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Stable isotope labeled peptides (SIL peptides), also known as heavy peptides, are chemically synthesized peptides with the native sequence, but some of the constituent amino acids are replaced by the stable isotope labeled amino acids, such as 12C by 13C, 14N by 15N, and 1H by 2H. Stable isotope labeled peptides are chemically and physically indistinguishable from their endogenous counterparts with respect to retention time, ionization efficiency and fragmentation mechanism.