See description of Compare Identification Summaries with Spectral Count .

To obtain a spectral count, right click on a Dataset with merged Identification Summaries and select the “Compare with SC” menu in the popup. This Dataset will be used as reference Dataset and Protein Set list as well as specifics peptides will ne defined there.

In the Spectral Count window, fill the name and description of your Spectral Count and press Next.

Then select the Identification Summaries on which you want to perform the Spectral Count and press Next.

Finally select the DataSet where shared peptides spectral count weight will be calculated and press OK.

A Spectral Count is created and added to the Quantitations Panel.

You can then display a Spectral Count, see viewspectralcount