The image above is stolen directly by/from Google Images. First thing that pops up if you look up "spectral counting". Anyway, I often get questions about using Proteome Discoverer for spectral counting. I have some slides that I cut from an iORBI I attended several years ago showing spectral counting in PD and this is what I send people.
I'm not a big fan of spectral counting, but it does have its place sometimes. The slides show you a comparison of spectral counting vs. quan of peaks at the MS1 intensity level as the limitations in dynamic range from spectral counting (with a very nice reference).
You can download the PPT slides here.
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