CAMERA: An Integrated
Strategy for Compound Spectra
Extraction and Annotation of Liquid Chromatography/Mass Spectrometry
Data Sets
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Abstract
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 bottleneck 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 modes, 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