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Table 1 DeCyder MS analysis for Q-TOF MS of recombinant parkin exposed to H2O2

From: Oxidation of the cysteine-rich regions of parkin perturbs its E3 ligase activity and contributes to protein aggregation

Domain (Residue #)

Peptide Sequence

Monoiostopioc M r 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

  1. 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.