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TABLE 1. Representative list of Cys-labeled peptide pairs obtained from E1 at pH 8.0 as identified by LC/MS/MS analysis

Peptide^a [M+H]⁺^b
Charge state^c Xcorr^d ${Delta}$ C_n^e Labeled residue^f

Calculated Measured

F.GC#KIAVNPL.R 928.5 928.9 2 2.577 0.105 C259

F.GC*KIAVNPL.R 971.5 972.0 2 2.510 0.088 C259

R.AVDC#SYGNIPISIDIPNAAFIR.T 2,364.7 2,363.7 2 4.494 0.975 C271

R.AVDC*SYGNIPISIDIPNAAFIR.T 2,407.7 2,406.5 2 3.292 NC^g C271

^a Residue modifications: *, 57.0 u (carboxamidomethylation); and #, 14.0 u (methylation). The amino acid residues appearing before and after the periods correspond to the residues proceeding and following the peptide in the protein sequence.

^b Average mass calculated based on the peptide sequence (calculated) and the deconvoluted mass-to-charge (m/z) ratio based on the measured centroid mass (measured).

^c Charge state of the precursor ion selected for CID.

^d The SEQUEST cross-correlation score (Xcorr) of the peptide is based on the match of the obtained product ion spectra to the theoretical ion distribution for the corresponding peptide contained in the database.

^e The SEQUEST difference of cross-correlation scores ( ${Delta}$ C_n) is the "difference" between the top two Xcorr values for a given product ion spectrum.

^f Labeled residues correspond to their position in the primary sequence of the E1 protein as determined by CID peptide fragmentation analysis.

^g NC, not calculated. Since SEQUEST could not match another peptide with the corresponding precursor ion mass and generated fragmentation pattern, the ${Delta}$ C_n could not be calculated.

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