Deisotoping (in the msconvert option) significantly improves search results for iTRAQ data. However, it also has very bad affects on the reporter ions. Is there a way to get msconvert to only do deisotoping for those spectra in which the m/z >= 140 (ie above the reporter ion levels)? Is this something that can be customized? If not, is there a good workaround to this problem -- eg running msconvert for ms2 below 140 (no desitoping) and again for above 140 (with deisotoping) and somehow merging the mzXML files?
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