Supporting data of “A Chemical Biology Approach for Cell Type-Specific Proteomic and Interactomic Profiling and the Identification of Neuroprotective HSP90 Client Proteins”

To simultaneously profile the proteome and interactome in specific cells ofcomplex tissues, we developed a chemical biology technique called MACSPI(Methionine Analog-based Cell-Specific Proteomics and Interactomics) anddemonstrated its utilities in the popular multicellular model organism <i>C. elegans</i>.Our approach involved utilizing an engineered methionine analog equipped with abio-orthogonal tag and a photo-crosslinker, along with cell-specific expression of amutant methionyl-tRNA synthetase (MetRS) capable of incorporating thismethionine analog into proteins. As a proof-of-concept, we profiled the proteomesand interactomes of the body wall muscles and the nervous system of <i>C. elegans</i>.Using click-chemistry, protein enrichment, and LC-MS/MS, we confirmed that our 3probe selectively labels proteins in target cells, enabling their proteomic profilingwithin whole-worm lysates. To capture transient protein-protein interactions (PPIs),we combined UV-induced photo-crosslinking with a dual-enrichment strategy. Bytagging endogenous chaperones like HSP90 with HA, we performed sequentialpurifications via both the bio-orthogonal handle and the HA epitope, successfullyidentifying precise, tissue-specific chaperone interactomes.We further optimized MACSPI for specific types of neurons, such as the eightdopaminergic (DA) neurons and six touch receptor neurons (TRNs), by increasingprobe concentration, labeling generations, and click chemistry reagentsconcentrations. This deep profiling revealed a poor correlation betweentranscriptomic and proteomic levels, underscoring the need for direct proteinmeasurement. Furthermore, to decipher the mechanism of neurodegenerativediseases like Parkinson's disease (PD), which increasingly affects the human agingpopulation, and to identify key genes with neuroprotective functions, we mappedproteomic and transcriptomic alterations in a PD model and compared those withour HSP90 interactome data to identify HSP90 client proteins that may haveneuroprotective effects and tested them in functional assays. Additionally, weprofiled the proteomic alterations induced by colchicine treatment, which causesmicrotubule depolymerization in <i>C. elegans</i>, and found that microtubule stabilitycontrols the protein level of many proteins. Ultimately, our work establishes apowerful platform for tissue-resolution interactomics and cell-resolutionproteomics, aiming to decipher the disease mechanism and identify key genes withneuroprotective functions based on the data obtained.The "Dataset for quantification" includes all the analyzed MS data. This dataset provides the data for the correlation analysis and the volcano plotting. "Dataset for pathway enrichment" dataset includes all the downstream analysis followed by the "Dataset for quantification". This dataset include the KEGG and GO term enrichment analysis.