Integrating chemoproteomics, subcellular localization annotations and experimental oxidation measurements to define the subcellular cysteinome and redoxome. Available at: https://www.sciencedirect.com/science/article/pii/S2451945623001861

The CysLoC Database and mass spectrometry processing were created and developed by Lisa Boatner.

About: Proteinaceous cysteines function as essential sensors of cellular redox state. Consequently, defining the cysteine redoxome is a key challenge for functional proteomic studies. While proteome-wide inventories of cysteine oxidation state are readily achieved using established, widely adopted proteomic methods such as OxICAT, Biotin Switch, and SP3-Rox, these methods typically assay bulk proteomes and therefore fail to capture protein localization-dependent oxidative modifications. Here we establish the local cysteine capture (Cys-LoC) and local cysteine oxidation (Cys-LOx) methods, which together yield compartment-specific cysteine capture and quantitation of cysteine oxidation state. Benchmarking of the Cys-LoC method across a panel of subcellular compartments revealed more than 3,500 cysteines not previously captured by whole-cell proteomic analysis. Application of the Cys-LOx method to LPS-stimulated immortalized murine bone marrow-derived macrophages (iBMDM), revealed previously unidentified, mitochondrially localized cysteine oxidative modifications upon pro-inflammatory activation, including those associated with oxidative mitochondrial metabolism.

Yan, T., Julio, A.R., Villanueva, M., Jones, A.E., Ball, A.B., Boatner, L.M., Turmon, A.C., Nguyễn, K.B., Yen, S.L., Desai, H.S. and Divakaruni, A.S., 2023. Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome. Cell Chemical Biology, 30(7), 811-827.

To run (specifically for post-processing FragPipe MS label free quantitation (LFQ) data with a mouse fasta file):

python3 230119_process.py -exp 'lfq' -lpm '463.2366;467.2529' -hpm '463.2366;467.2529' -proref '2022-10-04-decoys-contam-uniprot_mouse_swissprot_1042022.fasta.fas'