Data for: Nitric oxide contributes to protein homeostasis by S-nitrosylations of the chaperone HSPA8 and the ubiquitin ligase UBE2D
Description
DIB1: We generated nNOS+ SH-SY5Y cells that express nNOS at a level comparable to mouse brain, replicating the aging phenotype. nNOS+ and MOCK cells were exposed to proteostasis stress by treatment with rapamycin or serum-free starvation versus control. To analyze NO-mediated S-nitrosylations (SNO) and other reversible protein modifications including disulfides and sulfoxides we used complimentary proteomic approaches encompassing 2D-SNO-DIGE (differential gel electrophoresis), SNO-site identification (SNOSID), SNO Super-SILAC, SNO BIAM-Switch and Redox-BIAM switch. The redox proteomes were analyzed using hybrid liquid chromatography/mass spectrometry (LC/MS) on an LTQ Orbitrap XL (2D-SNO-DIGE, SNOSID, SNO-SILAC) or on a Thermo Scientific™ Q Exactive Plus (BIAM switch assays), the latter equipped with an ultra-high performance liquid chromatography unit and a Nanospray Flex Ion-Source. Full scan MS-data were acquired using Xcalibur, and raw mass spectra were analyzed using the proteomics software MaxQuant. The data are MaxQuant output files (Table 1 2D-SNO-DIGE, Table 2 SNOSID, Table 3 SNO-SILAC, Table 4 GO of SNO modified proteins, Table 5 SNO-BIAM switch, Table 6 Redox BIAM switch) providing essential information including peptide and protein identification, accession numbers, protein and gene names, sequence coverage and quantification values of each sample. Identifications from the reverse decoy database, identified by site only and known contaminants were excluded. The Excel file also contains Gene Ontology terms associated with the SNOed proteins (Table 4 and specified columns in Table 5 and 6). The GO overrepresentation analysis (Table 4) was performed with the Panther GO overrepresentation tool (http://www.pantherdb.org/). Excel Table 1: 2D-SNO DIGE Excel Table 2: SNOSID Excel Table 3: SNO-SILAC Excel Table 4: Gene ontology of redox modified proteins (pooled hits of 2D-DIGE, SNOSID and SNO-SILAC) Excel Table 5: SNO-BIAM switch Excel Table 6: Redox-BIAM switch DIB2 The data are MaxQuant output files (Table 1 SILAC, Table 3 LFQ proteome) of the Full Proteome including peptide and protein identification, accession numbers, protein and gene names, sequence coverage and SILAC or label free quantification (LFQ) values of each sample. Identifications from the reverse decoy database, identified by site only and known contaminants were excluded. The raw MS proteomics data of the Full Proteome have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD010538. Reviewer account details: Username: reviewer95719@ebi.ac.uk; Password: UR0ZlqWo. Excel Table 1: MaxQuant data of normalized SILAC proteome (vehicle versus 6h rapamycin) Excel Table 2: Gene Ontology analysis of significantly regulated proteins (SILAC experiment) Excel Table 3: MaxQuant data of label-free deep proteome (conditions: full medium, 24h serum-free, 24h rapamycin)