Table 1.

DeCyder MS analysis for Q-TOF MS of recombinant parkin exposed to H₂O₂

Domain (Residue #)	Peptide Sequence	Monoiostopioc Mr Calculated Observed		Modifications	Ratio
RING I	235NITCITCTDVR245	1326.59	1326.56	Cys-CAM (C); Cys-SO2H (C)	13.2
(238 - 293)	235NITCITCTDVR245	1333.55	1333.62	2 Cys-SO3H	n/a
	235NITCITCTDVRSPVLVFQCNSR256	2605.19	2605.18†	Cys-CAM; Cys-SO2H; Cys-SO3H	n/a
	246SPVLVFQCNSR256	1296.61	1296.58	Cys-SO3H	n/a
	257HVICLDCFHLYCVTRLNDR275	2367.09	2367.19*	Cys-SO3H	3.6
IBR	350VTCEGGNGLGCGFAFCRECK369	2154.86	2154.90	Cys-CAM; Cys-SO3H	n/a
(294 - 417)	370EAYHEGECSAVFEASGTTTQAYR392	2554.06	2554.09	Cys-SO3H	n/a
RING II	428NGGCMHMK435	956.31	956.33	2 Oxidation (Met); Cys-SO3H	n/a
(418 - 449)	428NGGCMHMKCPQPQCR442	1882.70	1882.77	2 Cys-CAM; 2 Oxidation (Met); Cys-SO3H	n/a
	436CPQPQCR442	862.34	862.40	Cys-SO2H	n/a
Others	130DSPPAGSPAGRSIYNSFYVYCK151	2410.09	2410.15	Cys-SO2H (C)	8.1
(1 - 237)	171QATLTLTQGPSCWDDVLIPNR191	2375.14	2375.15	Cys-SO3H (C)	n/a
	192MSGECQSPHCPGTSAEFFFK211	2236.89	2236.94	Cys-SO3H (C)	69.1
	192MSGECQSPHCPGTSAEFFFK211	2309.90	2309.93	Cys-CAM (C); Oxidation (Met); Cys-SO3H (C)	n/a

Notes: GST-parkin was exposed to 10 μM (unmarked), 50 μM (*), or 200 μM H₂O₂ (†). To compensate for intensity differences between elution profiles of individual experiments, normalization was performed using the measured intensity distribution of the entire peptide population. Our development of this algorithm represents a novel function of DeCyder MS v2.0. The ratio of peptide modification was calculated as the intensity of H₂O₂-exposed parkin compared to vehicle-treated control. Peptide sequences in these experiments are determined by mass fingerprint. Legend: n/a, not applicable (since peptide modifications were only identified for the H₂O₂-exposed samples); IBR, in-between RING domain; CAM, Carbamidomethyl; Cys, cysteine; Met, methionine.