searchMetlin              package:xcms              R Documentation

_S_e_a_r_c_h _M_e_t_l_i_n _O_n_l_i_n_e _D_a_t_a_b_a_s_e

_D_e_s_c_r_i_p_t_i_o_n:

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

_U_s_a_g_e:

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

_A_r_g_u_m_e_n_t_s:

  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()

_D_e_t_a_i_l_s:

     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 by'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 'A' and 'B' parameter

_V_a_l_u_e:

     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

_A_u_t_h_o_r(_s):

     H. Paul Benton, hpbenton@scripps.edu

_R_e_f_e_r_e_n_c_e_s:

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

