These types of modifications are typically located by comparative peptide mapping on either the FT-ICR, MALDI-Tof/Tof instruments, or by LC-MS/MS analysis.
- Comparative mapping of the peptide mass fingerprint of a control sample digestion (with no modification) to the modified sample digestion using µESI FT-ICR or MALDI-Tof/Tof MS. Masses that differ can be further analyzed by MS/MS.
- Comparison of the observed peptide mass fingerprint masses (µESI FT-ICR or MALDI-Tof/Tof) to the known protein sequence to locate peptides that do not match. MS/MS can be performed on these masses.
- Analyze the digest(s) by LC-MS/MS and do a database search locating for specific modifications.