TABLE 3.

Part A, cysteine containing peptides identified from MS/MS spectra with selected SEQUEST parameters shown for each peptide. Part B, Bioworks ShowOut view for peptide #1 in panel A, depicting the next two closest matches to the database. Subscripts denote the position of the cysteine within the 2-KPCC sequence. Symbols represent modifications to cysteine and are as follows: #, iodoacetamide; ∼, acrylamide; and @, BES

^a Calculated charge state based on the observed m/z value.

^b The X_corr value is the cross-correlation value from the search, or a measure of how closely an experimental MS/MS spectrum matches to a theoretical MS/MS spectrum for a given peptide in the database.

^c Delta Correlation value, dCn indicates how different the first hit is from the second hit in a database search. It is calculated as follows: (X_corr#1 − X_corr#2)/X_corr#1. A general rule of thumb is that a dCn of 0.1 or greater is good.

^d Relative Sp score. Sp is the preliminary score. After finding all peptides that match within the selected mass tolerance, SEQUEST dose a preliminary scoring of these candidates to reduce the list down to 500 for the final XS_corr analysis. Ideally the RSp value should be 1 on the best matches.