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Spectral counting is of interest to some scientists using Scaffold. Scaffold displays a number of data useful for spectral counting.
If you double click on any protein in the "Samples" view of Scaffold you will be taken to the "Proteins" view.
In the "Proteins" view listed in the upper left hand corner of the screen you will see a window with information about the protein. If you scroll to the right in that window you will see three columns: %Spectra, #Spectra, and #Unique. These are the outputs you can use for spectral counting.
The %Spectra column tells you the percentage of the total spectra assigned to that protein. This is useful because it is giving you a percentage of the whole rather than a specific count number, so you can compare these results against results from another sample.
The #Spectra column tells you the number of spectra associated with that protein. This is useful if you want to give specific numerical results. However, if the amount of sample loaded into your MS/MS machine differed then obviously your spectral counts will differ.
The #Unique refers to the number of unique spectra associated with that protein. This is not as useful as the others for spectral counting, but if you have a situation were it appears that a unique spectra is present in one sample and not another you may wish to report it.
The Percentage of total spectra (%Spectra), Number of total spectra (#Spectra), and Number of unique spectra (#Unique) are all exported in the peptide report, so if you like to use a spreadsheet to display your results you can find them there.
Some scientists like to use percentages of spectra (%Spectra) and number of spectra (#Spectra) to display their results. With those numbers you will know if there were differences in the overall protein concentration when compared to the other proteins in the sample (from %Spectra), and if the number of spectra was greatly increased or decreased between samples (from #Spectra).
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