Yes, my raw data have two "functions":1) "intact compound" m/z ; 2) fragment pattern. Then I'll process them using XCMS R-package. I'll check the Proteowizard's filters and learn more about these filters that you are telling me. I've been using MSconvertGUI to convert my raw data. Thank you so much. I was worry about that.
I'd like to know if exists a free-source converter or a R package to convert correctly these raw data into a mzXML or netCDF data, without the necessity of MassLynx software.
Thank you in advance.
Francisco J. Novais University of São Paulo, Brazil.