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Supplementary material The Supplementary Material for this article can be found online at: Abbreviations 2-D gel two-dimensional gel 2-ME 2-mercaptoethanol AD Alzheimers disease ALS amyotrophic lateral sclerosis A amyloid-beta BiotinHPDP N -[6-(biotinamido) hexyl]-3 -(2 -pyridyldithio) propionamide BME -mercaptoethanol BST biotin switch technique CAM carbamidomethyl group CBK photocaged bromomethyl ketone CIK4 iodomethyl CNS central nervous system CSF cerebrospinal fluid Ctrl control CuAAC copper(I)-catalyzed azidealkyne cycloaddition Cys cysteine CysTMT cysteine-reactive tandem mass tag CysTMTRAQ cysteine-reactive tandem mass tag and isobaric tags for relative and absolute quantitation DDA data-dependent acquisition DIA data-independent acquisition DTBA dithiobutylamine DTT dithiothreitol EBX ethynyl benziodoxolone ELISA enzyme-linked immunosorbent assay ERW3 fluoronitrobenzene ESI electrospray ionization FFI fatal familial insomnia FTD frontotemporal dementia HC healthy control HPDP N -[6-(biotinamido) hexyl]-3 -(2 -pyridyldithio) propionamide (biotinHPDP) HRMS1 high resolution MS1 IA immunoaffinity IAA iodoacetic acid IAM iodoacetamide iCAT isotope-coded affinity tag iodoTMT iodoacetyl isobaric tandem mass tags IPL inferior parietal lobule isoTOP-ABPP isotopic tandem orthogonal proteolysis-activity-based protein profiling iTRAQ isobaric tags for relative and absolute quantitation LFQ label free quantification MCI mild cognitive impairment MMTS methanethiosulfonate MND motor neuron disease MnSOD manganese superoxide dismutase MRM multiple reaction monitoring MS mass spectrometry MS multiple sclerosis MTRP multiplexed thiol reactivity profiling NaAsc sodium ascorbate ND neurodegenerative diseases NEM N -ethylmaleimide NLRP3, NOD-like receptor family pyrin domain containing 3 NMDA N -methyl -D-aspartate NOD nucleotide-binding and oligomerization domain NPH normal pressure hydrocephalus NPM N -propargylmaleimide OxcyscPILOT oxidized cysteine-selective combined precursor isotopic labeling and isobaric tagging Oxi-Cys oxidative cysteine PD Parkinsons disease PRM parallel reaction monitoring p-SRM pseudo- selected reaction monitoring PTM post-translational modification RAC resin-assisted capture RB2 chloropyridine ROS reactive oxygen species sCJD CreutzfeldtJakob disease SDSPAGE sodium dodecyl sulfate polyacrylamide-gel electrophoresis SH sulfhydryl SILAC stable isotope labeling by amino acids in cell culture S -NO S -nitrosylation SNO TRAP S -NO trapping by triaryl phosphine S -O 2 H S -sulfinylation S -O 3 H S -sulfonylation SOD1 superoxide dismutase type-1 S -OH S -sulfenylation SPS synchronous precursor selection SRM selected reaction monitoring S -SG S -glutathionylation SWATH-MS sequential window acquisition of all theoretical mass spectra TCA trichloroacetic acid TCEP Tris(2-carboxyethyl)phosphine TEV tobacco etch virus TMT isobaric tandem mass tags TOF time-of-flight TOP tandem orthogonal proteolysis TTP transthyretin UPLC ultra performance liquid chromatography XIC extracted ion chromatogram

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