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Clustering of MS2 Spectra for Metabolite Identification

Bioconductor version: Release (3.19)

CluMSID is a tool that aids the identification of features in untargeted LC-MS/MS analysis by the use of MS2 spectra similarity and unsupervised statistical methods. It offers functions for a complete and customisable workflow from raw data to visualisations and is interfaceable with the xmcs family of preprocessing packages.

Author: Tobias Depke [aut, cre], Raimo Franke [ctb], Mark Broenstrup [ths]

Maintainer: Tobias Depke <depke at>

Citation (from within R, enter citation("CluMSID")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

CluMSID DI-MS/MS Tutorial HTML R Script
CluMSID GC-EI-MS Tutorial HTML R Script
CluMSID LowRes Tutorial HTML R Script
CluMSID MTBLS Tutorial HTML R Script
CluMSID Tutorial HTML R Script
Reference Manual PDF


biocViews Clustering, Metabolomics, Preprocessing, Software
Version 1.20.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License MIT + file LICENSE
Depends R (>= 3.6)
Imports mzR, S4Vectors, dbscan, RColorBrewer, ape, network, GGally, ggplot2, plotly, methods, utils, stats, sna, grDevices, graphics, Biobase, gplots, MSnbase
System Requirements
Bug Reports
See More
Suggests knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr, CluMSIDdata, metaMS, metaMSdata, xcms
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CluMSID_1.20.0.tar.gz
Windows Binary
macOS Binary (x86_64) CluMSID_1.20.0.tgz
macOS Binary (arm64)
Source Repository git clone
Source Repository (Developer Access) git clone
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