CAMERA: An integrated strategy for compound spectra extraction and annotation of LC/MS data sets
By Carsten Kuhl, Ralf Tautenhahn, Christoph Böttcher, T. Larson, Steffen Neumann. Analytical Chemistry, 2011
1,079 citations recorded by the source corpus.
Liquid chromatography coupled to mass spectrometry is routinely used for metabolomics experiments. In contrast to the fairly routine and automated data acquisition steps, subsequent compound annotation and identification require extensive manual analysis and thus form a major bottle neck in data interpretation. Here we present CAMERA, a Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data. To evaluate the algorithms, we compared the annotation of CAMERA against a manually defined annotation for a mixture of known compounds spiked into a complex matrix at different concentrations. CAMERA successfully extracted accurate masses for 89.7% and 90.3% of the annotatable compounds in positive and negative ion mode, respectively. Furthermore, we present a novel annotation approach that combines spectral information of data acquired in opposite ion modes to further improve the annotation rate. We demonstrate the utility of CAMERA in two different, easily adoptable plant metabolomics experiments, where the application of CAMERA drastically reduced the amount of manual analysis.
Subfields: Ecology, Molecular Biology, Spectroscopy
View Paper: https://www.semanticscholar.org/paper/24c8e21623952ea62f388768b704f24135d6fdd6
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In Molecular Biology
- Steffen Neumann
- Bo Wen
- Marnix H. Medema
- Pieter C. Dorrestein
- T. Eisenberg
- Zhanlong Mei
- Siqi Liu
- Frank Madeo
In Spectroscopy
Citations in the corpus
- MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools (2019, background): “Most fragmented mass peaks (precursor ions) represent molecular ions, although fragmented mass peaks may also represent adducts of one and the same molecule, in source fragments or doubly-charged peaks [29].”
- IPO: a tool for automated optimization of XCMS parameters (2015, methodology): “IPO is continuously improved, optimization of additional XCMS methods will be implemented, other DoE evaluation techniques will be tested and additional identification of isotopic peaks with the R-package CAMERA [23] will be made available to further increase the power of IPO.”
- metaX: a flexible and comprehensive software for processing metabolomics data (2017, methodology): “LC-MS raw data files were converted to mzXML format using ProteoWizard (version 3.0.5941) [44] and then were processed by XCMS [4] and CAMERA [5] for peak picking and peak annotation, respectively.”