Proteomics

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Quantitative proteomic analysis reveals JMJD6 and DNAJB11 as endogenous substrates of E3 ligase RFFL

ABSTRACT: Immunoprecipitation experiments using anti-RFFL antibody. Samples were loaded in technical duplicates in EvoTips, and chromatographic separation was done on an in-house column and the 30 samples per day (SPD) method on Evosep One system (Evosep). Peptides were detected and fragmented using timsTOF Pro 2 mass spectrometer (Bruker Daltonics) in data-dependent mode with parallel accumulation serial fragmentation (PASEF) enabled. The raw data was analyzed using Fragpipe (v 22.0). MS/MS spectra were searched using MSFragger (v 4.1) against forward and reversed Homo sapiens UniProt sequence database (UP000005640) supplemented with common contaminants (total 20,979 sequences excluding decoys).

INSTRUMENT(S): timsTOF Pro 2

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Prof. S. Murty Srinivasula  

PROVIDER: MSV000096868 | MassIVE | Thu Jan 16 02:32:00 GMT 2025

SECONDARY ACCESSION(S): PXD059871

REPOSITORIES: MassIVE

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Quantitative Proteomic Analysis Reveals JMJD6 and DNAJB11 as Endogenous Substrates of E3 Ligase RFFL.

Narendradev Nikhil Dev ND   Marathe Soumitra S   Baboo Sabyasachi S   McClatchy Daniel B DB   Diedrich Jolene K JK   Jain Parul P   Purwar Rahul R   Yates John R JR   Srinivasula Srinivasa Murty SM  

Journal of proteome research 20250626

The ubiquitin-proteasome system contributes to protein quality control, involving E3 ligases that ubiquitinate proteins and leading to their degradation. The dysregulation of protein degradation results in the abnormal accumulation of proteins and is implicated in the pathology of diverse diseases, making targeted protein degradation a promising therapeutic strategy. Here, we focus on RFFL, an endosome-associated RING E3 ligase involved in mitochondrial homeostasis and the clearance of misfolded  ...[more]

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