simSearch                package:xcms                R Documentation

_U_n_r_e_s_t_r_i_c_t_e_d _p_r_e_c_u_r_s_o_r _M_e_t_l_i_n _S_e_a_r_c_h

_D_e_s_c_r_i_p_t_i_o_n:

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

_U_s_a_g_e:

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

_A_r_g_u_m_e_n_t_s:

  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()

_D_e_t_a_i_l_s:

     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.

_V_a_l_u_e:

     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

_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

