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

Research output: Contribution to journalArticleResearchpeer review

Authors

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

Research Organisations

External Research Organisations

  • Radboud University Medical Center
  • University of Freiburg
  • Institute of Cancer Research
  • University of Cambridge
  • University Medical Center Hamburg-Eppendorf
  • Comunidad de Madrid
  • Goethe University Frankfurt
  • Carl von Ossietzky University of Oldenburg
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Details

Original languageEnglish
Article number148411
JournalBiochimica et Biophysica Acta - Bioenergetics
Volume1862
Issue number7
Early online date17 Mar 2021
Publication statusPublished - 1 Jul 2021

Abstract

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.

Keywords

    Complexome profiling, Data visualization, Database, FAIR, Protein complex

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biophysics
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)
  • Cell Biology

Cite this

CEDAR, an online resource for the reporting and exploration of complexome profiling data. / van Strien, Joeri; Haupt, Alexander; Schulte, Uwe et al.
In: Biochimica et Biophysica Acta - Bioenergetics, Vol. 1862, No. 7, 148411, 01.07.2021.

Research output: Contribution to journalArticleResearchpeer review

van Strien, J, Haupt, A, Schulte, U, Braun, H-P, Cabrera-Orefice, A, Choudhary, JS, Evers, F, Fernandez-Vizarra, E, Guerrero-Castillo, S, Kooij, TWA, Páleníková, P, Pardo, M, Ugalde, C, Wittig, I, Wöhlbrand, L, Brandt, U, Arnold, S & Huynen, MA 2021, 'CEDAR, an online resource for the reporting and exploration of complexome profiling data', Biochimica et Biophysica Acta - Bioenergetics, vol. 1862, no. 7, 148411. https://doi.org/10.1016/j.bbabio.2021.148411, https://doi.org/10.15488/11674
van Strien, J., Haupt, A., Schulte, U., Braun, H.-P., Cabrera-Orefice, A., Choudhary, J. S., Evers, F., Fernandez-Vizarra, E., Guerrero-Castillo, S., Kooij, T. W. A., Páleníková, P., Pardo, M., Ugalde, C., Wittig, I., Wöhlbrand, L., Brandt, U., Arnold, S., & Huynen, M. A. (2021). CEDAR, an online resource for the reporting and exploration of complexome profiling data. Biochimica et Biophysica Acta - Bioenergetics, 1862(7), Article 148411. https://doi.org/10.1016/j.bbabio.2021.148411, https://doi.org/10.15488/11674
van Strien J, Haupt A, Schulte U, Braun HP, Cabrera-Orefice A, Choudhary JS et al. CEDAR, an online resource for the reporting and exploration of complexome profiling data. Biochimica et Biophysica Acta - Bioenergetics. 2021 Jul 1;1862(7):148411. Epub 2021 Mar 17. doi: 10.1016/j.bbabio.2021.148411, 10.15488/11674
van Strien, Joeri ; Haupt, Alexander ; Schulte, Uwe et al. / CEDAR, an online resource for the reporting and exploration of complexome profiling data. In: Biochimica et Biophysica Acta - Bioenergetics. 2021 ; Vol. 1862, No. 7.
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abstract = "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.",
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note = "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 Aut{\'o}noma 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 Fran{\c c}aise 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 ).",
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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 ).

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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.

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KW - Data visualization

KW - Database

KW - FAIR

KW - Protein complex

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