To search for symmetric and asymmetric arginine methylations within the hmSILAC peptide sequences, we defined new specifications in MaxQuant with the mass difference and residue specificities corresponding to neutral loss of light monomethylamine and dimethylamine [NH2CH3, 31.0421 Da; NH(CH3)2, 45.0578 Da] and loss of heavy monomethylamine and dimethylamine [NH2(13CD3), 35.0641 Da; NH(13CD3)2, 53.1018 Da] to the following variable modifications: di-methyl-K/R and di-methyl4-K/R. In addition, we added heavy methionine (Met4) and oxidized heavy methionine (OxMet4) as variable modifications. To search for symmetric and asymmetric arginine methylations within the SILAC dataset, we defined new specifications in MaxQuant with the mass difference and residue specificities corresponding to neutral loss of light monomethylamine and dimethylamine [NH2CH3, 31.0421 Da; NH(CH3)2, 45.0578 Da] and loss of heavy monomethylamine and dimethylamine [15NH2CH3, 32.0392 Da; 15NH(CH3)2, 46.0548 Da] to the following variable modification: di-methyl-R. Then, MaxQuant viewer was used for manual inspection of the MS2 spectra of the identified dimethylated peptides.

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