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Ludesi CEO talks at Quality Control in Proteomics Workshop
Photo of the main conference room taken during a switch of speakers in the plenary session.
From the 25th to the 27th of November the Quality Control in Proteomics Workshop took place in Hinxton, UK, as part of the ESF Frontiers of Functional Genomics Workshops. Organized by Lennart Martens and Henning Hermjakob from the EBI, the workshops main objective was to assemble a critical mass of representatives from the academic community, from industry (pharma, biotech start-ups, and consumables vendors), and from key scientific journals to discuss quality control (QC) strategies in proteomics.
The QC of data from different instruments and software is vitally important to ensure that what we are seeing is “real” and comparable to similar experiments. Too often we innovate and develop new instruments or workflows and forget to thoroughly validate that the output is correct, complete, and reproducible.
The proteomics community has only recently begun to adopt quality control of the different steps in the complex workflows employed when analysing a sample. As a result, efforts towards QC are currently specific to individual laboratories, resulting in widely divergent and incomparable strategies to verify the operational status of the instrumentation and analysis steps.
Needless to say that this workshop not only addressed this obvious weak-point in proteomics research today, but also represents a much-welcomed and exciting initiative from the community.
As a spotlight on 2D gel-based proteomics, Ludesi’s CEO Ola Forsstrom-Olsson was invited to speak about QC of 2D gel image analysis data. Apart from outlining the need for QC in this area, his talk focused on the new Gel IQ tool – a freely available tool that allows researchers to assess the quality of their data. The official report on the workshop nicely summarizes his talk:
“Dr. Ola Forsstrom-Olsson, from Ludesi, Sweden, presented a highly interesting, freely available application developed by his company to allow any user to perform a semi-automated quality control on their 2D gel image analysis. The software strikes a careful balance between the necessity to automatically call and match gel spots (due to the sheer amount of spots that need to be processed) and the need for manual validation of these automatic assignments for QC purposes. The software does this by first asking the user to specify a number of spots to evaluate manually. Subsequently, that number of spots will be randomly selected from the data, and will be shown in detail to the user. For each spot, the user has to grade the quality of the assignment, with the tool automatically progressing to subsequent spots. As soon as the manual validation quota is reached, the tool outputs the quality metrics, including a ‘combined correctness’ score.”
The development of free tools, such as Gel IQ, is vital to help scientists successfully QC their experiments and we’re happy to report that Gel IQ has so far been extremely well received by the community.
Gel IQ is freely downloadable at www.ludesi.com/free-tools and we will make sure to report more on it in the weeks to come!
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