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Shape step one illustrates the newest SICyLIA workflow so you can yourself evaluate cysteine oxidization in two ranged samples with the an entire proteome scale
Contour the first step illustrates the SICyLIA workflow to help you oneself examine cysteine oxidation in two ranged examples towards the a complete proteome scale
Proteomic quantification of around the world cysteine oxidization
Control and oxidatively stressed cells or tissue samples were extracted separately in the presence of either light ( 12 C2HcuatroINO) or stable isotope-labelled heavy ( 1step three C2D2H2INO) IAM to alkylate reduced cysteine thiols (SH), coupling a carbamidomethyl (CAM) group to the cysteine residue. After labelling, equal amounts of protein extracts were mixed using a label-swap replication strategy and treated with dithiothreitol (DTT) to reduce reversibly oxidised thiols, which were subsequently blocked with n-ethylmaleimide (NEM). Proteomes were then digested and peptides fractionated using off-line high pH reversed phase chromatography prior to UHPLC-MS/MS analysis on a Q-Exactive HF. Cysteine oxidation ratios are calculated using the MaxQuant computational platform 20 based on the abundance of light and heavy CAM-modified peptide pairs for each cysteine-containing unique peptide. As IAM reacts with reduced cysteine thiols, a -modification for a given peptide indicates increased cysteine oxidation. Whereas changes in the levels of reduced cysteine between samples undergoing a short-term treatment can be compared immediately (Fig. 1a ), different cell lines or tissues derived from different mice have distinct proteomes and require normalisation for protein levels. For relative protein quantification, stable isotope dimethyl labelling 26 was used in con labelling (Fig. 1b ). This method follows a comparable workflow as described above, streamlining these parallel procedures. As shown in Fig. 1b , a fraction of the lysates used to prepare IAM-labelled samples are digested and dimethylated with either light (H 12 CHO/NaBH3CN) or heavy (D 13 CDO/NaBD3CN) formaldehyde/sodium cyanoborohydride, mixed in equal ratios using a label-swap replication strategy for independent replicates, and subjected to high pH reversed phase chromatography fractionation before UHPLC-MS/MS analysis. Continue Reading