Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data

Annotates data from liquid chromatography coupled to mass spectrometry (LC/MS) metabolomics experiments. Based on a network algorithm (O.Senan, A. Aguilar- Mogas, M. Navarro, O. Yanes, R.GuimerĂ  and M. Sales-Pardo, Metabolomics Conference (2016), Dublin), 'CliqueMS' builds a weighted similarity network where nodes are features and edges are weighted according to the similarity of this features. Then it searches for the most plausible division of the similarity network into cliques (fully connected components). Finally it annotates metabolites within each clique, obtaining for each annotated metabolite the neutral mass and their features, corresponding to isotopes, ionization adducts and fragmentation adducts of that metabolite.

"cliqueMS" annotates processed LC/MZ data. This R package obtains annotation for isotopes, ion adducts and fragmentation adducts. The adduct's list can be supplied by the user or either use one of the package's lists.


Installation has been tested on Linux and Windows.

You can install "cliqueMS" from github with:


Usage and examples

For a tutorial on "cliqueMS" please check the vignette:



First version of cliqueMS.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.


0.3.0 by Oriol Senan Campos, 20 days ago

Report a bug at

Browse source code at

Authors: Oriol Senan Campos [aut, cre] , Antoni Aguilar-Mogas [aut] , Jordi Capellades [aut] , Miriam Navarro [aut] , Oscar Yanes [aut] , Roger GuimerĂ  [aut] , Marta Sales-Pardo [aut]

Documentation:   PDF Manual  

GPL (>= 2) license

Imports Rcpp, xcms, MSnbase, igraph, qlcMatrix, Matrix, methods

Suggests knitr, rmarkdown, testthat, CAMERA

Linking to Rcpp, BH, RcppArmadillo

System requirements: C++11

See at CRAN