Since TMT and iTRAQ work by measuring the reporter ions in the 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+, you will see a warning that quantitative data is not available. You will also not see the Spectrum tab in Scaffold's Proteins View if you don't include the MGF file.
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