Supplementary Figure 2: Fragment-ion types that are specific for disulfide-linked peptides and their contribution to disulfide bond identification. | Nature Methods

Supplementary Figure 2: Fragment-ion types that are specific for disulfide-linked peptides and their contribution to disulfide bond identification.

From: Mapping native disulfide bonds at a proteome scale

Supplementary Figure 2

(a-b) Illustration of the disulfide bond-specific fragment ions found in HCD spectra, including p ions (αp, bp, αp(-2), bp(-2), αp(+32), bp(+32), αp(-34) and βp(-34)), pb and py ions (e.g. αp(-2)b4 and αp(-2)y4). (c) An HCD spectrum in which disulfide bond-specific fragment ions are found (inset). (d) E-value separation of correct and random matches of disulfide-bonded peptides when different ion types are considered in the pLink search. The test data consisted of 1141 HCD spectra of disulfide-linked peptide pairs whose identities were known and 46526 HCD spectra of reduced and alkylated linear peptides from a trypsin-digested E. coli lysate. Solid and dashed lines denote forward (pos) and reverse (neg) database hits, respectively.

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