TY - JOUR

T1 - CEDAR, an online resource for the reporting and exploration of complexome profiling data

AU - van Strien, Joeri

AU - Haupt, Alexander

AU - Schulte, Uwe

AU - Braun, Hans-Peter

AU - Cabrera-Orefice, Alfredo

AU - Choudhary, Jyoti S

AU - Evers, Felix

AU - Fernandez-Vizarra, Erika

AU - Guerrero-Castillo, Sergio

AU - Kooij, Taco W A

AU - Páleníková, Petra

AU - Pardo, Mercedes

AU - Ugalde, Cristina

AU - Wittig, Ilka

AU - Wöhlbrand, Lars

AU - Brandt, Ulrich

AU - Arnold, Susanne

AU - Huynen, Martijn A

N1 - Funding Information: We would like to thank Arthur Pistorius for his assistance with deployment of the CEDAR website. This work was supported by grants from the Dutch Organisation for Health Research and Development (ZON-MW TOP grant number 91217009 ; MH., UB, SA and JS), the Netherlands Organisation for Scientific Research (NWO-VIDI 864.13.009 , TWAK and FE), Comunidad Autónoma de Madrid (ERDF-ESF Grant P2018/BAA-4403 ; CU), Instituto de Salud Carlos III -MINECO (European FEDER Funds Grant PI17-00048 ; CU), the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) (Project-ID 403222702 – SFB 1381; US) and under Germany's Excellence Strategy (CIBSS - EXC-2189 - Project ID 390939984; US), the Medical Research Council Core (Grant MC_UU_00015/5 ; EFV), the Association Française contre les Myopathies (AFM) (Grant 16086 ; EFV), the Deutsche Forschungsgemeinschaft ( SFB 815/Z1 ; IW), BMBF mitoNET — German Network for Mitochondrial Disorders ( 01GM1906D ; IW), Medical Research Council , UK ( MC_UU_00015/4 , PP), Marie Sklodowska-Curie ITN-REMIX grant (Grant 721757 ; PP), DFG grant ( Br 1829/16-1 ; HPB), and the CRUK Centre ( C309/A25144 ).

PY - 2021/7/1

Y1 - 2021/7/1

N2 - Complexome profiling is an emerging 'omics' approach that systematically interrogates the composition of protein complexes (the complexome) of a sample, by combining biochemical separation of native protein complexes with mass-spectrometry based quantitation proteomics. The resulting fractionation profiles hold comprehensive information on the abundance and composition of the complexome, and have a high potential for reuse by experimental and computational researchers. However, the lack of a central resource that provides access to these data, reported with adequate descriptions and an analysis tool, has limited their reuse. Therefore, we established the ComplexomE profiling DAta Resource (CEDAR, www3.cmbi.umcn.nl/cedar/), an openly accessible database for depositing and exploring mass spectrometry data from complexome profiling studies. Compatibility and reusability of the data is ensured by a standardized data and reporting format containing the "minimum information required for a complexome profiling experiment" (MIACE). The data can be accessed through a user-friendly web interface, as well as programmatically using the REST API portal. Additionally, all complexome profiles available on CEDAR can be inspected directly on the website with the profile viewer tool that allows the detection of correlated profiles and inference of potential complexes. In conclusion, CEDAR is a unique, growing and invaluable resource for the study of protein complex composition and dynamics across biological systems.

AB - Complexome profiling is an emerging 'omics' approach that systematically interrogates the composition of protein complexes (the complexome) of a sample, by combining biochemical separation of native protein complexes with mass-spectrometry based quantitation proteomics. The resulting fractionation profiles hold comprehensive information on the abundance and composition of the complexome, and have a high potential for reuse by experimental and computational researchers. However, the lack of a central resource that provides access to these data, reported with adequate descriptions and an analysis tool, has limited their reuse. Therefore, we established the ComplexomE profiling DAta Resource (CEDAR, www3.cmbi.umcn.nl/cedar/), an openly accessible database for depositing and exploring mass spectrometry data from complexome profiling studies. Compatibility and reusability of the data is ensured by a standardized data and reporting format containing the "minimum information required for a complexome profiling experiment" (MIACE). The data can be accessed through a user-friendly web interface, as well as programmatically using the REST API portal. Additionally, all complexome profiles available on CEDAR can be inspected directly on the website with the profile viewer tool that allows the detection of correlated profiles and inference of potential complexes. In conclusion, CEDAR is a unique, growing and invaluable resource for the study of protein complex composition and dynamics across biological systems.

KW - Complexome profiling

KW - Data visualization

KW - Database

KW - FAIR

KW - Protein complex

UR - http://www.scopus.com/inward/record.url?scp=85102647000&partnerID=8YFLogxK

U2 - 10.1016/j.bbabio.2021.148411

DO - 10.1016/j.bbabio.2021.148411

M3 - Article

C2 - 33722514

VL - 1862

JO - Biochimica et Biophysica Acta - Bioenergetics

JF - Biochimica et Biophysica Acta - Bioenergetics

SN - 0005-2728

IS - 7

M1 - 148411

ER -