xMSanalyzer statistics

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Citations per year

Number of citations per year for the bioinformatics software tool xMSanalyzer
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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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Popular tool citations

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

xMSanalyzer specifications

Information


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

Versioning


No version available

Publication for xMSanalyzer

xMSanalyzer citations

 (16)
library_books

Human Suction Blister Fluid Composition Determined Using High Resolution Metabolomics

2018
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. […]

library_books

Cohort profile: the Emory Cardiovascular Biobank (EmCAB)

2017
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 […]

call_split

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

2017
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 […]

library_books

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

2017
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, […]

library_books

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

2017
GigaScience
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 […]

library_books

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

2016
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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