Table 3. MS/MS Ion series of diadducted model peptides by naphthoquinones at pH 8.5.

Peptide	Modification	Precursor m/z[M+H]+	Ions Detected a	Supplemental Figure Ref.b
GRGDSPC	1,2-NQ c	1007.35 d	544.22 (b4 † ) e, 631.25 (b5 † ), 792.30 (y6 † ), 989.36 ([M+H]+ - H2O +X g )	9
GRGDSPC	1,4-NQ f	1007.35	728.29 (b6) e, 639.28 (y4), 989.35 ([M+H]+ - H2O +X)	15
DYKDDDDK	1,2-NQ	1329.47	1068.35 (b6 †† ), 1183.37 (b7 †† ), 607.33 (y5), 1013.41 ([M+H]+- X),1311.46 ([M+H]+ - H2O +X)	11
DYKDDDDK	1,4-NQ	1329.47	752.27 (b6), 867.30 (b7), 1013.40 ([M+H]+- X)	Not shown
DASFHSWG-NH2	1,2-NQ	1221.46	874.31 (b5 †† ), 961.34 (b6 †† ), 643.26 (y4 † ), 790. 33 (y5 † ),905.39 ([M+H]+- X), 1203.45 ([M+H]+ - H2O + X)	12
DASFHSWG-NH2	1,4-NQ	1221.46	961.34 (b6 †† ), 1147.42 (b7 †† ), 643.26 (y 4 † ), 790.36 (y5 † ),905.39 ([M+H]+- X), 1203.45 ([M+H]+ - H2O + X)	17
EFYAPWCG	1,2-NQ	1288.47	620.22 (y4 † ), 1270.45 ([M+H]+ - H2O + X)	13
EFYAPWCG	1,4-NQ	1288.47	794.35 (b6), 1213.4340 (b7 †† ), 778.26 (y4 †† ), 849.29 (y5 †† ), 1012.36 (y6 †† )	18

Product ion spectra for adducted peptides were indistinguishable between both pH conditions; more products were observed at pH 8.5 therefore ions series for the products at this pH was given.

^aObserved signals assigned as b- or y- ions for the diadducts are listed.

^bReference to detailed spectra corresponding to the appropriate ion series.

^cThe modifications are 1,2-naphthoquinone (monoadduct mass +158.04).

^dThe adducted masses were observed in incubations performed at both pHs; data are from pH 8.5 incubations.

^eIons in bold represent modification by a naphthoquinone. A bold b- or y- represents a monoadducted ion. Some of the diadduct MS/MS spectra had monoadduct fragment ions present that were absent in the monoadduct MS/MS spectra.

^fThe modifications are 1,4-naphthoquinone (monoadduct mass +158.04).

^gIn the detected fragment ion signals, X represents the mass of the adduct.