CAMERA

Version: 1.34.0

Website

http://bioconductor.org/packages/release/bioc/html/CAMERA.html

Description

CAMERA (Collection of Algorithms for MEtabolite pRofile Annotation) is designed as an add-on to XCMS, providing additional grouping based on retention time and chromatographic peak shape and isotopic peaks and adduct annotation. Features are first grouped by their retention times, using 60% of the FWHM around the centroid of the most intense feature that is not yet assigned a compound spectrum. Isotopic peaks are then detected by calculating a pairwise distance matrix and detecting isotopes exhibiting a 1.0033 m/z difference. Chromatographic peak shape is then used to improve spectral separation (pointwise pearson correlation of the intensities between the chromatographic peak boundaries between all pairs of features of a single EIC, pointwise pearson correlation of the intensities between the chromatographic peak boundaries between all pairs of features of all samples and isotope relationship between two features, which are then plotted as scores on a relationship graph using either the Highly-connected-subgraphs or label propagation community algorithms). Adducts, common neutral losses and cluster ions are then annotated using a dynamic rule set, which is then matched against m/z differences. Annotations made in positive and negative mode are then combined and compounds that are detected in both are verified using a novel algorithm and a cross-polarity rule table.

Functionality

• Annotation/MS/Level 4 - Unequivocal Molecular Formula

Instrument Data Type

• MS/LC-MS

Approaches

• Metabolomics/Untargeted

Computer Skills

Advanced

Software Type

R Package

Interface

Command line interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R

Dependencies

R (≥ 2.1.0), methods, Biobase, xcms (>= 1.13.5), igraph

Input Formats - Open

mzData, mzML, mzXML, netCDF

Input Formats - Proprietary

Published

2009

Last Updated

2017

License

GPL (≥ 2)

Paper

http://www.ncbi.nlm.nih.gov/pubmed/22111785

PMID

22111785