Dear colleagues,
I’m using an Agilent 6230 LC/TOF to detect the mass of antibodies but encountering some discrepancies in the results.
My antibody has an N-terminal glutamine (Q). When analyzing the Fab2 fragment (after IdeS digestion) using the Agilent 6230, the main peak was observed at 98,551 Da, which matches the theoretical mass without pyroglutamate (pyroQ) formation. However, when I used the Waters G2 LC-QTOF to analyze the same sample, the main peak shifted to 98,538 Da, which suggests pyroQ formation. I did peptide mapping later confirmed the presence of pyroQ.
Has anyone experienced a similar issue? Any insights or advice would be greatly appreciated.
I attached the deconvoluted spectra.
Agilent 6230:
Deconvolution method: BioConfirmIntactProtein-Default.m
Waters G2:
Deconvolution method: MaxEnt1
