MetaboAnnotation: simplifying metabolite annotation

We present the R package MetaboAnnotation designed to assist the end-user in
metabolite annotation. Specifically, MetaboAnnotation provides the high level
functions matchValues() and matchSpectra() to perform MS1 and MS2-based
annotation. The former involves matching of measured m/z values and/or retention
times of LC–MS features against reference values; the latter a comparison of
potentially generated experimental MS2 spectra against reference spectra, either
from in-house or external libraries. The result objects returned by these
functions bundle the query and target spectra and internally represent the
relationships between them in a data frame that also contains the score for each
match. Filtering, sub-setting, re-ordering and extracting matches, all
potentially error prone operations, are all handled by these result
objects. Finally an interactive, shiny-based, validation of matching results
is also available with the validateMatchedSpectra() function. The package is a
central component of a complete ecosystem facilitating metabolite annotation and
is available on Bioconductor.