CEDAR, an online resource for the reporting and exploration of complexome profiling data

Strien, Joeri van; Haupt, Alexander; Schulte, Uwe; Braun, Hans-Peter; Cabrera‐Orefice, Alfredo; Choudhary, Jyoti; Evers, Felix; Fernández-Vizarra, Erika; Guerrero–Castillo, Sergio; Kooij, Taco W. A.; Páleníková, Petra; Pardo, Mercedes; Ugalde, Cristina; Wittig, Ilka; Wöhlbrand, Lars; Brandt, Ulrich; Arnold, Susanne; Huynen, Martijn

doi:10.1016/j.bbabio.2021.148411

Cited by 30 publications

(14 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The complexome profiling datasets were deposited in the CEDAR database, accession code CRX32 (http://www3.cmbi.umcn.nl/cedar/browse/experiments/CRX32; van Strien et al , 2021).…”

Section: Data Availabilitymentioning

confidence: 99%

Ablation of mitochondrial DNA results in widespread remodeling of the mitochondrial complexome

et al. 2021

Self Cite

View full text Add to dashboard Cite

So-called q0 cells lack mitochondrial DNA and are therefore incapable of aerobic ATP synthesis. How cells adapt to survive ablation of oxidative phosphorylation remains poorly understood. Complexome profiling analysis of q0 cells covered 1,002 mitochondrial proteins and revealed changes in abundance and organization of numerous multiprotein complexes including previously not described assemblies. Beyond multiple subassemblies of complexes that would normally contain components encoded by mitochondrial DNA, we observed widespread reorganization of the complexome. This included distinct changes in the expression pattern of adenine nucleotide carrier isoforms, other mitochondrial transporters, and components of the protein import machinery. Remarkably, ablation of mitochondrial DNA hardly affected the complexes organizing cristae junctions indicating that the altered cristae morphology in q0 mitochondria predominantly resulted from the loss of complex V dimers required to impose narrow curvatures to the inner membrane. Our data provide a comprehensive resource for in-depth analysis of remodeling of the mitochondrial complexome in response to respiratory deficiency.

show abstract

“…The complexome profiling datasets were deposited in the CEDAR database, accession code CRX32 (http://www3.cmbi.umcn.nl/cedar/browse/experiments/CRX32; van Strien et al , 2021).…”

Section: Data Availabilitymentioning

confidence: 99%

Ablation of mitochondrial DNA results in widespread remodeling of the mitochondrial complexome

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…Other proteomics data analysis tools e.g., Perseus and proteome discoverer have also been used to analyze complexome profiling data [17,87]. ComPrAn R package to study protein assemblies [28] CEDAR Online resource of CP data [89] ComplexFinder Machine-learning based prediction of novel protein complexes [90] Furthermore, ComPrAn stands out as an additional tool to analyze complexomes and was initially developed for qDGMS data [28]. This freely available R-package provides analysis on peptide-level data, normalization, and clustering tools for protein-level data, include functions to compare changes of protein complex composition between two SILAC labeled samples and produce publication-ready figures.…”

Section: Discussionmentioning

confidence: 99%

“…Recently, the complexome profiling Data Resource (CEDAR) repository was installed. CEDAR includes a storage and information sharing platform to support the reuse of complexome profiling data [89]. Many researchers also uploaded their mass spectrometry raw data into the Proteomics Identification database (PRIDE) together with analysis data for reuse by the scientific community [77].…”

Section: Discussionmentioning

confidence: 99%

Complexome Profiling: Assembly and Remodeling of Protein Complexes

Wittig

Malacarne

2021

IJMS

Self Cite

View full text Add to dashboard Cite

Many proteins have been found to operate in a complex with various biomolecules such as proteins, nucleic acids, carbohydrates, or lipids. Protein complexes can be transient, stable or dynamic and their association is controlled under variable cellular conditions. Complexome profiling is a recently developed mass spectrometry-based method that combines mild separation techniques, native gel electrophoresis, and density gradient centrifugation with quantitative mass spectrometry to generate inventories of protein assemblies within a cell or subcellular fraction. This review summarizes applications of complexome profiling with respect to assembly ranging from single subunits to large macromolecular complexes, as well as their stability, and remodeling in health and disease.

show abstract

“…All these under-explored results thus represent a valuable source of information, which could be reused and further mined by other researchers. To achieve this purpose, the ComplexomE profiling DAta Resource (CEDAR) has recently been established as the first website for depositing and sharing CP data ( van Strien et al, 2021 ). A standardized format containing the minimum information required for a CP experiment (MIACE) ensures compatibility and correct retrieval of data.…”

Section: Complexome Profilingmentioning

confidence: 99%

Complexome Profiling—Exploring Mitochondrial Protein Complexes in Health and Disease

Cabrera‐Orefice

Potter²,

Evers

et al. 2022

Front. Cell Dev. Biol.

Self Cite

View full text Add to dashboard Cite

Complexome profiling (CP) is a state-of-the-art approach that combines separation of native proteins by electrophoresis, size exclusion chromatography or density gradient centrifugation with tandem mass spectrometry identification and quantification. Resulting data are computationally clustered to visualize the inventory, abundance and arrangement of multiprotein complexes in a biological sample. Since its formal introduction a decade ago, this method has been mostly applied to explore not only the composition and abundance of mitochondrial oxidative phosphorylation (OXPHOS) complexes in several species but also to identify novel protein interactors involved in their assembly, maintenance and functions. Besides, complexome profiling has been utilized to study the dynamics of OXPHOS complexes, as well as the impact of an increasing number of mutations leading to mitochondrial disorders or rearrangements of the whole mitochondrial complexome. Here, we summarize the major findings obtained by this approach; emphasize its advantages and current limitations; discuss multiple examples on how this tool could be applied to further investigate pathophysiological mechanisms and comment on the latest advances and opportunity areas to keep developing this methodology.

show abstract

CEDAR, an online resource for the reporting and exploration of complexome profiling data

Cited by 30 publications

References 48 publications

Ablation of mitochondrial DNA results in widespread remodeling of the mitochondrial complexome

Ablation of mitochondrial DNA results in widespread remodeling of the mitochondrial complexome

Complexome Profiling: Assembly and Remodeling of Protein Complexes

Complexome Profiling—Exploring Mitochondrial Protein Complexes in Health and Disease

Contact Info

Product

Resources

About