searchMetlin {xcms}R Documentation

Search Metlin Online Database

Description

A method for searching MS^2 data against the accurate MS^2 METLIN database

Usage

searchMetlin(object, ppmfrag=10, ppmMZ= 5, file, MS1data=FALSE,
metXML="metlin", ...)

Arguments

object An xcmsFragment object generated by xcmsRaw.collect
ppmfrag Error in ppm for each fragment
ppmMZ Error in ppm for precursor mass
file Name of the results file
MS1data Should accurate mass alone be search as well
metXML location of metlin like XML file or "metlin" as a default
... 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 metXML parameter.

The search first identifies precursors that match entries in the current METLIN databass using the specified error given by 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 byppmfrag. 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 A and B parameter

Value

A data frame with the following columns:

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

Author(s)

H. Paul Benton, hpbenton@scripps.edu

References

H. Paul Benton, D.M. Wong, S.A.Strauger, G. Siuzdak "XCMS^2" Analytical Chemistry 2008


[Package xcms version 1.14.1 Index]