I am learning about data dependent acquisition (DDA) mode in mass spectrometry from this online resource. I have come across the following statement:

In DDA mode, the mass spectrometer selects the most intense peptide ions in a first stage of tandem mass spectrometry, and then they are fragmented and analyzed in a second stage of tandem mass spectrometry.

I am not sure what is meant by the "most intense peptide ions". Does most intense refer to the most abundant peptide ions? Any insights are appreciated.

  • 1
    $\begingroup$ I don't have a source at the moment (and hence a comment instead of an answer), but I would imagine the authors of that resource are referring to the most intense peptide ion m/z (mass/charge ratio) signal as measured by area under the curve (AUC). The software picks the largest peak(s) and targets them for further analysis during the second mass spec run. This can also be done manually. $\endgroup$
    – MattDMo
    Commented Apr 10, 2022 at 16:40


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