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 adducts list can be supplied by the user or either use one of the package's lists.


Installation has been tested on Linux, Windows and macOS.

You can install "cliqueMS" from github with:


Also, you can install it from CRAN with:


Usage and examples

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




New methods for functions 'anClique' and 'createNetwork'. Methods 'anClique.XCMSnExp' and 'createNetwork.XCMSnExp' developed for mz processed objects of class 'XCMSnExp' from xcms package. In addition, a new internal function has been created to compute cosine similarity. Therefore, now the installation of package 'CAMERA' is in 'Suggests', because is only needed for analysing processed mzdata with the older 'xcmsSet' class of 'xcms'.


Function "getAnnotation" now it is more accurate, because for isotopic features, it uses charge information from "getIsotopes" function.


Function "computeCliques" corrected, there was a small bug in the "step" variable. Function "getIsotopes" corrected, bug when "filterIso" leave no isotopes in the group. In function "filterIso", small bug corrected. maxGrade parameter was not working correctly, fixed for function "getIsotopes".

0.2.2 Function "getIsotopes" updated: there was a bug when the sample had no isotopes, now corrected. Function "getAnnotation" updated: there was a bug when the sample had no isotopes, now corrected.

0.2.1 First version of cliqueMS

Reference manual

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0.3.1 by Oriol Senan Campos, 2 months 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