pLink-SS software was used to initially identify spectra containing disulfide-linked peptides, as previously described (133). Precursor and fragment tolerances were set to 10 ppm, variable modifications of Cys carbamidomethylation, and Ser/Thr phosphorylation. Once a spectrum containing a disulfide-linked peptide was identified, the spectrum was redrawn using a custom R script and manually annotated to include disulfide fragmentation mass shifts of −33.987 atomic mass units (amu) (dehydroalanine) and +31.971 amu (disulfohydryl) at both Cys residues (134).

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