When building a spectrum library, you may specify post-translational modifications to peptides going into the library. This information is included in the SSL file that is passed to BlibBuild.
Each type of modification is indicated by a unique code enumerated in the table below. The 'modification sequence' is a string of codes that is as long as the peptide sequence. Each position in the modification sequence corresponds to the same position in the peptide sequence. For example, if the peptide YGPSQPLK has a phosphorylation on the serine, the modification sequence would be 000p0000. If the same sequence had a second phosphorylation on the tyrosine and a dimethylation on the lysine, the modification sequence would be p00p000d.
Modification Codes Modification m/z change Code phosphorylation +80 p oxidation +16 o acytylation +42 a dimethylation +28 d monomethylation +14 m trimethylation +42 t sulfation +79.9 s carbanlyation +43 c