How does Scaffold calculate the peptide mass values displayed in the Spectrum Report?
Each peptide has four mass values associated with it in Scaffold’s Spectrum Report. These are Observed m/z, Actual peptide mass (AMU), Calculated peptide mass (AMU), and Actual minus calculated peptide mass (AMU). Although it is not directly a mass, the Spectrum charge is a very important part of Scaffold’s mass calculations. Observed m/z = Observed mass charge given by the MS/MS machine Actual peptide mass (AMU) = (Observed m/z)*Spectrum charge – Spectrum charge*(1 proton). This is the actual weight of the Observed m/z spectrum. Calculated peptide mass (AMU) = Sum(amino acid weights) + 1 proton. This is the summation of amino acid weights for the peptide, plus one proton weight. Scaffold is really reporting the Calculated mass for the ionized peptide. Actual minus calculated peptide mass (AMU) = (Actual peptide mass) – (Calculated peptide mass – 1 proton). It is important to remember that 1 proton mass (in AMU) is subtracted from what Scaffold calls the Calculated peptide mass before
