\name{searchMetlin}
\alias{searchMetlin}
\alias{searchMetlin,xcmsFragments-method}
\title{Search Metlin Online Database}
\description{
  A method for searching \eqn{MS^2} data against the accurate \eqn{MS^2} METLIN database
}
\usage{
searchMetlin(object, ppmfrag=10, ppmMZ= 5, file, MS1data=FALSE,
metXML="metlin", ...)
}
\arguments{
  \item{object}{An xcmsFragment object generated by xcmsRaw.collect}
  \item{ppmfrag}{Error in ppm for each fragment}
  \item{ppmMZ}{Error in ppm for precursor mass}
  \item{file}{Name of the results file}
  \item{MS1data}{Should accurate mass alone be search as well}
  \item{metXML}{location of metlin like XML file or "metlin" as a
    default}
  \item{...}{Arguments to plot.metlin()}
}
\details{
  This method automates the task of MS/MS comparison to a reference library. By default the METLIN database is used however this can be changed with the \code{metXML} parameter. 

  The search first identifies precursors that match entries in the current METLIN databass using the specified error given by \code{ppmMZ}. Once a matching m/z value is found, MS/MS data is searched. Each fragment is identified and comparied to the reference fragments with error specified by\code{ppmfrag}. Each match is done using a score schema of the difference and similarity of the two spectra. This value is the equiovacated against the possible maximum and minimum.
  
  For each match a plot of the two MS/MS spectra are given. These are found using the \code{A} and \code{B} parameter
}
\value{
  A data frame with the following columns:

\item{A}{Location of the plot}
\item{B}{Seconded number locator for plot}
\item{Precursor Ion}{M/Z of the precursor Ion}
\item{rtmin}{Start of rt window}
\item{rtmax}{End of rt window}
\item{CollisionEnergy experiment"}{Collision energy of the experiment}
\item{CollisionEnergy Reference}{Collision energy of the reference}
\item{Percentage Match"}{Match percentage of the reference spectra to the experimental spectra}
\item{Metlin Mass}{The mass of the reference precursor ion}
\item{# matching"}{The number of matching fragment}
\item{# non-matching}{The number of non-matching fragments}
\item{Total # Ref ion}{The total number of fragment reference ions}
\item{Metlin ID Name}{Name of the identified meatbolite}
\item{Ionization}{Is the reference spectra in '-' mode or '+' mode}
\item{Adduct}{Is the reference spectra an adduct of the precursor}

}
\references{
  H. Paul Benton, D.M. Wong, S.A.Strauger, G. Siuzdak "XC\eqn{MS^2}"
  Analytical Chemistry 2008
}
\author{H. Paul Benton, \email{hpbenton@scripps.edu}}
\keyword{methods}