I have been working on the labeling of cysteine thiol residues using a differential alkylation technique (NEM and Biotin Maleimide), during the whole process before performing the trypsin digestion step I took samples to perform a native SDS-PAGE and verify the protein is labeled. After verifying the protein is labeled I proceed with the following steps until I reach the LC-MS analysis. I have been improving the final amount of protein injected into the LC-MS equipment (40 ug of protein, recommended by other authors).

After performing the LC-MS analysis, the number of cysteine oxidation sites detected by the equipment is too low (around 10-13 sites).

Do you have a technique to verify the efficiency of the labeling using biotin maleimide?

Thank you for your comments in advance