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

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CEDAR, an online resource for the reporting and exploration of complexome profiling data. / van Strien, Joeri; Haupt, Alexander; Schulte, Uwe; Braun, Hans-Peter; Cabrera-Orefice, Alfredo; Choudhary, Jyoti S; Evers, Felix; Fernandez-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 A.

in: BBA-BIOENERGETICS, Jahrgang 1862, Nr. 7, 01.07.2021, S. 148411.

Publikationen: SCORING: Beitrag in Fachzeitschrift/Zeitung › SCORING: Zeitschriftenaufsatz › Forschung › Begutachtung

Harvard

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', BBA-BIOENERGETICS, Jg. 1862, Nr. 7, S. 148411. https://doi.org/10.1016/j.bbabio.2021.148411

APA

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. BBA-BIOENERGETICS, 1862(7), 148411. https://doi.org/10.1016/j.bbabio.2021.148411

Vancouver

van Strien J, Haupt A, Schulte U, Braun H-P, Cabrera-Orefice A, Choudhary JS et al. CEDAR, an online resource for the reporting and exploration of complexome profiling data. BBA-BIOENERGETICS. 2021 Jul 1;1862(7):148411. https://doi.org/10.1016/j.bbabio.2021.148411

Bibtex

@article{3386e366c90b4b26a182fbc1b424f4ca,
title = "CEDAR, an online resource for the reporting and exploration of complexome profiling data",
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 = "Databases, Factual, Humans, Multiprotein Complexes/metabolism, Proteins/metabolism, Proteome/analysis, Software",
author = "{van Strien}, Joeri and Alexander Haupt and Uwe Schulte and Hans-Peter Braun and Alfredo Cabrera-Orefice and Choudhary, {Jyoti S} and Felix Evers and Erika Fernandez-Vizarra and Sergio Guerrero-Castillo and Kooij, {Taco W A} and Petra P{\'a}len{\'i}kov{\'a} and Mercedes Pardo and Cristina Ugalde and Ilka Wittig and Lars W{\"o}hlbrand and Ulrich Brandt and Susanne Arnold and Huynen, {Martijn A}",
note = "Copyright {\textcopyright} 2021 The Authors. Published by Elsevier B.V. All rights reserved.",
year = "2021",
month = jul,
day = "1",
doi = "10.1016/j.bbabio.2021.148411",
language = "English",
volume = "1862",
pages = "148411",
journal = "BBA-BIOENERGETICS",
issn = "0005-2728",
publisher = "Elsevier",
number = "7",

}

RIS

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 - Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.

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 - Databases, Factual

KW - Humans

KW - Multiprotein Complexes/metabolism

KW - Proteins/metabolism

KW - Proteome/analysis

KW - Software

U2 - 10.1016/j.bbabio.2021.148411

DO - 10.1016/j.bbabio.2021.148411

M3 - SCORING: Journal article

C2 - 33722514

VL - 1862

SP - 148411

JO - BBA-BIOENERGETICS

JF - BBA-BIOENERGETICS

SN - 0005-2728

IS - 7

ER -