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Ayoubi R, Ryan J, Gonzalez Bolivar S, Alende C, Ruiz Moleon V, Fotouhi M, Alqazzaz M, Southern K, Alshafie W, Baker MR, Ball AR, Callahan D, Cooper JA, Crosby K, Harvey KJ, Houston DW, Kumaran R, Rego M, Schofield C, Wu H, Biddle MS, Brown CM, Kahn RA, Bandrowski A, Virk HS, Edwards AM, McPherson PS, Laflamme C. A consensus platform for antibody characterization. Nat Protoc 2024:10.1038/s41596-024-01095-8. [PMID: 39690206 DOI: 10.1038/s41596-024-01095-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 10/18/2024] [Indexed: 12/19/2024]
Abstract
Antibody-based research applications are critical for biological discovery. Yet there are no industry standards for comparing the performance of antibodies in various applications. We describe a knockout cell line-based antibody characterization platform, developed and approved jointly by industry and academic researchers, that enables the systematic comparison of antibody performance in western blot, immunoprecipitation and immunofluorescence. The scalable protocols, which require minimal technological resources, consist of (1) the identification of appropriate cell lines for antibody characterization studies, (2) development/contribution of isogenic knockout controls, and (3) a series of antibody characterization procedures focused on the most common applications of antibodies in research. We provide examples of expected outcomes to guide antibody users in evaluating antibody performance. Central to our approach is advocating for transparent and open data sharing, enabling a community effort to identify specific antibodies for all human proteins. Mid-level graduate students with training in biochemistry and prior experience in cell culture and microscopy can complete the protocols for a specific protein within 1 month while working part-time on this effort. Antibody characterization is needed to meet standards for resource validation and data reproducibility, which are increasingly required by journals and funding agencies.
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Affiliation(s)
- Riham Ayoubi
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, the Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Joel Ryan
- Advanced BioImaging Facility, McGill University, Montreal, Quebec, Canada
| | - Sara Gonzalez Bolivar
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, the Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Charles Alende
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, the Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Vera Ruiz Moleon
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, the Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Maryam Fotouhi
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, the Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Mona Alqazzaz
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Kathleen Southern
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, the Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Walaa Alshafie
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, the Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | | | | | | | | | | | | | - Douglas W Houston
- Developmental Studies Hybridoma Bank, Department of Biology, The University of Iowa, Iowa City, IA, USA
| | | | | | | | - Hai Wu
- ABclonal Technology, Woburn, MA, USA
| | - Michael S Biddle
- NIHR Respiratory Biomedical Research Centre, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Claire M Brown
- Advanced BioImaging Facility, McGill University, Montreal, Quebec, Canada
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Anita Bandrowski
- Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
| | - Harvinder S Virk
- NIHR Respiratory Biomedical Research Centre, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Aled M Edwards
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Peter S McPherson
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, the Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Carl Laflamme
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, the Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.
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