I am trying XCMS online and although everything seems to be working, I believe there may be a problem. The issue is that my data was acquired on a Thermo LTQ-FT, thus I have two kinds of MS1 scans, with one scan in the iontrap, and one scan in the FT cell. Is it possible to have XCMS online just process one type of data at a time? For example, just the odd or even scans?
Alternatively, can one of the mzXML converters do this? Neither Proteowizard or Readw seem to have this function.