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.

In the Spectral Count Result Table, you will find three types of Spectral Count : Basic, Specific and Weighted, and an overview column to rapidly compare the Spectral Count between the different Identification Summaries.

The overview is based on the Basic Spectral Count, but it can be changed thanks to the Column Buttons. This button allow to change the visibility of the columns too.

If you sort the column Overview by clicking on its header. You will be able to easily find the proteins with Spectral Counts different from one Identification Summary to another.

You can later display again an already generated Spectral Count, see viewspectralcount