RT Journal Article
SR Electronic
T1 Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topology
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.05.05.490733
DO 10.1101/2022.05.05.490733
A1 Ying Zhu
A1 Kerem Can Akkaya
A1 Diogo Borges Lima
A1 Cong Wang
A1 Martin Lehmann
A1 Fan Liu
YR 2022
UL http://biorxiv.org/content/early/2022/05/05/2022.05.05.490733.abstract
AB The specific functions of cellular organelles and sub-compartments depend on their protein content, which can be characterized by spatial proteomics approaches. However, many spatial proteomics methods are limited in their ability to resolve organellar sub-compartments, profile multiple sub-compartments in parallel, and/or characterize membrane-associated proteomes. Here, we develop a cross-link assisted spatial proteomics (CLASP) strategy that addresses these shortcomings. Using human mitochondria as a model system, we show that CLASP can elucidate spatial proteomes of all mitochondrial sub-compartments and provide topological insight into the mitochondrial membrane proteome in a single experiment. Biochemical and imaging-based follow-up studies demonstrate that CLASP allows discovering mitochondria-associated proteins and revising previous protein sub-compartment localization and membrane topology data. This study extends the scope of cross-linking mass spectrometry beyond protein structure and interaction analysis towards spatial proteomics, establishes a method for concomitant profiling of sub-organelle and membrane proteomes, and provides a resource for mitochondrial spatial biology.Competing Interest StatementFL is on the advisory board of Absea Biotechnology Ltd.