xMSanalyzer statistics

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Citations per year

Number of citations per year for the bioinformatics software tool xMSanalyzer

Tool usage distribution map

This map represents all the scientific publications referring to xMSanalyzer per scientific context
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Associated diseases

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


No version available

Publication for xMSanalyzer

xMSanalyzer citations


Human Suction Blister Fluid Composition Determined Using High Resolution Metabolomics

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

[…] iquid 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. […]


Cohort profile: the Emory Cardiovascular Biobank (EmCAB)

BMJ Open
PMCID: 5778297
PMID: 29288185
DOI: 10.1136/bmjopen-2017-018753

[…] internal standards and maintained in an autosampler maintained at 4°C until injection. Electrospray ionisation is used in the positive ion mode. Data are extracted using apLCMS with modifications by xMSanalyzer as m/z features, where an m/z feature is defined by m/z (mass-to-charge ratio), retention time and ion intensity (integrated ion intensity for the chromatographic peak). Identities of many […]


Yale school of public health symposium on lifetime exposures and human health: the exposome; summary and future reflections

Hum Genomics
PMCID: 5723043
PMID: 29221465
DOI: 10.1186/s40246-017-0128-0
call_split See protocol

[…] Extraction of ultra-high resolution mass spectral data can be effectively obtained with software language tools such as apLCMS [] and XCMS []. A wrapper function in xMSanalyzer [] allows re-extraction of the same data with different parameter settings to improve capture of signals with different characteristics, and also provides quality control, batch normalizat […]


Plasma metabolomics reveals membrane lipids, aspartate/asparagine and nucleotide metabolism pathway differences associated with chloroquine resistance in Plasmodium vivax malaria

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

[…] 10-minute 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, […]


From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

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

[…] tries 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 a […]


Low‐dose oral cadmium increases airway reactivity and lung neuronal gene expression in mice

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

[…] tography 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 to re […]

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

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