID: 29425024
DOI: 10.1021/acs.analchem.7b04073

[…] chromatography (ultimate 3000, dionex, sunnyvale, ca) and fourier transform mass spectrometry (q-exactive, thermo scientific, waltham, ma). data was extracted using aplcms with modifications by xmsanalyzer. see si for details. the metabolomics data set is available upon request to the corresponding authors., statistical analysis, network/pathway analysis, and metabolite set enrichment […]

PMCID: 4669660
PMID: 26702339
DOI: 10.1016/j.csbj.2015.10.005

[…] of ions that are trapped and oscillate in a chamber. the computational aspects of metabolomics are also in rapid progress, including open source feature extraction tools (xcms , openms , aplcms , xmsanalyzer ), databases of metabolites (human metabolome database , , metlin , pubchem , chebi ), and data analysis tools (xcms online , metaboanalyst , mummichog ). it should be noted […]

PMCID: 4302260
PMID: 25468946
DOI: 10.2337/dc14-2033

[…] metabolomics data analysis. feature and sample quality assessment was performed based on coefficient of variation (cv) and pearson correlation, respectively, based on the technical replicates using xmsanalyzer (). metabolites with cv >50% in our samples were excluded from further analyses. potential metabolite identities were determined by performing an online search (10 ppm mass accuracy) […]

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xMSanalyzer in publications

PMCID: 5559093
PMID: 28813452
DOI: 10.1371/journal.pone.0182819

[…] gradient used in this study cannot resolve structural isomers and isobaric species []. peak detection, noise removal, and alignment was performed using aplcms v6.0.1[] and xcms v1.44[] with xmsanalyzer v2.0.4[], yielding a data table with accurate mass (m/z), retention time and intensity for each m/z feature across all samples. an m/z feature is defined as the unique combination of m/z, […]

PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] to be user friendly by providing a file-based operation and a wrapper function for a single command line batch process of lc-ms data, but still requires some computational knowledge to operate. xmsanalyzer [] is an r package for improving feature detection that integrates with existing packages such as aplcms and xcms. it systematically re-extracts features with multiple parameter settings […]

PMCID: 4945833
PMID: 27401458
DOI: 10.14814/phy2.12821

[…] and positive electrospray ionization on a high field qexactive ms (thermo, waltham, massachusetts) set to a scan range of 85–1275 m/z (soltow et al. ). chemical features were extracted using xmsanalyzer (uppal et al. ) with aplcms (yu et al. ). identities and μmol/l abundances were established by ms/ms and coelution with authentic heavy‐isotope labeled standards and/or by comparison […]

PMCID: 4721204
PMID: 26792212
DOI: 10.1186/s40168-016-0147-4

[…] fisher, san diego, ca) from m/z 85 to 1275 over 10 min. peak extraction, noise removal, and quantification of ion intensities were performed by an adaptive processing software package (aplcms) with xmsanalyzer designed for use with lc-ftms data []. for clarification, data extracted on m/z features, which are not definitively identified metabolites, will be referred to as “features” […]

PMCID: 4657040
PMID: 26596774
DOI: 10.1038/srep17221

[…] using anion exchange and c18 chromatography combined with the thermo orbitrap-velos (thermo fisher, san diego, ca) mass spectrometer using an m/z range of 85 to 850. the data was pre-processed using xmsanalyzer in combination with aplcms. for each feature, there were three readings per subject. an average metabolite intensity value was calculated from the non-zero readings for each individual. […]

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xMSanalyzer institution(s)
BimCore, School of Medicine, Emory University, Atlanta, GA, USA

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