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Citations per year

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Popular tool citations

chevron_left Isotopic labeling protein quantification Metabolite identification Chromatogram alignment Data normalization Peak detection Peak detection Peak alignment Peak alignment Metabolite quantification Spectral visualization chevron_right
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Protocols

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XCMS specifications

Information


Unique identifier OMICS_06038
Name XCMS
Alternative names centWave, XCMS Online
Software type Toolkit/Suite
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
Version 3.2.0
Stability Stable
Requirements
methods, plyr, RColorBrewer, BiocGenerics, Biobase, testthat, S4Vectors, BiocStyle, R(>=2.14.0), lattice, multtest, caTools, magrittr, rgl, pander, faahKO, BiocParallel(>=1.8.0), MSnbase(>=2.5.10), mzR(>=2.13.1), ProtGenerics, RANN, MassSpecWavelet(>=1.5.2), knitr(>=1.1.0), msdata, ncdf4, microbenchmark
Maintained Yes

Subtool


  • Massifquant

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Information


Unique identifier OMICS_06038
Name XCMS
Alternative names centWave, XCMS Online
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • Massifquant

Publications for XCMS

XCMS in pipelines

 (15)
2018
PMCID: 5918566
PMID: 29713366
DOI: 10.1186/s13007-018-0301-z

[…] masslynx 4.1. signals derived from esi (+) and esi (−) were processed separately. peak peaking, grouping and signalling corrections were processed with r software for statistical computing using the xcms package for relative quantification []. partial least-squares (pls), heatmap construction and clustering were performed with metaboanalyst 3.0 []. the kruskal–wallis test (p < 0.05) […]

2017
PMCID: 5665457
PMID: 28798136
DOI: 10.1242/dmm.030411

[…] data were converted to netcdf file format with fileconverter software available in xcalibur (thermo fisher scientific, bremen, germany). deconvolution was performed using the freely available xcms software as described previously (; ). data were exported from xcms as a .csv file for further data analysis. the quality of data was assessed by applying qc data as previously described (), […]

2016
PMCID: 5025507
PMID: 27729833
DOI: 10.1007/s11306-016-1109-3

[…] (nonlinear dynamics, newcastle upon tyne, uk) for peak picking and run alignment. in addition, raw data was converted into mzxml-format using proteowizard (chambers et al. ) for processing with the ‚xcms’-package for r (https://masspec.scripps.edu/xcms/download.php) according to previously published protocols (patti et al. ; tautenhahn et al. ; smith et al. ; benton et al. ). after extraction […]

2016
PMCID: 5126694
PMID: 27897248
DOI: 10.1038/srep37976

[…] were set to 280 °c, 280 °c, and 240 °c, respectively. the detector voltage was 0.92 kv. the ionization mode was electron impact (ei) at 70 ev., for lc-ms, peak alignment was achieved with xcms. for ce-ms, peak deconvolution, detection and area integration were performed by using agilent masshunter qualitative and quantitative analysis software. for gc-ms, the molecular features […]

2015
PMCID: 4423578
PMID: 25952148
DOI: 10.1186/1471-2105-16-S7-S2

[…] quantities. ideally, solutions would focus on one of the several complex individual steps for data processing []. however, most are released as end-to-end solutions (e.g., superhirn [], maxquant [], xcms [], and skyline []). this makes comparison to other competing algorithms virtually impossible, and is at least partially responsible for the lack of critical evaluations in the literature [], […]


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XCMS in publications

 (499)
PMCID: 5964348
DOI: 10.1128/mBio.00820-18

[…] chemical repertoire induced by ralsolamycin, we analyzed fungal cultures using ultrahigh-performance liquid chromatography coupled to high-resolution mass spectrometry (uhplc-hrms) using the program xcms (). principal-component analyses of all samples showed that f. fujikuroi metabolism is shifted most in response to gmi1000-conditioned, high-nitrogen medium (). using the metaxcms package (), […]

PMCID: 5944135
PMID: 29743024
DOI: 10.1186/s12870-018-1295-4

[…] was set to 70,000. the mass range scanned was 150–1000 m/z. the maximum injection time was 100 ms. sheath gas and aux flow rates were 32 and 7 arb, respectively. the raw data were processed by the xcms online platform [], using parameters suggested for the orbitrap instrument, with minor modifications. the peak lists were further processed in r [], using ggplot2 []. for quantification of major […]

PMCID: 5941619
PMID: 29743087
DOI: 10.1186/s12944-018-0750-4

[…] were randomized to reduce the systematic error associated with measurements variability. urine specimens were sequentially analyzed in sets of 15 samples/day., lc-ms data were analyzed with the xcms online software (https://xcmsonline.scripps.edu) to identify and line up features [–]. the alignment applied a 0.2 min retention time and a 0.002 da mass tolerance window., a pilot trial […]

PMCID: 5940876
PMID: 29740146
DOI: 10.1038/s41598-018-25588-1

[…] uplc system coupled to a xevo® g2 qtof-ms using leucine enkephalin as lockspray® for accurate mass calibration. data was processed, aligned, and analyzed using masslynxtm (waters, milford, ma), xcms online, metaboanalyst, and r., internal standards (1 µm 4-nitrobenzoic acid) were added to culture media (500 μl) that was deproteinized as above and then evaporated in a speed-vac […]

PMCID: 5940898
PMID: 29739963
DOI: 10.1038/s41598-018-25086-4

[…] throughout the sequence., lc–ms raw data files were converted to mzml files using the open-source msconvert tool from the proteowizard library, mzml files were processed using the r package xcms (r version 3.3.1., xcms version 1.50.0) to detect, deconvolute and align features (molecular entities with a unique and a specific retention time). parameter settings for xcms processing […]


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XCMS institution(s)
Leibniz Institute of Plant Biochemistry, Department of Stress and Developmental Biology, Halle, Germany

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