findPeaks.MS1-methods          package:xcms          R Documentation

_C_o_l_l_e_c_t_i_n_g _M_S_1 _p_r_e_c_u_r_s_o_r _p_e_a_k_s

_D_e_s_c_r_i_p_t_i_o_n:

     Collecting Tandem MS or MS$^n$ Mass Spectrometry precursor peaks
     as annotated in XML raw file

_A_r_g_u_m_e_n_t_s:

  object: 'xcmsRaw' object

_D_e_t_a_i_l_s:

     Some mass spectrometers can acquire MS1 and MS2 (or MS$^n$ scans)
     quasi simultanously, e.g. in data dependent tandem MS or DDIT
     mode.

     Since xcmsFragments attaches _all_ MS$^n$ peaks to MS1 peaks in
     xcmsSet, it is important that findPeaks and xcmsSet do not miss
     any MS1 precursor peak.

     To be sure that all MS1 precursor peaks are in an xcmsSet,
     findPeaks.MS1 does not do an actual peak picking, but simply uses
     the annotation stored in mzXML, mzData or mzML raw files.

     This relies on the following XML tags:

     mzData: ' <spectrum id="463"> <spectrumInstrument msLevel="2">
     <cvParam cvLabel="psi" accession="PSI:1000039"
     name="TimeInSeconds" value="92.7743"/> </spectrumInstrument>
     <precursor msLevel="1" spectrumRef="461"> <cvParam cvLabel="psi"
     accession="PSI:1000040" name="MassToChargeRatio" value="462.091"/>
     <cvParam cvLabel="psi" accession="PSI:1000042" name="Intensity"
     value="366.674"/> </precursor> </spectrum> '

     mzXML: ' <scan num="17" msLevel="2" retentionTime="PT1.5224S">
     <precursorMz precursorIntensity="125245">220.1828003</precursorMz>
          </scan> '  

     Several mzXML and mzData converters are known to create incomplete
     files, either without intensities (they will be set to 0) or
     without the precursor retention time (then a reasonably close rt
     will be chosen. NYI).

_V_a_l_u_e:

     A matrix with columns:

mz, mzmin, mzmax: annotated MS1 precursor selection mass 

rt, rtmin, rtmax: annotated MS1 precursor retention time 

into, maxo, sn: annotated MS1 precursor intensity 

_M_e_t_h_o_d_s:


     _o_b_j_e_c_t = "_x_c_m_s_R_a_w" ' findPeaks.MS1(object) '


_A_u_t_h_o_r(_s):

     Steffen Neumann, sneumann@ipb-halle.de

_S_e_e _A_l_s_o:

     'findPeaks-methods' 'xcmsRaw-class'

