1
|
de Marco A, Berrow N, Lebendiker M, Garcia-Alai M, Knauer SH, Lopez-Mendez B, Matagne A, Parret A, Remans K, Uebel S, Raynal B. Quality control of protein reagents for the improvement of research data reproducibility. Nat Commun 2021; 12:2795. [PMID: 33990604 PMCID: PMC8121922 DOI: 10.1038/s41467-021-23167-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 04/19/2021] [Indexed: 11/23/2022] Open
Abstract
Proteins and peptides are amongst the most widely used research reagents but often their quality is inadequate and can result in poor data reproducibility. Here we propose a simple set of guidelines that, when correctly applied to protein reagents should provide more reliable experimental data.
Collapse
Affiliation(s)
- Ario de Marco
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipava, Vipava, Slovenia
| | - Nick Berrow
- Protein Expression Core Facility, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mario Lebendiker
- Protein Purification Facility, Wolfson Centre for Applied Structural Biology, Edmund J. Safra Campus - The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Maria Garcia-Alai
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Hamburg, Germany
| | - Stefan H Knauer
- Biochemistry IV - Biopolymers, University of Bayreuth, Bayreuth, Germany
| | - Blanca Lopez-Mendez
- Protein Production and Characterization Platform, Novo Nordisk Foundation Center for Protein Research, Copenhagen, Denmark
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Department of Life Sciences, University of Liège, Building B6C, Allée du 6 Août, 13, Liège, Belgium
| | - Annabel Parret
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Hamburg, Germany
| | - Kim Remans
- Protein Expression and Purification Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | | | - Bertrand Raynal
- Institut Pasteur, Plateforme de Biophysique moléculaire, Department of Structural Biology and Chemistry, Paris, France.
| |
Collapse
|
2
|
Lebendiker M, Danieli T, de Marco A. The Trip Adviser guide to the protein science world: a proposal to improve the awareness concerning the quality of recombinant proteins. BMC Res Notes 2014; 7:585. [PMID: 25178166 PMCID: PMC4161829 DOI: 10.1186/1756-0500-7-585] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 07/31/2014] [Indexed: 11/24/2022] Open
Abstract
In many research articles, where protein purification is required for various assays, (protein-protein interactions, activity assays, etc.), we always have access to the final results, but seldom have access to the raw data required for an accurate evaluation of the protein quality. This data is extremely important on one hand to critically evaluate the quality of the proteins used in the described research and, on the other hand, to allow other laboratories to safely use the described procedure in a reproducible manner. We herby propose to include a standardized methodology that can easily be incorporated in research papers. Moreover, this methodology can be utilized as a “quality control” ladder, where the more information given, will lead to a higher ranking of the article. This “quality control” stamp will allow researchers retrieving relevant and useful materials and methods in the field of protein research.
Collapse
Affiliation(s)
| | | | - Ario de Marco
- Department of Biomedical Sciences and Engineering, University of Nova Gorica, Glavni Trg 9, SI-5261 Vipava, Slovenia.
| |
Collapse
|
3
|
Buckle AM, Bate MA, Androulakis S, Cinquanta M, Basquin J, Bonneau F, Chatterjee DK, Cittaro D, Gräslund S, Gruszka A, Page R, Suppmann S, Wheeler JX, Agostini D, Taussig M, Taylor CF, Bottomley SP, Villaverde A, de Marco A. Recombinant protein quality evaluation: proposal for a minimal information standard. Stand Genomic Sci 2011; 5:195-7. [PMID: 22180821 PMCID: PMC3235516 DOI: 10.4056/sigs.1834511] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Ashley M. Buckle
- The Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Australia
- Corresponding authors: Ario de Marco, University of Nova Gorica (UNG), Rožna Dolina (Nova Gorica), Slovenia. Tel. 0039.3493542056;
| | - Mark A. Bate
- The Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Australia
| | - Steve Androulakis
- Monash eResearch Centre, Monash University, Clayton, Victoria, Australia
| | | | - Jerome Basquin
- Max Planck Institute of Biochemistry, Department of Structural Cell Biology, Martinsried, Germany
| | - Fabien Bonneau
- Max Planck Institute of Biochemistry, Department of Structural Cell Biology, Martinsried, Germany
| | - Deb K. Chatterjee
- Protein Expression Laboratory, SAIC-Frederick Inc., National Cancer Institute, Frederick, MD USA
| | | | - Susanne Gräslund
- Structural Genomics Consortium, Karolinska Institutet, Department of Medical Biophysics and Biochemistry, Stockholm, Sweden
| | | | - Rebecca Page
- Brown University, Department of Molecular Biology, Cell Biology and Biochemistry, Providence, RI, USA
| | - Sabine Suppmann
- Max Planck Institute of Biochemistry, Microchemistry Core Facility, Martinsried, Germany
| | - Jun X. Wheeler
- National Institute for Biological Standards and Control, Health Protection Agency, Hertfordshire, UK
| | | | - Mike Taussig
- Protein Technologies Group, Babraham Bioscience Technologies, Cambridge UK
| | - Chris F. Taylor
- The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Stephen P. Bottomley
- The Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Australia
| | - Antonio Villaverde
- Institute for Biotechnology and Biomedicine and Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain
| | - Ario de Marco
- Department Environmental Sciences, University of Nova Gorica, Nova Gorica, Slovenia
- Corresponding authors: Ario de Marco, University of Nova Gorica (UNG), Rožna Dolina (Nova Gorica), Slovenia. Tel. 0039.3493542056;
| |
Collapse
|