Bio-Rad has announced that 10 of 17 labs participating in phase two of the 2D Gel Reproducibility Initiative ran gels of the same sample and generated images within a 95 per cent confidence level.
Phase 2 was coordinated by representatives from Bio-Rad, Cil Biotech, Nonlinear Dynamics and Novartis Institutes for Biomedical Research.
Results of phase two will be submitted for publication to a peer-reviewed journal.
Completed deliverables of phase two included a standard sample (Hela-cell lysate), a vendor-independent protocol for running the gels and a reference master gel image.
Labs can use the sample and standard protocol and refer to the standard image to validate the performance and reproducibility of their 2D process.
'The study provides members of the 2D-gel community with a reference standard so researchers can ascertain whether or not they have performed their experiments correctly and reproducibly,' said study participant Maxey Chung, an associate professor of biochemistry at the National University of Singapore.
'Once they are satisfied with the runs with the standard sample, they can run their samples with confidence that any issue that may arise is due to the sample rather than the 2D technique itself.' As part of its global campaign for 2010, Bio-Rad plans to conduct wet-lab clinics for its customers to point out potential pitfalls and recommended solutions for reproducible results.
According to Kumar, there were three main takeaways from the phase two study: complex proteomics methods such as 2D can benefit greatly from the availability of reference materials; users can gain confidence in being able to generate reproducible data based on peer-to-peer review and feedback - an iterative approach will help reduce potential issues; and availability of reference images for intra- and inter-lab studies could reduce bias.
Proposed next steps for this project include: recommending standard protocol to validate performance; distribution of test standards and kits; creation of central image repository; providing global education to produce high quality and highly reproducible data; expansion of study under more stringent conditions Bio-Rad coordinated the participants' involvement in phase two, including qualifying and enrolling labs and supplying reagents for 2D gel experiments based on the request from participating labs.
The labs completed their 2D gel experiments on their own platforms with reagents from multiple vendors and a common Hela-cell lysate prepared by Cilbiotech.
Nonlinear Dynamics analysed the participants' 2D gels using Samespots software and determined the 95 per cent confidence level using Principal Component Analysis (PCA).
In the first phase, Dr Hans Voshol of the Novartis Institutes for Biomedical Research demonstrated the intra-lab reproducibility of 2D gels.
