simSearch {xcms}R Documentation

Unrestricted precursor Metlin Search

Description

A method for searching MS^2 data against the METLIN Database without a precursor restraint.

Usage

simSearch(object, ppmfrag=20, percent=50, file, fullReport=FALSE, ...)

Arguments

object An xcmsFragment object generated by xcmsRaw.collect
ppmfrag Error on fragment masses in ppm
percent Percentage thresthold to use for identification
file Name of the output files
fullReport Should a full report be generated
... Arguments to plot.metlin()

Details

This method searches the METLIN database for similar MS/MS spectra and ranks them on a fragment score and a neutral loss score. Both of these scores work on a score_fun method. The search takes xcmsFragment objects and searches the database with an unrestricted precursor, thereby searching all spectra in the METLIN database. The percent variable can be used to remove spectra that are below the accepted percentage similarity. The percentage similarity is an independant variable for both the fragment search and the neutral loss search. The method generates two files when the fullReport variable is set to TRUE. The default file shows the top 5 m/z's most frequently matched. This gives a guide as fragments and neutral losses which should be inspected with a formula calculator. The second file which is printed to a variable and or to the second file is a full report of the data. This report includes metabolite names from the METLIN database and gives both the fragment score and the neutral loss score thereby giving a confidence to the likelyhood of the possible molecule/family of molecules.

Value

A data frame with the following columns:

m/z Precursor m/z of the Experimental spectra
rtmin Start of the rt window
rtmax End of the rt window
Experiment Collision Energy Experimental spectra Collision Energy
Fragment Score Score of the Fragments
Neutral Score Score of the Neutral loss
Common Neutral loss m/z of the most matching neutral loss
Common Fragment m/z of the most matching fragment
Compound Name Name of the compound from METLIN
Metlin Mass The mass as reported by METLIN
Collision Energy The collision energy of the metlin spectra

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]