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

