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X13CMS specifications


Unique identifier OMICS_06730
Name X13CMS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for X13CMS

X13CMS citations


Identifying off target effects of etomoxir reveals that carnitine palmitoyltransferase I is essential for cancer cell proliferation independent of β oxidation

PLoS Biol
PMCID: 5892939
PMID: 29596410
DOI: 10.1371/journal.pbio.2003782

[…] hplc system. mass spectrometry detection was carried out on an agilent 6540 q-tof coupled with an esi source operated in negative mode. isotopic labeling was assessed comprehensively by using the x13cms software []. the identity of each metabolite was confirmed by matching retention times and ms/ms fragmentation data to standard compounds. the isotopologue distribution patterns presented […]


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

[…] that show a clear pattern of isotopic enrichment. however, the approach requires the labeled fraction to be fully labeled and the tracer to be highly pure to get the proper isotopic distributions. x13cms [] and george [], both run on the r platform using gc-ms output. the former algorithm iterates over ms signals in each mass spectra using the mass difference due to the label, while the latter […]


Lactate Metabolism is Associated with Mammalian Mitochondria

Nat Chem Biol
PMCID: 5069139
PMID: 27618187
DOI: 10.1038/nchembio.2172

[…] for features detection (peakwidth = 20–200 s and ppm = 10) and obiwarp method for retention time correction. the output object, xcmsset(), containing labeled and unlabeled data was then submitted to x13cms for the isotopic labeling analysis. the peaks corresponding to the isotoplogues of each base peak were identified according to the following inputs: i.) the mass difference between 13c and 12c […]


Stable Isotope Assisted Evaluation of Different Extraction Solvents for Untargeted Metabolomics of Plants

Int J Mol Sci
PMCID: 4964393
PMID: 27367667
DOI: 10.3390/ijms17071017

[…] for global yet specific detection of features derived from biological origin. to this end, several software tools have been developed for lc-hrms data processing during the last few years such as x13cms [], mzmatch-iso [], hitime [], iroa—company (avaliable online: http://iroatech.com, last accessed may 2016), allocator [] and metextract [,]., some of these tools have been designed to use […]


Evidence that 2 hydroxyglutarate is not readily metabolized in colorectal carcinoma cells

PMCID: 4665876
PMID: 26629338
DOI: 10.1186/s40170-015-0139-z

[…] re extracted as described above., raw data was converted to mzxml by using msconvert and then analyzed with the xcms software (peakwidth = 5–140 s and ppm = 12) []. for isotope analysis, our in-house x13cms software package was utilized and isotopic labeling patterns were identified with the following parameters: mass of 12c = 12.000000 da, mass difference between 13c and 12c = 1.003355 da, ppm =  […]


Untargeted Profiling of Tracer Derived Metabolites Using Stable Isotopic Labeling and Fast Polarity Switching LC–ESI HRMS

Anal Chem
PMCID: 4255957
PMID: 25372979
DOI: 10.1021/ac503290j

[…] software tools designed for the untargeted detection and analysis of isotope patterns of metabolites derived from native and partly isotopically labeled tracers are available (e.g., mzmatch-iso, x13cms). however, to the best of our knowledge, no tools for the automated global and highly selective detection of only those metabolites derived from native and labeled tracers with nonoverlapping […]

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X13CMS institution(s)
Departments of Genetics, Medicine, and Chemistry, Washington University School of Medicine, St Louis, MO, USA

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