Table 2 Quantification of targeted lysine modifications TIMING: 3–4 days for each run

 1. Synthesize peptides containing targeted lysine modifications as internal calibrators.

 ▲CRITICAL The purity of the synthetic peptides should be greater than 98% to ensure accurate quantification.

 2. Mix known concentrations of synthetic peptide into samples to be analyzed.

 3. Run samples with known synthetic peptides and samples without synthetic peptides through steps 1–54.

 4. Compare the areas of GC or LC peaks of the targeted modifiers in these samples.

 5. Calculate the levels of modifications in these samples by comparing with the internal peptide calibrator.

 6. Alternatively, obtain a working curve by running various levels of synthetic peptides through steps 1–54, and compare areas of GC or LC peaks of samples with the working curve.