Terminology Comparison: Legacy Scaffold and Scaffold 4

With the incorporation of protein clusters, we have modified and added new terms to capture different types of evidence, total and exclusive for example. These new terms particularly affect the display options in the Samples view that most Scaffold users are familiar with. Check the following definitions of the terms and table of correspondence with Scaffold 3.

New Terminology
Unique Peptides Peptides with different amino acids sequences, regardless of any modifications
Unique Spectra Spectra that differ in amino acid sequence, charge state or modification
Exclusive Associated with a single protein group
Total Associated with a protein group, whether it i shared with other protein groups


Terminology comparison between Scaffold 3 and 4
Scaffold 3 Term Scaffold 4 Term Description
Number of Unique Peptides Exclusive Unique Peptide Count Number of different amino acid sequences that are only associated with this protein
Number of Unique Spectra Exclusive Unique Spectrum Count Number of unique spectra associated only with this protein
Number of Assigned Spectra Exclusive Spectrum Count Number of spectra associated with this protein
Unweighted Spectrum Count Total Spectrum Count Total number of spectra associated with this protein including those shared with other proteins
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