Download Explanation of Scaffold`s Display Options - Proteome Software

Explanation of Scaffold’s Display Options
% of total spectra: This is the percentage of the total number of spectra which is assigned to the protein in
question. This number is the number of assigned spectra for this protein divided by the total spectra in the
sample (as seen in the Load Data View).
Assigned spectra: This is the number of spectra which Protein Prophet assigns to the protein in question.The
peptides represented by these spectra may also be present in the sample from a different protein, but the
program assigns each spectrum to only the protein (or protein group) for which there is the most evidence,
so in this display option, spectra are counted only once.
Unique Peptides: This is the number of distinct amino acid sequences represented in the peptides that match
to a protein. Peptides with the same a.a. sequence but different charges, or with different modifications are
grouped together and counted only once in this count.
Unique Spectra: Two spectra are unique if they match different peptides (even if the peptides overlap) or
match two different charge states of the same peptide or match both a peptide and a modified form of the
peptide. The number of unique spectra is a count of these unique spectra. Only peptides that are "good" or
"valid" and are assigned to a given protein count.
Percentage coverage: The percentage of all amino acids in the protein sequence that were detected in the
sample.
Unweighted spectrum count: This is all of the spectral counts which could possibly be assigned to a protein
regardless of whether or not Protein Prophet actually assigned the spectra to these proteins. Spectra
matching a shared peptide are counted in each protein containing that peptide.
Quantitative Values (=Normalized spectral counts): Our protein normalizing entails averaging the unweighted
spectral counts for all of the MS-samples and then multiplying the spectrum counts in each sample by the
average divided by the individual sample's sum.
In all cases, the proteins listed depend on the filter values selected at the top of the window. For the
displayed proteins, the actual values of all options except Protein ID Probability depend on the setting for the
minimum peptide probability filter.