Since TMT and iTRAQ work by measuring the reporter ion peaks in mass spectra, it is important to include the spectrum data along with the mzIdentML (MZID) in the form of an MGF file. If the MGF file is not present when you try to load your data into Scaffold Q+S, you will see a warning that quantitative data is not available. You will also not be able to visualize spectra in the Spectrum tab of Scaffold's Proteins View if you don't include the MGF file.
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