Table 1

Protein fingerprinting results obtained from the mass spectrometric analysis of tryptic peptides and protein alignment using ProFound

Gel SectionIncub.Protein IdentifiedPeptides AlignedCoverageProbabilityMS/MS Peptides
h %
∼55-kDa band0CYP3A216330.62
μS Epoxide
HMM Bands0none
Ubiquitin (8 kDa)0Ubiquitin7671.0

The ∼55 kDa band and the HMM bands were determined in samples without added ubiquitin. The ubiquitin band was analyzed in a separate sample that contained 100 μM ubiquitin. Probability values for multiple hits on the same or very closely related gene product were summed. For example, in the case of the ∼55-kDa band, ProFound identified two separate entries for CYP3A2 and assigned each a probability of 0.31. The last column identifies the number of peptides for which sequence information was obtained by MS/MS analysis that confirmed that the peptide was from the indicated CYP3A protein. CYP3A1 and CYP3A23 are 98.6% identical. As such, we were typically unable to distinguish peptides from these two proteins using this analysis.