Annotation of LC/MS
metabolomics data

About CliqueMS

CliqueMS is a network-based algorithm that annotates isotopes, in-source adducts and fragments from LC/MS data


What CliqueMS can do

Annotate your samples one-by-one. Reduce the complexity of the data. Group the signals that are likely to belong to the same metabolite. For each group, up to five different annotations ranked by score.


CliqueMS transforms the spectral data into a network. Within this network it finds groups according to a probabilistic algorithm. Each group is a clique, and represents all the signals (isotopes, adducts and fragments) belonging to the same metabolite.

Flexible Annotation

For each group, CliqueMS provides up to five different annotations from all possible annotations within that group. Those top-five annotations are ranked through a score, which is computed by an adduct list that contains the frequency of the putative adducts. CliqueMS can use the build-in adduct list and also a custom list.

Single samples

CliqueMS annotates samples one-by-one. Even in large samples, the whole process is very fast.


CliqueMS is available as a web application or as a R package.

CliqueMS Web

Online annotation of samples.

CliqueMS Web is a Shiny Web application (GLP-3). Easy and intuitive, with all the features of CliqueMS in a graphical application.

CliqueMS R package

Annotation of large number of samples.

R package cliqueMS is recommended for users that need to annotate a large number of samples. Compatible with Linux, MacOS or Windows.

Go to CliqueMS R package Bioconductor repository


Go to CliqueMS R package Tutorial



Contribute to CliqueMS

If you want to contribute to the development of CliqueMS, or have any comment please contact. Also if you experience any problem while working with CliqueMS Web or the CliqueMS R package.

Send Us A Message

Send a mail to the developers

Additional Information
CliqueMS developer's web

CliqueMS Github

CliqueMS Article

Go to CliqueMS article