findAdducts-methods          package:CAMERA          R Documentation

_C_a_l_c_u_l_a_t_e _A_d_d_u_c_t_s _a_n_d _A_n_n_o_t_a_t_e _L_C/_E_S_I-_M_S _S_p_e_c_t_r_a

_D_e_s_c_r_i_p_t_i_o_n:

     Annotate adducts (and fragments) for a xsAnnotate object. Returns
     a xsAnnotate object with annotated pseudospectra.

_U_s_a_g_e:

      findAdducts(object,ppm=5,mzabs=0.015,multiplier=3,polarity=NULL)

_A_r_g_u_m_e_n_t_s:

  object: the 'xsAnnotate' object

     ppm: ppm error for the search

   mzabs: allowed variance for the search

multiplier: highest number(n) of allowed clusterion [nM+ion] 

polarity: Which polarity mode was used for measuring of the ms sample

_D_e_t_a_i_l_s:

     Adducts (and fragments) are annotated for a xsAnnotate object. For
     every pseudospectra group, generated bei groupFWHM and groupCorr,
     all possible Adducts are calculated and mapped to the peaks. If at
     least two adducts match, a possible molecule-mass for the group
     can be calculated. After the annotation every masshypothese is
     checked against the charge of the calculated isotopes. It is
     recommend to call findIsotopes() before the annotation step.

_A_u_t_h_o_r(_s):

     Carsten Kuhl <ckuhl@ipb-halle.de>

_E_x_a_m_p_l_e_s:

      library(CAMERA)
      file <- system.file('mzdata/MM14.mzdata', package = "CAMERA")
      xs   <- xcmsSet(file, method="centWave", ppm=30, peakwidth=c(5,10))
      an   <- xsAnnotate(xs)
      an   <- groupFWHM(an)
     # an <- groupCorr(an,xs) # optional but very recommended step

      an <- findIsotopes(an)  # optional but recommended.
      an <- findAdducts(an,polarity="positive")
      peaklist <- getPeaklist(an) # get the annotated peak list

