CliqueMS new R package for the annotation of adducts and fragments in LC-MS

July 09, 2019, 12:21:29 PM

Dear Forum Members,

I want to use this sub-forum for announcing CliqueMS, a new package for the annotation of isotopes, adducts and fragments in LC-MS untargeted metabolomics. CliqueMS is based on a network algorithm for grouping features that are likely to belong to the same metabolite. Then, within each group it annotates isotopes, adducts and some fragments in a flexible way.

Last package version can be installed from the github:
https://github.com/osenan/cliquems

Moreover, there is an online Application for those that do not use R, called CliqueMS Web:
http://cliquems.seeslab.net/

For both the package and the Web Application there are tutorials to learn how to perform the analysis. For those who want to know all details I link the publication of the algorithm:
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz207/5418951

As the developer of the package, I will be happy to answer questions and doubts regarding the use of CliqueMS.

Kind regards,
Oriol Senan

Re: CliqueMS new R package for the annotation of adducts and fragments in LC-MS

Reply #1 – July 17, 2019, 09:41:24 PM

Thanks for sharing, Osenan.

I've been using different packages for annotation of isotopes, adducts, dimers and fragments.
There are, of course, many ways that this can be done. From using just exact mass; examination of co-elution peak shape; and correlations of peak areas.

I'd be interested in looking at how your network algorithm can improve our annotations.

Look forward to some interesting discussions in the future!

Cheers,
Corey

Re: CliqueMS new R package for the annotation of adducts and fragments in LC-MS

Reply #2 – July 18, 2019, 07:49:50 AM

Thanks for your answer,

Exactly, looking for some interesting discussions on annotation and other metabolomics topics!

Oriol