Hi Antonio, You are correct and you will need access to the MS2 spectra. Indeed, that is the incentive argued by Griffin, that MS2 fragment intensity gives some advantage to quantification in MS2-based methods for overlapping signals. However, there is a lot more literature out there (and far more recent than the Griffin paper) regarding the benefits and limitations of MS1 and MS2 quantification. Also, MS1 quantification algorithms have improved a lot over the past several years. Some algorithms might even be able to deconvolve overlapping MS1 signals. In any case, the extent to which overlapping MS1 signals interfere with the overall quantification results is 1) sample dependent, and 2) a matter of debate. Ultimately there isn't a perfect solution, and cases for which any procedure, whether MS1-based or MS2-based, might be better suited. Cheers, Mike
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