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Protocols

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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Versioning


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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 citations

 (325)
library_books

Conserved Responses in a War of Small Molecules between a Plant Pathogenic Bacterium and Fungi

2018
MBio
PMCID: 5964348
DOI: 10.1128/mBio.00820-18

[…] ing Student’s t test or analysis of variance (ANOVA) followed by Tukey-Kramer analysis to show significant differences. Untargeted metabolomics analyses were performed from four replicates within the XCMS and metaXCMS software packages implemented in the R language (https://github.com/spraker/Spraker_XCMS_analysis_Fusarium). For analyses of known F. fujikuroi metabolites, the MAVEN software packag […]

library_books

Endophytic fungi from the roots of horseradish (Armoracia rusticana) and their interactions with the defensive metabolites of the glucosinolate myrosinase isothiocyanate system

2018
BMC Plant Biol
PMCID: 5944135
PMID: 29743024
DOI: 10.1186/s12870-018-1295-4

[…] on 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 […]

library_books

Assessing the Zoantharian Diversity of the Tropical Eastern Pacific through an Integrative Approach

2018
Sci Rep
PMCID: 5940898
PMID: 29739963
DOI: 10.1038/s41598-018-25086-4

[…] ntamination 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 were set […]

library_books

Simultaneous quantification of serum monounsaturated and polyunsaturated phosphatidylcholines as potential biomarkers for diagnosing non small cell lung cancer

2018
Sci Rep
PMCID: 5940703
PMID: 29740076
DOI: 10.1038/s41598-018-25552-z

[…] Technologies, USA) and Analyst TF (version 1.7.1, AB SCIEX, USA) qualitative analysis software. MS raw data files were converted to the mzXML format using ProteoWizard and processed by the R package XCMS (version 1.41.0), which can perform peak finding, filtering, alignment, and scaling. The R package CAMERA was used for peak annotation after XCMS data processing. The cutoff for match score was s […]

library_books

Proteomics integrated with metabolomics: analysis of the internal causes of nutrient changes in alfalfa at different growth stages

2018
BMC Plant Biol
PMCID: 5935980
PMID: 29728056
DOI: 10.1186/s12870-018-1291-8

[…] The raw MS data (wiff.scan files) were converted to MzXML files using ProteoWizard MSConvert and processed using XCMS [–] for feature detection, retention time correction and alignment. Metabolites were identified via accuracy mass (< 25 ppm) matching and secondary spectrogram matching (score > 0.8). The results […]

call_split

Tissue storage affects lipidome profiling in comparison to in vivo microsampling approach

2018
Sci Rep
PMCID: 5934459
PMID: 29725071
DOI: 10.1038/s41598-018-25428-2
call_split See protocol

[…] Raw LC/MS data sets were processed using XCMS package software for peak extraction, grouping, retention time correction, and peak filling–. All parameters for XCMS analysis were optimized by IPO package. Extracted peaks were annotated with t […]

Citations

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

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