Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

Exercise MSMS4: answers


  1. Are all four reporter ions being used?
    No, looks like only 114 and 116 labels were used
  2. Why are some ratios shown in bold face?
    These are ratios that are significantly different from 1. (details)
  3. Would normalisation a good idea for this example?
    Definitely not. All the indications are that this is a test sample with a ratio of approx 1:2. Normalisation should only be used when the average ratio is expected to be 1.
  4. How is iTRAQ modification to Tyr used in the method?
    Any match with iTRAQ(Y) is excluded from quantitation because this reaction is slower than iTRAQ (K) and iTRAQ (N-term), so likely to be incomplete, which could give a skewed ratio.


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